RiceWiki - User contributions [en]

Os01g0121700

2014-06-09T12:41:43Z

Liangliangbig: /* References */

Please input one-sentence summary here.

==Annotated Information==
The name of the gene is half-size adenosine triphosphate-binding cassette transporter subgroup G,OsABCG1or OsWBC1,is a Putative ATP-binding-cassette protein，belongs to the ABC transporter superfamily.
===Function===
ATP-binding cassette transporters (ABC transporters) are transmembrane proteins that utilize the energy of adenosine triphosphate (ATP) binding and hydrolysis to carry out certain biological processes including translocation of various substrates across membranes and non-transport-related processes such as translation of RNA and DNA repair. They transport a wide variety of substrates across extra- and intracellular membranes, including metabolic products, lipids and sterols, and drugs. Proteins are classified as ABC transporters based on the sequence and organization of their ATP-binding cassette (ABC) domain(s).

ABC proteins are characterized by a highly conserved amino acid region, the ATP binding cassette, also known as the nucleotide binding domain (NBD). This domain contains conserved motifs known as Walker A and Walker B sequences, an ABC signature motif, an H loop, and a Q loop . Half-size ABC proteins consist of only one core unit, while full-size ABC proteins have two or more core units. Full-size ABC proteins can function alone, whereas half-size ABC proteins must form homo- or heterodimers to function as transporters.
===Mechanism of function===
The general mechanism for the transport cycle of ABC transporters has not been fully elucidated but substantial structural and biochemical data has accumulated to support a model in which ATP binding and hydrolysis is coupled to conformational changes in the transporter. The resting state of all ABC transporters has the NBDs in an open dimer configuration, with low affinity for ATP. This open conformation possesses a chamber accessible to the interior of the transporter. The transport cycle is initiated by binding of substrate to the high-affinity site on the TMDs, which induces conformational changes in the NBDs and enhances the binding of ATP. Two molecules of ATP bind, cooperatively, to form the closed dimer configuration. The closed NBD dimer induces a conformational change in the TMDs such that the TMD opens, forming a chamber with an opening opposite to that of the initial state. The affinity of the substrate to the TMD is reduced, thereby releasing the substrate. Hydrolysis of ATP follows and then sequential release of Pi and then ADP restores the transporter to its basal configuration. Although a common mechanism has been suggested, the order of substrate binding, nucleotide binding and hydrolysis, and conformational changes, as well as interactions between the domains is still debated.
===Expression===
ATP-binding cassette transporters (ABC transporters) are members of a protein superfamily that is one of the largest and oldest families with representatives in all extant phyla from prokaryotes to humans.

===Evolution===
Adenosine triphosphate (ATP)-binding cassette (ABC) proteins exist in a wide range of organisms from prokaryotes to eukaryotes.Genome wide analysis of model plants such as Arabidopsis and rice (Oryza sativa L.) has revealed that plants have more than 120 ABC proteins, much more than animals or insects.

You can also add sub-section(s) at will.

==Labs working on this gene==
1. Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, 2-11 Nishi, Inada, Obihiro, Hokkaido 080-8555, Japan.

==References==
1. Shuichi Matsuda;Atsushi Funabiki;Kaoru Furukawa;Nozomi Komori;Masanori Koike;Yoshihiko Tokuji;Itsuro Takamure;Kiyoaki Kato Genome-wide analysis and expression profiling of half-size ABC protein subgroup G in rice in response to abiotic stress and phytohormone treatments Molecular Genetics and Genomics, 2012, 287(10): 819-835

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0121700|
Description = ABC transporter related domain containing protein|
Version = NM_001048413.1 GI:115434239 GeneID:4326045|
Length = 6489 bp|
Definition = Oryza sativa Japonica Group Os01g0121700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:1223012..1229500|
CDS = 1224084..1224269,1224578..1224662,1224763..1224975,1225114..1225334,1225511..1225642 ,1226218..1226494,1226887..1227088,1227779..1227911,1228241..1228391 ,1228484..1228674,1229167..1229382|
GCID = <gbrowseImage1>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatgggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatga</cdnaseq>|
AA = <aaseq>MEVRGLGQLLAALAAALFVRAVAGPGPALLPPADDEDSDADPEA GGEGGGVPPVTIRWARITCALKNKRGDVARFLLSNASGEAKSGRLLALMGPSGSGKTT LLNVLAGQLTASPSLHLSGFLYINGRPISEGGYKIAYVRQEDLFFSQLTVRETLSLAA ELQLRRTLTPERKESYVNDLLFRLGLVNCADSIVGDAKVRGISGGEKKRLSLACELIA SPSIIFADEPTTGLDAFQAEKVMETLRQLAEDGHTVICSIHQPRGSVYGKFDDIVLLS EGEVIYMGPAKEEPLLYFASLGYHCPDHVNPAEFLADLISVDYSSAESVQSSRKRIEN LIEEFSNKVAITESNSSLTNPEGSEFSPKLIQKSTTKHRRGWWRQFRLLFKRAWMQAF RDGPTNKVRARMSVASAIIFGSVFWRMGKTQTSIQDRMGLLQVTAINTAMAALTKTVG VFPKERAIVDRERAKGSYALGPYLSSKLLAEIPIGAAFPLIFGSILYPMSKLHPTFSR FAKFCGIVTVESFAASAMGLTVGAMAPTTEAAMALGPSLMTVFIVFGGYYVNPDNTPV IFRWIPKVSLIRWAFQGLCINEFKGLQFEQQHSYDIQTGEQALERFSLGGIRIADTLV AQGRILMFWYWLTYLLLKKNRPKYQQLLPPSEEDQNKQQVKEVK</aaseq>|
DNA = <dnaseqindica>5232..5417#4839..4923#4526..4738#4167..4387#3859..3990#3007..3283#2413..2614#1590..1722#1110..1260#827..1017#119..334#ccccccccccccctcgtcttcctcctcttcactcctcgtcgcacgcgacgtgaaccttccagaagcttctagaacagtcgtcaggcctctctccgctcgtcccccgcgcgcgcgcgagatggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggtgagtcgctctgcctcgaatcatccattccgttccctctcgccggaggagtcgcattggtcggcggcgctgcgcgcacggaaagaaaaaaaaaatcatctgcttaggattagccaggagagccgcgtgctgtctgagagactgacactgggccctacctgtcgatgtggcactgactcatcacattttagatgaacaggttgctgaaatttgtttcgcacttccgctgttggctaacgggctaagtaattgcgtggcattctgcagtctgtatgtagaattgtatattaatttgcgtcgaacaagtaatttgcgaaatttgtttcacactttcaccgtctgcactctgcagcttcaatcagtagatgaacacaccgaagctgtgtattctgtatgtagaattgtacattgagtgccatcaataatcggaatttcttgcttctgcgcgtctctgggtgattgttgtaatggttataacgtgctgcatgccaggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagtaagcttaagctatgcttcttcagttggctttcacaattttttagtcaggtttacagagaagagctatactcattgcttttccttgtgtaggattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggtaagttatccatgatggtatatggtctgctttctaaagaaaaagttatccatgatggttaaaatgttcgaagaaattgaaccaattggttttagtgcactacatcaaatgttggatacgaacttgtagtttctagcactggtggagaaaatctgtcaaattacacatgaaaagcattgttattttggtgctcagatagatgacaagtatgctaagtttttcaattgatgggcagaacctacataatatctatcgctgtctgttcaagtatttccctttttattttgtatcaccaggtatttatttctttttattataactggttgtaggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtacttttacctgactgtagtgtttatttaacccttccttggttgaataagcattctcatctcctcttaatgttttcgttaggaaatacatgactagttgcaagcaaatgttctgatcacttcttcaaatctactgtttctttgtaaatttgtgccatgcttcttttttttattggaaccagcacgagaatgtgctttttcattaaatatagcaggagaaaaatacagcccctaagggcaaagaaaaagaaaatttgtagccatgccggattcaagtgaaaatagattgccaatactgcgatagttgcattaaaatggcttcaatagatacaccacatttttctcatgccacaagaattgctttaagatgatgcatgtttcttgtactaagactgctactctaatggttaacacatgacatatcataatcttggtggcatctttaatcaagcaccatggtattgggacttgccttattagatttgtcattgaatgctgcaaacaaaatatattcttgatatgatatacaagctacatcccttctggacaaagtgttgcacatttactttatctgaagtgttgagcttccatgattagagatagcgcattcattggtcctttgatgtgacaaaagtgcaaaacataagtgagattgcataaactttgttcacatatgtgccatccttttaggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggttggtattcgctcaccttttcctttacttggcatttcctgttgttttcgatgtgtgcattgtactgattttatttagactgtaatactctactaccttggtgcataacatgatagtggtcatatttgtccttgttagtggcactatccaaaattccagtgtacggtatgctagaattttactcagaattttaattaggcatgcagattctggcttgtgtacttgttcacaccataatggagattatcttgcttttataagttcttttatctattatcagatgtgttggtttctatattctatgtatactgtcaatatgctatgctgcttgtttttctgcctgctattattgcttatcaataacttgagtttgattacttcatatttttcaggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggttttattaaaattcatttaattctcagttgcagcttcctcttttaatctgcttcccgctgcttctttaaatcaagttgatatgtttatttattatttgctgtggaagttatcagatactcgtgaggcttcctttcaaaaaaatcgtttttcttacatattcttttagcctgagtaaactatatacataatgtaatgaatttaggaggtttagatcgaacatgttactatatttgagtttggatccatgatttagtttttgccaaatctgtgcctcaaaaaggtgtaatacgcaactgcccatgaaacatacttgtaaacaaaaaagaaacactttgctaatggaactatgaggatttggattgtggttgattgtaaacaaaaaggaaacactttgctaatggaactataaggatttggattgtggttgaggttatctgactaatgttcaagccttttatagtttgcctgggtacccattaataatctgagcgcagttgcttagatggggtttagctaaagatttactgccacgctgttgtgtctgatattggaataggaccttctgtgttttaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtagaatatgttggattttttatgactcgttgagttgaatttgctaggttgcacatgcttcagattttggacttacattcattctcttcctaatattgactttggtacaagctttttcattgtgtctgagcatttttctgattttgatctgtccctttttcaatttatgagttaaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctaggtaagtattatcctccctctaatttagaaatgaatctgaggcactttattacatgccacgcagaaatagtagaatatcgatagttcgatactattttgtttatgctccatcaaacaacattccatgctacactttcagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatggtaaccctcttccttatatcatattttggctcctaagctaggtgggaccgtgggatagttaatgaccctatatttcaactttgtttgccattgatttcagggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggtacggttgttcatgtggacctgcaaaaggcagttttacatttttactgttacaaaaatgcagacacacacttggttaagtgccagtgagatattgctcgacctaagttaatgtttgaatgataatgcactcaaacagaaaattggcccagacactattcatgtgttatcatcacattcaattaaaaatctgaattgaaaattttccttgaattgtaactggggcctgggtaaaaaggtgaacctttggcatatctttcttctatggaggggaagtgatctgcttttgacacattacttctatggcaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatgaagtgctgccagcaacattttgccagcaaaggtaaaagagacattagcattaaccacgtttcacacaatggtcctaatctcctgaaatattttttgtcaggatgtactgcaattagaaaacgtaactgttgtatcatattgagcattagttgtatggccctttttgtagttaatattctttttgtagcatctgaatgggaaattatggcctaaataattttgggggtagcaagcattccttcattctatagtcttgcatctatagaagacttatccccattcccagaatgactgtcttgttatcaagcacatcgtttttagttgcccagaaatgcattgtcatcaagttgttgtacccacttagattaacattgctagaagccgagaactctgaagcctttataagatctaattgctacagatatggtgtttgggaagtagtttagttgacagtagcataaatcaggaatcatgacccatgttgtaaacttcaagatccatgcatcttgtgtttcttgtgacctctaggcactcaattctgcaattgcttcaagtcttgaacccttgagcccatttgagtagctttgctgatgatgccatatactaatatctccttgaccatgtgccaactgatggcagctagggatctgcactagcattcaggctatgtgataaacaacttagccaatagtatgatagtactataatttctcctctttgccaattgctaactgttttctttttttttttcttatcagagagaagctgcaccttcttcacagcatctcggcatgagaatgagaggatcactaaatcatgcggcaataaaacaattagccgcccaagcccatcactttgaagcagtacatcaactcaactgaatgattaatttcctcttttcttttttgtcaagcaagtactcgtagtaatagtattcaactcaataatgggagatggccggtgttggttggaagcgacgagtcgctgcattcgatgtgattacttctaaactatttattgttccatgattccttccctgaataaatcaccggccaaaatgtgccatgtggact</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048413.1 RefSeq:Os01g0121700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0121700

2014-06-09T12:41:07Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
The name of the gene is half-size adenosine triphosphate-binding cassette transporter subgroup G,OsABCG1or OsWBC1,is a Putative ATP-binding-cassette protein，belongs to the ABC transporter superfamily.
===Function===
ATP-binding cassette transporters (ABC transporters) are transmembrane proteins that utilize the energy of adenosine triphosphate (ATP) binding and hydrolysis to carry out certain biological processes including translocation of various substrates across membranes and non-transport-related processes such as translation of RNA and DNA repair. They transport a wide variety of substrates across extra- and intracellular membranes, including metabolic products, lipids and sterols, and drugs. Proteins are classified as ABC transporters based on the sequence and organization of their ATP-binding cassette (ABC) domain(s).

ABC proteins are characterized by a highly conserved amino acid region, the ATP binding cassette, also known as the nucleotide binding domain (NBD). This domain contains conserved motifs known as Walker A and Walker B sequences, an ABC signature motif, an H loop, and a Q loop . Half-size ABC proteins consist of only one core unit, while full-size ABC proteins have two or more core units. Full-size ABC proteins can function alone, whereas half-size ABC proteins must form homo- or heterodimers to function as transporters.
===Mechanism of function===
The general mechanism for the transport cycle of ABC transporters has not been fully elucidated but substantial structural and biochemical data has accumulated to support a model in which ATP binding and hydrolysis is coupled to conformational changes in the transporter. The resting state of all ABC transporters has the NBDs in an open dimer configuration, with low affinity for ATP. This open conformation possesses a chamber accessible to the interior of the transporter. The transport cycle is initiated by binding of substrate to the high-affinity site on the TMDs, which induces conformational changes in the NBDs and enhances the binding of ATP. Two molecules of ATP bind, cooperatively, to form the closed dimer configuration. The closed NBD dimer induces a conformational change in the TMDs such that the TMD opens, forming a chamber with an opening opposite to that of the initial state. The affinity of the substrate to the TMD is reduced, thereby releasing the substrate. Hydrolysis of ATP follows and then sequential release of Pi and then ADP restores the transporter to its basal configuration. Although a common mechanism has been suggested, the order of substrate binding, nucleotide binding and hydrolysis, and conformational changes, as well as interactions between the domains is still debated.
===Expression===
ATP-binding cassette transporters (ABC transporters) are members of a protein superfamily that is one of the largest and oldest families with representatives in all extant phyla from prokaryotes to humans.

===Evolution===
Adenosine triphosphate (ATP)-binding cassette (ABC) proteins exist in a wide range of organisms from prokaryotes to eukaryotes.Genome wide analysis of model plants such as Arabidopsis and rice (Oryza sativa L.) has revealed that plants have more than 120 ABC proteins, much more than animals or insects.

You can also add sub-section(s) at will.

==Labs working on this gene==
1. Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, 2-11 Nishi, Inada, Obihiro, Hokkaido 080-8555, Japan.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0121700|
Description = ABC transporter related domain containing protein|
Version = NM_001048413.1 GI:115434239 GeneID:4326045|
Length = 6489 bp|
Definition = Oryza sativa Japonica Group Os01g0121700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:1223012..1229500|
CDS = 1224084..1224269,1224578..1224662,1224763..1224975,1225114..1225334,1225511..1225642 ,1226218..1226494,1226887..1227088,1227779..1227911,1228241..1228391 ,1228484..1228674,1229167..1229382|
GCID = <gbrowseImage1>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatgggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatga</cdnaseq>|
AA = <aaseq>MEVRGLGQLLAALAAALFVRAVAGPGPALLPPADDEDSDADPEA GGEGGGVPPVTIRWARITCALKNKRGDVARFLLSNASGEAKSGRLLALMGPSGSGKTT LLNVLAGQLTASPSLHLSGFLYINGRPISEGGYKIAYVRQEDLFFSQLTVRETLSLAA ELQLRRTLTPERKESYVNDLLFRLGLVNCADSIVGDAKVRGISGGEKKRLSLACELIA SPSIIFADEPTTGLDAFQAEKVMETLRQLAEDGHTVICSIHQPRGSVYGKFDDIVLLS EGEVIYMGPAKEEPLLYFASLGYHCPDHVNPAEFLADLISVDYSSAESVQSSRKRIEN LIEEFSNKVAITESNSSLTNPEGSEFSPKLIQKSTTKHRRGWWRQFRLLFKRAWMQAF RDGPTNKVRARMSVASAIIFGSVFWRMGKTQTSIQDRMGLLQVTAINTAMAALTKTVG VFPKERAIVDRERAKGSYALGPYLSSKLLAEIPIGAAFPLIFGSILYPMSKLHPTFSR FAKFCGIVTVESFAASAMGLTVGAMAPTTEAAMALGPSLMTVFIVFGGYYVNPDNTPV IFRWIPKVSLIRWAFQGLCINEFKGLQFEQQHSYDIQTGEQALERFSLGGIRIADTLV AQGRILMFWYWLTYLLLKKNRPKYQQLLPPSEEDQNKQQVKEVK</aaseq>|
DNA = <dnaseqindica>5232..5417#4839..4923#4526..4738#4167..4387#3859..3990#3007..3283#2413..2614#1590..1722#1110..1260#827..1017#119..334#ccccccccccccctcgtcttcctcctcttcactcctcgtcgcacgcgacgtgaaccttccagaagcttctagaacagtcgtcaggcctctctccgctcgtcccccgcgcgcgcgcgagatggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggtgagtcgctctgcctcgaatcatccattccgttccctctcgccggaggagtcgcattggtcggcggcgctgcgcgcacggaaagaaaaaaaaaatcatctgcttaggattagccaggagagccgcgtgctgtctgagagactgacactgggccctacctgtcgatgtggcactgactcatcacattttagatgaacaggttgctgaaatttgtttcgcacttccgctgttggctaacgggctaagtaattgcgtggcattctgcagtctgtatgtagaattgtatattaatttgcgtcgaacaagtaatttgcgaaatttgtttcacactttcaccgtctgcactctgcagcttcaatcagtagatgaacacaccgaagctgtgtattctgtatgtagaattgtacattgagtgccatcaataatcggaatttcttgcttctgcgcgtctctgggtgattgttgtaatggttataacgtgctgcatgccaggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagtaagcttaagctatgcttcttcagttggctttcacaattttttagtcaggtttacagagaagagctatactcattgcttttccttgtgtaggattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggtaagttatccatgatggtatatggtctgctttctaaagaaaaagttatccatgatggttaaaatgttcgaagaaattgaaccaattggttttagtgcactacatcaaatgttggatacgaacttgtagtttctagcactggtggagaaaatctgtcaaattacacatgaaaagcattgttattttggtgctcagatagatgacaagtatgctaagtttttcaattgatgggcagaacctacataatatctatcgctgtctgttcaagtatttccctttttattttgtatcaccaggtatttatttctttttattataactggttgtaggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtacttttacctgactgtagtgtttatttaacccttccttggttgaataagcattctcatctcctcttaatgttttcgttaggaaatacatgactagttgcaagcaaatgttctgatcacttcttcaaatctactgtttctttgtaaatttgtgccatgcttcttttttttattggaaccagcacgagaatgtgctttttcattaaatatagcaggagaaaaatacagcccctaagggcaaagaaaaagaaaatttgtagccatgccggattcaagtgaaaatagattgccaatactgcgatagttgcattaaaatggcttcaatagatacaccacatttttctcatgccacaagaattgctttaagatgatgcatgtttcttgtactaagactgctactctaatggttaacacatgacatatcataatcttggtggcatctttaatcaagcaccatggtattgggacttgccttattagatttgtcattgaatgctgcaaacaaaatatattcttgatatgatatacaagctacatcccttctggacaaagtgttgcacatttactttatctgaagtgttgagcttccatgattagagatagcgcattcattggtcctttgatgtgacaaaagtgcaaaacataagtgagattgcataaactttgttcacatatgtgccatccttttaggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggttggtattcgctcaccttttcctttacttggcatttcctgttgttttcgatgtgtgcattgtactgattttatttagactgtaatactctactaccttggtgcataacatgatagtggtcatatttgtccttgttagtggcactatccaaaattccagtgtacggtatgctagaattttactcagaattttaattaggcatgcagattctggcttgtgtacttgttcacaccataatggagattatcttgcttttataagttcttttatctattatcagatgtgttggtttctatattctatgtatactgtcaatatgctatgctgcttgtttttctgcctgctattattgcttatcaataacttgagtttgattacttcatatttttcaggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggttttattaaaattcatttaattctcagttgcagcttcctcttttaatctgcttcccgctgcttctttaaatcaagttgatatgtttatttattatttgctgtggaagttatcagatactcgtgaggcttcctttcaaaaaaatcgtttttcttacatattcttttagcctgagtaaactatatacataatgtaatgaatttaggaggtttagatcgaacatgttactatatttgagtttggatccatgatttagtttttgccaaatctgtgcctcaaaaaggtgtaatacgcaactgcccatgaaacatacttgtaaacaaaaaagaaacactttgctaatggaactatgaggatttggattgtggttgattgtaaacaaaaaggaaacactttgctaatggaactataaggatttggattgtggttgaggttatctgactaatgttcaagccttttatagtttgcctgggtacccattaataatctgagcgcagttgcttagatggggtttagctaaagatttactgccacgctgttgtgtctgatattggaataggaccttctgtgttttaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtagaatatgttggattttttatgactcgttgagttgaatttgctaggttgcacatgcttcagattttggacttacattcattctcttcctaatattgactttggtacaagctttttcattgtgtctgagcatttttctgattttgatctgtccctttttcaatttatgagttaaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctaggtaagtattatcctccctctaatttagaaatgaatctgaggcactttattacatgccacgcagaaatagtagaatatcgatagttcgatactattttgtttatgctccatcaaacaacattccatgctacactttcagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatggtaaccctcttccttatatcatattttggctcctaagctaggtgggaccgtgggatagttaatgaccctatatttcaactttgtttgccattgatttcagggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggtacggttgttcatgtggacctgcaaaaggcagttttacatttttactgttacaaaaatgcagacacacacttggttaagtgccagtgagatattgctcgacctaagttaatgtttgaatgataatgcactcaaacagaaaattggcccagacactattcatgtgttatcatcacattcaattaaaaatctgaattgaaaattttccttgaattgtaactggggcctgggtaaaaaggtgaacctttggcatatctttcttctatggaggggaagtgatctgcttttgacacattacttctatggcaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatgaagtgctgccagcaacattttgccagcaaaggtaaaagagacattagcattaaccacgtttcacacaatggtcctaatctcctgaaatattttttgtcaggatgtactgcaattagaaaacgtaactgttgtatcatattgagcattagttgtatggccctttttgtagttaatattctttttgtagcatctgaatgggaaattatggcctaaataattttgggggtagcaagcattccttcattctatagtcttgcatctatagaagacttatccccattcccagaatgactgtcttgttatcaagcacatcgtttttagttgcccagaaatgcattgtcatcaagttgttgtacccacttagattaacattgctagaagccgagaactctgaagcctttataagatctaattgctacagatatggtgtttgggaagtagtttagttgacagtagcataaatcaggaatcatgacccatgttgtaaacttcaagatccatgcatcttgtgtttcttgtgacctctaggcactcaattctgcaattgcttcaagtcttgaacccttgagcccatttgagtagctttgctgatgatgccatatactaatatctccttgaccatgtgccaactgatggcagctagggatctgcactagcattcaggctatgtgataaacaacttagccaatagtatgatagtactataatttctcctctttgccaattgctaactgttttctttttttttttcttatcagagagaagctgcaccttcttcacagcatctcggcatgagaatgagaggatcactaaatcatgcggcaataaaacaattagccgcccaagcccatcactttgaagcagtacatcaactcaactgaatgattaatttcctcttttcttttttgtcaagcaagtactcgtagtaatagtattcaactcaataatgggagatggccggtgttggttggaagcgacgagtcgctgcattcgatgtgattacttctaaactatttattgttccatgattccttccctgaataaatcaccggccaaaatgtgccatgtggact</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048413.1 RefSeq:Os01g0121700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0121700

2014-06-09T12:39:41Z

Liangliangbig: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
The name of the gene is half-size adenosine triphosphate-binding cassette transporter subgroup G,OsABCG1or OsWBC1,is a Putative ATP-binding-cassette protein，belongs to the ABC transporter superfamily.
===Function===
ATP-binding cassette transporters (ABC transporters) are transmembrane proteins that utilize the energy of adenosine triphosphate (ATP) binding and hydrolysis to carry out certain biological processes including translocation of various substrates across membranes and non-transport-related processes such as translation of RNA and DNA repair. They transport a wide variety of substrates across extra- and intracellular membranes, including metabolic products, lipids and sterols, and drugs. Proteins are classified as ABC transporters based on the sequence and organization of their ATP-binding cassette (ABC) domain(s).

ABC proteins are characterized by a highly conserved amino acid region, the ATP binding cassette, also known as the nucleotide binding domain (NBD). This domain contains conserved motifs known as Walker A and Walker B sequences, an ABC signature motif, an H loop, and a Q loop . Half-size ABC proteins consist of only one core unit, while full-size ABC proteins have two or more core units. Full-size ABC proteins can function alone, whereas half-size ABC proteins must form homo- or heterodimers to function as transporters.
===Mechanism of function===
The general mechanism for the transport cycle of ABC transporters has not been fully elucidated but substantial structural and biochemical data has accumulated to support a model in which ATP binding and hydrolysis is coupled to conformational changes in the transporter. The resting state of all ABC transporters has the NBDs in an open dimer configuration, with low affinity for ATP. This open conformation possesses a chamber accessible to the interior of the transporter. The transport cycle is initiated by binding of substrate to the high-affinity site on the TMDs, which induces conformational changes in the NBDs and enhances the binding of ATP. Two molecules of ATP bind, cooperatively, to form the closed dimer configuration. The closed NBD dimer induces a conformational change in the TMDs such that the TMD opens, forming a chamber with an opening opposite to that of the initial state. The affinity of the substrate to the TMD is reduced, thereby releasing the substrate. Hydrolysis of ATP follows and then sequential release of Pi and then ADP restores the transporter to its basal configuration. Although a common mechanism has been suggested, the order of substrate binding, nucleotide binding and hydrolysis, and conformational changes, as well as interactions between the domains is still debated.
===Expression===
ATP-binding cassette transporters (ABC transporters) are members of a protein superfamily that is one of the largest and oldest families with representatives in all extant phyla from prokaryotes to humans.

===Evolution===
Adenosine triphosphate (ATP)-binding cassette (ABC) proteins exist in a wide range of organisms from prokaryotes to eukaryotes.Genome wide analysis of model plants such as Arabidopsis and rice (Oryza sativa L.) has revealed that plants have more than 120 ABC proteins, much more than animals or insects.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0121700|
Description = ABC transporter related domain containing protein|
Version = NM_001048413.1 GI:115434239 GeneID:4326045|
Length = 6489 bp|
Definition = Oryza sativa Japonica Group Os01g0121700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:1223012..1229500|
CDS = 1224084..1224269,1224578..1224662,1224763..1224975,1225114..1225334,1225511..1225642 ,1226218..1226494,1226887..1227088,1227779..1227911,1228241..1228391 ,1228484..1228674,1229167..1229382|
GCID = <gbrowseImage1>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatgggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatga</cdnaseq>|
AA = <aaseq>MEVRGLGQLLAALAAALFVRAVAGPGPALLPPADDEDSDADPEA GGEGGGVPPVTIRWARITCALKNKRGDVARFLLSNASGEAKSGRLLALMGPSGSGKTT LLNVLAGQLTASPSLHLSGFLYINGRPISEGGYKIAYVRQEDLFFSQLTVRETLSLAA ELQLRRTLTPERKESYVNDLLFRLGLVNCADSIVGDAKVRGISGGEKKRLSLACELIA SPSIIFADEPTTGLDAFQAEKVMETLRQLAEDGHTVICSIHQPRGSVYGKFDDIVLLS EGEVIYMGPAKEEPLLYFASLGYHCPDHVNPAEFLADLISVDYSSAESVQSSRKRIEN LIEEFSNKVAITESNSSLTNPEGSEFSPKLIQKSTTKHRRGWWRQFRLLFKRAWMQAF RDGPTNKVRARMSVASAIIFGSVFWRMGKTQTSIQDRMGLLQVTAINTAMAALTKTVG VFPKERAIVDRERAKGSYALGPYLSSKLLAEIPIGAAFPLIFGSILYPMSKLHPTFSR FAKFCGIVTVESFAASAMGLTVGAMAPTTEAAMALGPSLMTVFIVFGGYYVNPDNTPV IFRWIPKVSLIRWAFQGLCINEFKGLQFEQQHSYDIQTGEQALERFSLGGIRIADTLV AQGRILMFWYWLTYLLLKKNRPKYQQLLPPSEEDQNKQQVKEVK</aaseq>|
DNA = <dnaseqindica>5232..5417#4839..4923#4526..4738#4167..4387#3859..3990#3007..3283#2413..2614#1590..1722#1110..1260#827..1017#119..334#ccccccccccccctcgtcttcctcctcttcactcctcgtcgcacgcgacgtgaaccttccagaagcttctagaacagtcgtcaggcctctctccgctcgtcccccgcgcgcgcgcgagatggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggtgagtcgctctgcctcgaatcatccattccgttccctctcgccggaggagtcgcattggtcggcggcgctgcgcgcacggaaagaaaaaaaaaatcatctgcttaggattagccaggagagccgcgtgctgtctgagagactgacactgggccctacctgtcgatgtggcactgactcatcacattttagatgaacaggttgctgaaatttgtttcgcacttccgctgttggctaacgggctaagtaattgcgtggcattctgcagtctgtatgtagaattgtatattaatttgcgtcgaacaagtaatttgcgaaatttgtttcacactttcaccgtctgcactctgcagcttcaatcagtagatgaacacaccgaagctgtgtattctgtatgtagaattgtacattgagtgccatcaataatcggaatttcttgcttctgcgcgtctctgggtgattgttgtaatggttataacgtgctgcatgccaggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagtaagcttaagctatgcttcttcagttggctttcacaattttttagtcaggtttacagagaagagctatactcattgcttttccttgtgtaggattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggtaagttatccatgatggtatatggtctgctttctaaagaaaaagttatccatgatggttaaaatgttcgaagaaattgaaccaattggttttagtgcactacatcaaatgttggatacgaacttgtagtttctagcactggtggagaaaatctgtcaaattacacatgaaaagcattgttattttggtgctcagatagatgacaagtatgctaagtttttcaattgatgggcagaacctacataatatctatcgctgtctgttcaagtatttccctttttattttgtatcaccaggtatttatttctttttattataactggttgtaggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtacttttacctgactgtagtgtttatttaacccttccttggttgaataagcattctcatctcctcttaatgttttcgttaggaaatacatgactagttgcaagcaaatgttctgatcacttcttcaaatctactgtttctttgtaaatttgtgccatgcttcttttttttattggaaccagcacgagaatgtgctttttcattaaatatagcaggagaaaaatacagcccctaagggcaaagaaaaagaaaatttgtagccatgccggattcaagtgaaaatagattgccaatactgcgatagttgcattaaaatggcttcaatagatacaccacatttttctcatgccacaagaattgctttaagatgatgcatgtttcttgtactaagactgctactctaatggttaacacatgacatatcataatcttggtggcatctttaatcaagcaccatggtattgggacttgccttattagatttgtcattgaatgctgcaaacaaaatatattcttgatatgatatacaagctacatcccttctggacaaagtgttgcacatttactttatctgaagtgttgagcttccatgattagagatagcgcattcattggtcctttgatgtgacaaaagtgcaaaacataagtgagattgcataaactttgttcacatatgtgccatccttttaggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggttggtattcgctcaccttttcctttacttggcatttcctgttgttttcgatgtgtgcattgtactgattttatttagactgtaatactctactaccttggtgcataacatgatagtggtcatatttgtccttgttagtggcactatccaaaattccagtgtacggtatgctagaattttactcagaattttaattaggcatgcagattctggcttgtgtacttgttcacaccataatggagattatcttgcttttataagttcttttatctattatcagatgtgttggtttctatattctatgtatactgtcaatatgctatgctgcttgtttttctgcctgctattattgcttatcaataacttgagtttgattacttcatatttttcaggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggttttattaaaattcatttaattctcagttgcagcttcctcttttaatctgcttcccgctgcttctttaaatcaagttgatatgtttatttattatttgctgtggaagttatcagatactcgtgaggcttcctttcaaaaaaatcgtttttcttacatattcttttagcctgagtaaactatatacataatgtaatgaatttaggaggtttagatcgaacatgttactatatttgagtttggatccatgatttagtttttgccaaatctgtgcctcaaaaaggtgtaatacgcaactgcccatgaaacatacttgtaaacaaaaaagaaacactttgctaatggaactatgaggatttggattgtggttgattgtaaacaaaaaggaaacactttgctaatggaactataaggatttggattgtggttgaggttatctgactaatgttcaagccttttatagtttgcctgggtacccattaataatctgagcgcagttgcttagatggggtttagctaaagatttactgccacgctgttgtgtctgatattggaataggaccttctgtgttttaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtagaatatgttggattttttatgactcgttgagttgaatttgctaggttgcacatgcttcagattttggacttacattcattctcttcctaatattgactttggtacaagctttttcattgtgtctgagcatttttctgattttgatctgtccctttttcaatttatgagttaaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctaggtaagtattatcctccctctaatttagaaatgaatctgaggcactttattacatgccacgcagaaatagtagaatatcgatagttcgatactattttgtttatgctccatcaaacaacattccatgctacactttcagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatggtaaccctcttccttatatcatattttggctcctaagctaggtgggaccgtgggatagttaatgaccctatatttcaactttgtttgccattgatttcagggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggtacggttgttcatgtggacctgcaaaaggcagttttacatttttactgttacaaaaatgcagacacacacttggttaagtgccagtgagatattgctcgacctaagttaatgtttgaatgataatgcactcaaacagaaaattggcccagacactattcatgtgttatcatcacattcaattaaaaatctgaattgaaaattttccttgaattgtaactggggcctgggtaaaaaggtgaacctttggcatatctttcttctatggaggggaagtgatctgcttttgacacattacttctatggcaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatgaagtgctgccagcaacattttgccagcaaaggtaaaagagacattagcattaaccacgtttcacacaatggtcctaatctcctgaaatattttttgtcaggatgtactgcaattagaaaacgtaactgttgtatcatattgagcattagttgtatggccctttttgtagttaatattctttttgtagcatctgaatgggaaattatggcctaaataattttgggggtagcaagcattccttcattctatagtcttgcatctatagaagacttatccccattcccagaatgactgtcttgttatcaagcacatcgtttttagttgcccagaaatgcattgtcatcaagttgttgtacccacttagattaacattgctagaagccgagaactctgaagcctttataagatctaattgctacagatatggtgtttgggaagtagtttagttgacagtagcataaatcaggaatcatgacccatgttgtaaacttcaagatccatgcatcttgtgtttcttgtgacctctaggcactcaattctgcaattgcttcaagtcttgaacccttgagcccatttgagtagctttgctgatgatgccatatactaatatctccttgaccatgtgccaactgatggcagctagggatctgcactagcattcaggctatgtgataaacaacttagccaatagtatgatagtactataatttctcctctttgccaattgctaactgttttctttttttttttcttatcagagagaagctgcaccttcttcacagcatctcggcatgagaatgagaggatcactaaatcatgcggcaataaaacaattagccgcccaagcccatcactttgaagcagtacatcaactcaactgaatgattaatttcctcttttcttttttgtcaagcaagtactcgtagtaatagtattcaactcaataatgggagatggccggtgttggttggaagcgacgagtcgctgcattcgatgtgattacttctaaactatttattgttccatgattccttccctgaataaatcaccggccaaaatgtgccatgtggact</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048413.1 RefSeq:Os01g0121700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os06g0229800

2014-06-08T13:37:54Z

Liangliangbig: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

[[File:map location.jpg]]

Fig.1. Genetic map of chromosome 6 in rice

This gene,which has been proposed to be involved in the biosynthesis of amylopectin.It is a single copy gene via Southern blot analysis.The product of this gene only have one ORF, which belongs to glycosyl transferase family. Genomic DNA contains seven introns and eight exons. full-length of cDNA is 2409bp,and the enzyme protein composed of 803 amino acids.

[[File:cDNA of alk.jpg]]

Fig.2. Demonstration of genome sequence and cDNA sequence of alk

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

Gelatinization temperature (GT), an important parameter for rice cooking quality, is the critical temperature at which the starch granules start to lose crystallinity and birefringence by irreversible expanding and to change the starch surface from polarized to soluble state called starch paste.

Map-based cloning and sequence analysis of the ALK genes from different rice varieties, and base substitutions in coding sequence may cause the alteration in GT.Comparison between the DNA sequences from different rice varieties, together with the results obtained with digestion of the rice seeds in alkali solution, indicates that the base substitutions in coding sequence of ALK may cause the alteration in GT.

[[File:comparison.jpg]]

Fig.3. Comparison between the conserved DNA fragments of ALK in 9 rice varieties. The different nucleotides are shown inbold. Numbers above the plus sign indicate the nucleotide position fromATG in ALK of Shuangke Zao.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Fig.4. Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

Map-based cloning and sequence analysis of the ALK in different rice varieties revealed that base substitutions of G264 to C264 and GACGAG259-264 to AGCTTA259-264, which cause amino acids changes of Glu88 to Asp88 and Asp87Glu88 to Ser87Leu88, may result in the alteration of enzymatic activity of SSSII, which will finally alter the fine structure of crystalline lamellae of amylopectin and GT of rice.

[[File:relationship.jpg]]

Fig.5. Relationships between the primary amino acid sequences of SSSII in several plant species. The dendrogram was generated by the program CLUSTAL W. Accession numbers of source sequences are AY133248 for A. tauschii, AF155217 for wheat, AY133250 for barley, AF019296 for maize SSSIIb, AF019297 for maize SSSIIa, and AY423717 for rice.

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T13:34:49Z

Liangliangbig: /* Function */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

[[File:map location.jpg]]

Fig.1. Genetic map of chromosome 6 in rice

This gene,which has been proposed to be involved in the biosynthesis of amylopectin.It is a single copy gene via Southern blot analysis.The product of this gene only have one ORF, which belongs to glycosyl transferase family. Genomic DNA contains seven introns and eight exons. full-length of cDNA is 2409bp,and the enzyme protein composed of 803 amino acids.

[[File:cDNA of alk.jpg]]

Fig.2. Demonstration of genome sequence and cDNA sequence of alk

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

Gelatinization temperature (GT), an important parameter for rice cooking quality, is the critical temperature at which the starch granules start to lose crystallinity and birefringence by irreversible expanding and to change the starch surface from polarized to soluble state called starch paste.

Map-based cloning and sequence analysis of the ALK genes from different rice varieties, and base substitutions in coding sequence may cause the alteration in GT.Comparison between the DNA sequences from different rice varieties, together with the results obtained with digestion of the rice seeds in alkali solution, indicates that the base substitutions in coding sequence of ALK may cause the alteration in GT.

[[File:comparison.jpg]]

Fig.3. Comparison between the conserved DNA fragments of ALK in 9 rice varieties. The different nucleotides are shown inbold. Numbers above the plus sign indicate the nucleotide position fromATG in ALK of Shuangke Zao.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T13:31:55Z

Liangliangbig: /* Function */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

[[File:map location.jpg]]

Fig.1. Genetic map of chromosome 6 in rice

This gene,which has been proposed to be involved in the biosynthesis of amylopectin.It is a single copy gene via Southern blot analysis.The product of this gene only have one ORF, which belongs to glycosyl transferase family. Genomic DNA contains seven introns and eight exons. full-length of cDNA is 2409bp,and the enzyme protein composed of 803 amino acids.

[[File:cDNA of alk.jpg]]

Fig.2. Demonstration of genome sequence and cDNA sequence of alk

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

Gelatinization temperature (GT), an important parameter for rice cooking quality, is the critical temperature at which the starch granules start to lose crystallinity and birefringence by irreversible expanding and to change the starch surface from polarized to soluble state called starch paste.

Map-based cloning and sequence analysis of the ALK genes from different rice varieties, and base substitutions in coding sequence may cause the alteration in GT.Comparison between the DNA sequences from different rice varieties, together with the results obtained with digestion of the rice seeds in alkali solution, indicates that the base substitutions in coding sequence of ALK may cause the alteration in GT.

[[File:comparison.jpg]]

Comparison between the conserved DNA fragments of ALK in 9 rice varieties. The different nucleotides are shown inbold. Numbers above the plus sign indicate the nucleotide position fromATG in ALK of Shuangke Zao.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T13:17:41Z

Liangliangbig: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

[[File:map location.jpg]]

Fig.1. Genetic map of chromosome 6 in rice

This gene,which has been proposed to be involved in the biosynthesis of amylopectin.It is a single copy gene via Southern blot analysis.The product of this gene only have one ORF, which belongs to glycosyl transferase family. Genomic DNA contains seven introns and eight exons. full-length of cDNA is 2409bp,and the enzyme protein composed of 803 amino acids.

[[File:cDNA of alk.jpg]]

Fig.2. Demonstration of genome sequence and cDNA sequence of alk

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

File:CDNA of alk.jpg

2014-06-08T13:16:30Z

Liangliangbig: Demonstration of genome sequence and cDNA sequence of alk

Demonstration of genome sequence and cDNA sequence of alk

Os06g0229800

2014-06-08T13:15:41Z

Liangliangbig: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

[[File:map location.jpg]]

Fig.1. Genetic map of chromosome 6 in rice

This gene,which has been proposed to be involved in the biosynthesis of amylopectin.It is a single copy gene via Southern blot analysis.The product of this gene only have one ORF, which belongs to glycosyl transferase family. Genomic DNA contains seven introns and eight exons. full-length of cDNA is 2409bp,and the enzyme protein composed of 803 amino acids.

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T12:53:30Z

Liangliangbig: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

[[File:map location.jpg]]

Fig.1. Genetic map of chromosome 6 in rice

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

File:Map location.jpg

2014-06-08T12:51:40Z

Liangliangbig: genetic map of chromosome6

genetic map of chromosome6

Os06g0229800

2014-06-08T12:50:08Z

Liangliangbig: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T12:49:31Z

Liangliangbig: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
ALK (alkali degeneration gene) ,located on chromosome 6,previous studies have demonstrated that acl(t), a determinator of the profile for amylopectin chain-length of subspecies Japonica and Indica, alk(t)and SSSIIa were all mapped to the same locus.

===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T12:40:52Z

Liangliangbig: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, RT-PCR analysis demonstrated that ALK is expressed only in rice seeds,expression of the gene product is not detected in the blade tissues. In addition, no difference was detected at transcriptional level (fig. 5) among the rice varieties with high and low GT, suggesting that the alterations at the SSSII in different rice varieties may mainly affect its enzymatic activities.

[[File:expressionRT.jpg]]

Fig. 2. (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

File:Location of alk.jpg

2014-06-08T12:37:23Z

Liangliangbig: Genetic (a) and physical map (b) of ALK. All molecular markers are located on short arm of rice chromosome 6. (a) Letters and numbers above the vertical lines represent molecular markers and numbers below the vertical line represent the recombinants in a

Genetic (a) and physical map (b) of ALK. All molecular markers are located on short arm of rice chromosome 6. (a) Letters and numbers above the vertical lines represent molecular markers and numbers below the vertical line represent the recombinants in a 1352 F2 mapping population. (b) The horizontal line represents the nucleotide sequence between the molecular markers a and M5522. Predicted ORF in and near the 9.1 kb region are shown as open box.Numbers below the horizontal line and below the ORF indicate the nucleotide position according to the sequence of Nipponbare PAC clone P0525F01 (DDBJ accession number, AP003509).

File:ExpressionRT.jpg

2014-06-08T12:33:18Z

Liangliangbig: (a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

(a) Transcriptional levels of predicted ALK in different tissues of several rice varieties. (b) Transcriptional levels of Actin in different tissues of several rice varieties.

File:Relationship.jpg

2014-06-08T12:31:07Z

Liangliangbig: Relationships between the primary amino acid sequences of SSSII in several plant species. The dendrogram was generated by the program CLUSTAL W. Accession numbers of source sequences are AY133248 for A. tauschii, AF155217 for wheat, AY133250 for barley, A

Relationships between the primary amino acid sequences of SSSII in several plant species. The dendrogram was generated by the program CLUSTAL W. Accession numbers of source sequences are
AY133248 for A. tauschii, AF155217 for wheat, AY133250 for barley, AF019296 for maize SSSIIb, AF019297 for maize SSSIIa, and AY423717 for rice.

File:Comparison.jpg

2014-06-08T12:30:13Z

Liangliangbig: Comparison between the conserved DNA fragments of ALK in 9 rice varieties. The different nucleotides are shown inbold. Numbers above the plus sign indicate the nucleotide position fromATG in ALK of Shuangke Zao.

Comparison between the conserved DNA fragments of ALK in 9 rice varieties. The different nucleotides are shown inbold. Numbers above the plus sign indicate the nucleotide position fromATG in ALK of Shuangke Zao.

Os06g0229800

2014-06-08T11:45:41Z

Liangliangbig: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties[1].

===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T11:44:04Z

Liangliangbig: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

alk cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinization in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties.

===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T09:03:39Z

Liangliangbig: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T09:02:44Z

Liangliangbig: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Lin SY, Nagamura Y, kurata N, et al.DNA markers tightly linked to genes,Ph,alk and Rc.Rice Genet Newsletter,1994,11:108

2. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

3. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

4. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:45:10Z

Liangliangbig: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. Umemoto, T., et al., Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics, 2002. 104(1): p. 1-8.

2. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

3. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:40:33Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice development. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:40:04Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are important in rice developmen. The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:35:50Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute

Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences

Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:34:37Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

3、T. Umemoto ，Tohoku National Agricultural Experiment Station, Omagari, Akita 014-0102, Japan

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:02:33Z

Liangliangbig: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:02:05Z

Liangliangbig: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.
In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T07:00:30Z

Liangliangbig: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.
In five different plants: wheat, goat grass species, barley, maize and rice, the phylogenetic tree of SS Ⅱ shows that : SS Ⅱ of rice have a nearer evolutionary kinship with maize SS Ⅱa , which up to 69.8%.However, it have further relationship with barley SS Ⅱ.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]
Figure:Phylogenetic trees of SSⅡ from 5 different plant species(The number values represent the branch length)

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T06:28:09Z

Liangliangbig: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.
[[File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg]]

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

File:Phylogenetic trees of SSⅡ from 5 different plant species.jpg

2014-06-08T06:26:58Z

Liangliangbig: Phylogenetic trees of SSⅡ from 5 different plant species .PS:The number values represent the branch length

Phylogenetic trees of SSⅡ from 5 different plant species .PS:The number values represent the branch length

Os06g0229800

2014-06-08T06:10:29Z

Liangliangbig: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-08T06:08:54Z

Liangliangbig: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

[[File:1.jpg]]===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:55:13Z

Liangliangbig: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:54:45Z

Liangliangbig: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.
2. Guoyu Zhang;Zhijun Cheng;Xin Zhang;Xiuping Guo;Ning Su;Ling Jiang;Long Mao;Jianmin Wan. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch,Genome, 2011, 54(6): 448-459

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:52:44Z

Liangliangbig: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
1. 高振宇, 曾大力, 崔霞等. 水稻稻米糊化温度控制基因ALK的图位克隆及其序列分析. 中国科学(C辑), 2003, 33(6):481-487.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:51:50Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:50:56Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding
2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development. (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:49:31Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection.
They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:48:20Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

2、Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences
Jianmin Wan, His group is mainly engaged in rice gene mapping, cloning and cultivar selection. They focus on rice heading date, hybrid sterility, protein trafficking,and other traits which are related in rice important development (Germination, Plant Height, Panicle development, Starch biosynthesis). The lab also commit themselves to building high-density new molecular marker map, conducting fine mapping of genes related to the new, map-based cloning, conducting genetic transformation and function identification, as well as doing research of rice functional genomics, proteomics and bioinformatics, establishing and improving the design of efficient molecular breeding system, combined with conventional breeding to cultivate new varieties of high-quality rice with powerful market competitiveness.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T07:29:32Z

Liangliangbig: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
1、China National Rice Research Institute
Gao Zhenyu, Research:
（1） rice functional genomics
Genetic characteristics of important agronomic traits in rice, screening mutant libraries and build genetic populations, combined with genomics and transcriptomics gene / QTL mapping and cloning, and conduct functional analysis.
（2） Rice Molecular Genetics and Breeding
Use of existing genetic resources, gene / QTL polymerization and molecular breeding, creating a new high yield and quality of rice germplasm breeding

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-07T06:53:12Z

Liangliangbig: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
According to comparison of genomic DNA sequences among nine rice varieties, S-type varieties: Double Branch early, Minghui 63 and Zhaiyeqing,have G at the 264 site.While in C-type varieties(Ningxia early japonica, Chunjiang 06, No. 6 Nipponbare Yang Rice (indica)),have a C at the 264 site. So, the replace of G264 to C264 cause the amino acid change from Glu to Asp of SSS Ⅱ enzyme protein, which may be the genetic basis leading to pasting temperature change. Study the phylogenesis of five different plants including goats grass, wheat, barley, maize and rice, it shows that rice SSS Ⅱ and SSS Ⅱ a and b of maize is nearer relatively in evolutionary kinship, while is distantly related with goat grass species.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-06T12:43:18Z

Liangliangbig: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
===Function===
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-06T12:42:34Z

Liangliangbig: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.
===Expression===
ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-06T12:41:38Z

Liangliangbig: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

ALK gene is a single copy gene, and it has a specific expression in the seed of rice,RT-PCR results showed that expression of the gene product is not detected in the blade tissues.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0229800

2014-06-06T12:24:53Z

Liangliangbig: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
ALK gene encodes a soluble starch synthase Ⅱ, controlling the temperature of rice pasting .The encoding amino acid product of ALK gene may cause a change in starch synthase activity, thus affecting the synthesis of amylopectin branch chain of medium length, so that the crystal layer structure changes, resulting in the final performance of pasting temperature change.

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0229800|
Description = Similar to Starch synthase IIA|
Version = NM_001063751.1 GI:115467233 GeneID:4340567|
Length = 4946 bp|
Definition = Oryza sativa Japonica Group Os06g0229800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:6747359..6752304|
CDS = 6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 ,6749923..6749967,6750384..6750557,6751025..6751981|
GCID = <gbrowseImage1>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:6747359..6752304
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq>|
AA = <aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq>|
DNA = <dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063751.1 RefSeq:Os06g0229800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os01g0121700

2014-06-06T11:59:54Z

Liangliangbig: /* Annotated Information */

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==Annotated Information==
===Function===
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The name of the gene is half-size adenosine triphosphate-binding cassette transporter subgroup G,OsABCG1or OsWBC1,
===Expression===
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===Evolution===
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==Labs working on this gene==
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==References==
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==Structured Information==
{{JaponicaGene|
GeneName = Os01g0121700|
Description = ABC transporter related domain containing protein|
Version = NM_001048413.1 GI:115434239 GeneID:4326045|
Length = 6489 bp|
Definition = Oryza sativa Japonica Group Os01g0121700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:1223012..1229500|
CDS = 1224084..1224269,1224578..1224662,1224763..1224975,1225114..1225334,1225511..1225642 ,1226218..1226494,1226887..1227088,1227779..1227911,1228241..1228391 ,1228484..1228674,1229167..1229382|
GCID = <gbrowseImage1>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:1223012..1229500
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatgggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatga</cdnaseq>|
AA = <aaseq>MEVRGLGQLLAALAAALFVRAVAGPGPALLPPADDEDSDADPEA GGEGGGVPPVTIRWARITCALKNKRGDVARFLLSNASGEAKSGRLLALMGPSGSGKTT LLNVLAGQLTASPSLHLSGFLYINGRPISEGGYKIAYVRQEDLFFSQLTVRETLSLAA ELQLRRTLTPERKESYVNDLLFRLGLVNCADSIVGDAKVRGISGGEKKRLSLACELIA SPSIIFADEPTTGLDAFQAEKVMETLRQLAEDGHTVICSIHQPRGSVYGKFDDIVLLS EGEVIYMGPAKEEPLLYFASLGYHCPDHVNPAEFLADLISVDYSSAESVQSSRKRIEN LIEEFSNKVAITESNSSLTNPEGSEFSPKLIQKSTTKHRRGWWRQFRLLFKRAWMQAF RDGPTNKVRARMSVASAIIFGSVFWRMGKTQTSIQDRMGLLQVTAINTAMAALTKTVG VFPKERAIVDRERAKGSYALGPYLSSKLLAEIPIGAAFPLIFGSILYPMSKLHPTFSR FAKFCGIVTVESFAASAMGLTVGAMAPTTEAAMALGPSLMTVFIVFGGYYVNPDNTPV IFRWIPKVSLIRWAFQGLCINEFKGLQFEQQHSYDIQTGEQALERFSLGGIRIADTLV AQGRILMFWYWLTYLLLKKNRPKYQQLLPPSEEDQNKQQVKEVK</aaseq>|
DNA = <dnaseqindica>5232..5417#4839..4923#4526..4738#4167..4387#3859..3990#3007..3283#2413..2614#1590..1722#1110..1260#827..1017#119..334#ccccccccccccctcgtcttcctcctcttcactcctcgtcgcacgcgacgtgaaccttccagaagcttctagaacagtcgtcaggcctctctccgctcgtcccccgcgcgcgcgcgagatggaggtcaggggtctgggccagctcctggccgcgctcgccgcggcgctgttcgtccgcgccgtcgccggcccgggcccggcgctcctccctccggccgacgacgaggactccgacgccgacccggaggccggcggggaaggaggcggcgtgcctccggtgacgataaggtgggcccgcatcacctgcgccctcaagaacaagcgcggcgacgtggtgagtcgctctgcctcgaatcatccattccgttccctctcgccggaggagtcgcattggtcggcggcgctgcgcgcacggaaagaaaaaaaaaatcatctgcttaggattagccaggagagccgcgtgctgtctgagagactgacactgggccctacctgtcgatgtggcactgactcatcacattttagatgaacaggttgctgaaatttgtttcgcacttccgctgttggctaacgggctaagtaattgcgtggcattctgcagtctgtatgtagaattgtatattaatttgcgtcgaacaagtaatttgcgaaatttgtttcacactttcaccgtctgcactctgcagcttcaatcagtagatgaacacaccgaagctgtgtattctgtatgtagaattgtacattgagtgccatcaataatcggaatttcttgcttctgcgcgtctctgggtgattgttgtaatggttataacgtgctgcatgccaggcgaggtttttgctgtcaaatgcgtctggggaggcgaaatcggggaggctgcttgcgctcatggggccatcagggtccggtaaaacgactctgctcaatgtgcttgctggtcagctcacagcatcaccttctttgcacctttctgggtttctgtacatcaatggccgacctatctcagaaggtggctataagtaagcttaagctatgcttcttcagttggctttcacaattttttagtcaggtttacagagaagagctatactcattgcttttccttgtgtaggattgcttacgtgaggcaagaggaccttttcttctcacagcttactgttcgtgaaacgctctcgcttgctgctgaacttcagcttcgccgcacgttgactcctgagaggaaggaaagctatgttaatgaccttttgtttcgtcttgggctggtaagttatccatgatggtatatggtctgctttctaaagaaaaagttatccatgatggttaaaatgttcgaagaaattgaaccaattggttttagtgcactacatcaaatgttggatacgaacttgtagtttctagcactggtggagaaaatctgtcaaattacacatgaaaagcattgttattttggtgctcagatagatgacaagtatgctaagtttttcaattgatgggcagaacctacataatatctatcgctgtctgttcaagtatttccctttttattttgtatcaccaggtatttatttctttttattataactggttgtaggttaactgtgctgactcaattgtgggtgatgcaaaagtacgtggaataagtgggggtgaaaagaagcgtctctcccttgcgtgtgaactgattgctagcccttctatcatctttgcagacgaaccaactactggtacttttacctgactgtagtgtttatttaacccttccttggttgaataagcattctcatctcctcttaatgttttcgttaggaaatacatgactagttgcaagcaaatgttctgatcacttcttcaaatctactgtttctttgtaaatttgtgccatgcttcttttttttattggaaccagcacgagaatgtgctttttcattaaatatagcaggagaaaaatacagcccctaagggcaaagaaaaagaaaatttgtagccatgccggattcaagtgaaaatagattgccaatactgcgatagttgcattaaaatggcttcaatagatacaccacatttttctcatgccacaagaattgctttaagatgatgcatgtttcttgtactaagactgctactctaatggttaacacatgacatatcataatcttggtggcatctttaatcaagcaccatggtattgggacttgccttattagatttgtcattgaatgctgcaaacaaaatatattcttgatatgatatacaagctacatcccttctggacaaagtgttgcacatttactttatctgaagtgttgagcttccatgattagagatagcgcattcattggtcctttgatgtgacaaaagtgcaaaacataagtgagattgcataaactttgttcacatatgtgccatccttttaggtcttgatgcgttccaggcagagaaggtcatggaaactcttagacagcttgcagaagatggacacacggtgatatgttctatacatcagccaagaggttcagtttatggcaaatttgatgatattgtactactgtcagagggagaagttatatacatggggccagcaaaagaggaaccgttattgtactttgcatcattggggttggtattcgctcaccttttcctttacttggcatttcctgttgttttcgatgtgtgcattgtactgattttatttagactgtaatactctactaccttggtgcataacatgatagtggtcatatttgtccttgttagtggcactatccaaaattccagtgtacggtatgctagaattttactcagaattttaattaggcatgcagattctggcttgtgtacttgttcacaccataatggagattatcttgcttttataagttcttttatctattatcagatgtgttggtttctatattctatgtatactgtcaatatgctatgctgcttgtttttctgcctgctattattgcttatcaataacttgagtttgattacttcatatttttcaggtatcattgtccagatcatgtgaaccctgctgagttcttggctgatctcatttctgttgattatagttctgctgaaagtgtgcagtcatcacggaaaaggattgaaaacctcattgaagaattttctaataaagttgcaattactgaaagcaacagttcgctgacaaatccagaaggctctgaattttctcccaaacttattcagaagtccaccaccaagcatagacgtgggtggtggagacaattccgtttgctgtttaagagagcatggatgcaggttttattaaaattcatttaattctcagttgcagcttcctcttttaatctgcttcccgctgcttctttaaatcaagttgatatgtttatttattatttgctgtggaagttatcagatactcgtgaggcttcctttcaaaaaaatcgtttttcttacatattcttttagcctgagtaaactatatacataatgtaatgaatttaggaggtttagatcgaacatgttactatatttgagtttggatccatgatttagtttttgccaaatctgtgcctcaaaaaggtgtaatacgcaactgcccatgaaacatacttgtaaacaaaaaagaaacactttgctaatggaactatgaggatttggattgtggttgattgtaaacaaaaaggaaacactttgctaatggaactataaggatttggattgtggttgaggttatctgactaatgttcaagccttttatagtttgcctgggtacccattaataatctgagcgcagttgcttagatggggtttagctaaagatttactgccacgctgttgtgtctgatattggaataggaccttctgtgttttaggctttccgtgatggaccaacaaacaaagtgagagcaagaatgtccgttgcttcagcaatcatatttggatctgtgttctggcgaatggggaaaactcagacttccatacaagacaggatgggacttcttcaggtagaatatgttggattttttatgactcgttgagttgaatttgctaggttgcacatgcttcagattttggacttacattcattctcttcctaatattgactttggtacaagctttttcattgtgtctgagcatttttctgattttgatctgtccctttttcaatttatgagttaaggtaactgctataaacacagcaatggctgcactgacaaagacagtaggagttttcccgaaagagcgggctatagttgacagagaacgggccaaaggttcctatgcactaggaccatacctttcttctaagttgttggctgaaattcctattggggctgcattcccattgatatttggatccattctttatccaatgtctaaacttcatcctacattttctaggtaagtattatcctccctctaatttagaaatgaatctgaggcactttattacatgccacgcagaaatagtagaatatcgatagttcgatactattttgtttatgctccatcaaacaacattccatgctacactttcagatttgccaagttctgtggcatcgtgactgttgaatcatttgctgcatcagccatgggccttactgttggagctatggctcctacaacagaagccgccatggcccttggaccatcccttatgacagttttcattgtatttggaggatactatgttaaccctgataatacccccgtcatttttcgctggatcccaaaagtatccctaattagatggtaaccctcttccttatatcatattttggctcctaagctaggtgggaccgtgggatagttaatgaccctatatttcaactttgtttgccattgatttcagggccttccaagggctttgcattaatgagttcaaaggtttgcaatttgagcaacagcattcctatgacattcaaactggtgaacaggtacggttgttcatgtggacctgcaaaaggcagttttacatttttactgttacaaaaatgcagacacacacttggttaagtgccagtgagatattgctcgacctaagttaatgtttgaatgataatgcactcaaacagaaaattggcccagacactattcatgtgttatcatcacattcaattaaaaatctgaattgaaaattttccttgaattgtaactggggcctgggtaaaaaggtgaacctttggcatatctttcttctatggaggggaagtgatctgcttttgacacattacttctatggcaggccctggagaggttttcattaggaggaatccgcattgcagacacgcttgtggcacagggtagaattctgatgttctggtactggttaacctaccttcttctgaagaaaaacaggccaaagtatcagcagcttctaccaccatctgaggaagatcaaaataagcagcaagttaaggaagtgaaatgaagtgctgccagcaacattttgccagcaaaggtaaaagagacattagcattaaccacgtttcacacaatggtcctaatctcctgaaatattttttgtcaggatgtactgcaattagaaaacgtaactgttgtatcatattgagcattagttgtatggccctttttgtagttaatattctttttgtagcatctgaatgggaaattatggcctaaataattttgggggtagcaagcattccttcattctatagtcttgcatctatagaagacttatccccattcccagaatgactgtcttgttatcaagcacatcgtttttagttgcccagaaatgcattgtcatcaagttgttgtacccacttagattaacattgctagaagccgagaactctgaagcctttataagatctaattgctacagatatggtgtttgggaagtagtttagttgacagtagcataaatcaggaatcatgacccatgttgtaaacttcaagatccatgcatcttgtgtttcttgtgacctctaggcactcaattctgcaattgcttcaagtcttgaacccttgagcccatttgagtagctttgctgatgatgccatatactaatatctccttgaccatgtgccaactgatggcagctagggatctgcactagcattcaggctatgtgataaacaacttagccaatagtatgatagtactataatttctcctctttgccaattgctaactgttttctttttttttttcttatcagagagaagctgcaccttcttcacagcatctcggcatgagaatgagaggatcactaaatcatgcggcaataaaacaattagccgcccaagcccatcactttgaagcagtacatcaactcaactgaatgattaatttcctcttttcttttttgtcaagcaagtactcgtagtaatagtattcaactcaataatgggagatggccggtgttggttggaagcgacgagtcgctgcattcgatgtgattacttctaaactatttattgttccatgattccttccctgaataaatcaccggccaaaatgtgccatgtggact</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048413.1 RefSeq:Os01g0121700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]