Difference between revisions of "Os06g0229800"
(→References) |
(→Function) |
||
| Line 4: | Line 4: | ||
===Function=== | ===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 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=== | ===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. | 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. | ||
Revision as of 11:44, 8 June 2014
Please input one-sentence summary here.
Contents
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.
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
| Gene Name |
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 | |
| Location |
Chromosome 6:6747359..6752304 |
| Sequence Coding Region |
6747562..6747891,6748021..6748689,6748789..6748857,6749547..6749624,6749707..6749817 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008399:6747359..6752304 source=RiceChromosome06 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008399:6747359..6752304 source=RiceChromosome06 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtga</cdnaseq> |
| Protein Sequence |
<aaseq>MSSAVVASSTTFLVALASSASRGGPRRGRVVGVAAPPALLYDGR AGRLALRAPPPPRPRPRRRDAGVVRRADDGENEAAVERAGEDDDEEEEFSSGAWQPPR SRRGGVGKVLKRRGTVPPVGRYGSGGDAARVRGAAAPAPAPTQDAASSKNGALLSGRD DDTPASRNGSVVTGADKPAAATPPVTITKLPAPDSPVILPSVDKPQPEFVIPDATAPA PPPPGSNPRSSAPLPKPDNSEFAEDKSAKVVESAPKPKATRSSPIPAVEEETWDFKKY FDLNEPDAAEDGDDDDDWADSDASDSEIDQDDDSGPLAGENVMNVIVVAAECSPWCKT GGLGDVAGALPKALARRGHRVMVVVPRYGDYAEAQDVGIRKYYKAAGQDLEVKYFHAF IDGVDFVFIDAPLFRHRQDDIYGGNRQEIMKRMILFCKAAVEVPWHVPCGGVPYGDGN LVFLANDWHTALLPVYLKAYYRDNGMMQYTRSVLVIHNIAYQGRGPVDEFPYMELPEH YLDHFKLYDPVGGEHANIFGAGLKMADRVVTVSPGYLWELKTTEGGWGLHDIIRENDW KMNGIVNGIDYREWNPEVDVHLQSDGYANYTVASLDSSKPRCKAALQRELGLEVRDDV PLIGFIGRLDGQKGVDIIGDAMPWIAGQDVQLVLLGSGRRDLEVMLQRFEAQHNSKVR GWVGFSVKMAHRITAGADVLVMPSRFEPCGLNQLYAMAYGTVPVVHAVGGLRDTMSAF DPFEDTGLGWTFDRAEPHKLIEALGHCLETYRKYKESWRGLQVRGMSQDLSWDHAAEL YEEVLVKAKYQW</aaseq> |
| Gene Sequence |
<dnaseqindica>204..533#663..1331#1431..1499#2189..2266#2349..2459#2565..2609#3026..3199#3667..4623#gcgcacgctttacaggtggctcccccgccgtctcccccgcgtgccctcctcgccgtcgtcgctcgctgcccatttcatcccccgcacggcacgcgcgggacgaaagcaaagcacgcgcacacactcaaacccgcgcctcctccgctctcgtccgtcgcttcggttcggttccggctcgatcggggaggttcctcggggcgaccatgtcgtcggccgtcgtcgcgtcatccaccacgttcctcgtcgcgctcgcctcttcggcgtcacggggagggcccaggagggggagggtggtgggcgtggccgcgccgccggccctgctttacgacggccgcgccggaaggctagccctacgggcgccgcctccgccccggcctcggcctcggcgtcgggatgcgggcgtggtgcgccgcgcggatgatggggagaacgaggcggcggtggagcgggcgggtgaggacgacgacgaggaggaggagttctcttcgggcgcgtggcagccgccccgctcgcgtcgcggcggcgtcggcaaggtgggttggtggtgtcgatcggggcgccgagatcgtcgtgctcgagaggtgttctctgctttgattcgctttgatgttttcatttgaaaccgacgcgtgtgcttgcgcgtgcgcgcgctgtgtttgcaggtcttgaagcggaggggcaccgtcccgcccgtcggccggtacggctccggcggtgatgcggcgagagtgcgcggggcggccgcgccggcgccggcgccgacacaggacgccgcctcaagtaagaacggagcgcttctcagcggccgcgacgacgacacacctgcctcacggaacggatcggtcgttaccggcgccgacaagcctgccgccgccacgccgccggtgaccataacgaagctcccagcgccggactcccccgtgatccttccatccgtagacaagccgcagccggagttcgtcatcccagacgcgacggcgccggcgccgccaccgcccggttcaaatcccaggtcgtccgctcctctccccaagcctgacaattcggaatttgcagaggataagagcgcaaaagttgttgagagtgctccgaagccaaaggcgactagatcttcccctattcctgcggtagaagaggagacgtgggatttcaagaaatattttgatctgaacgaaccggacgccgcggaggatggcgatgacgatgatgactgggctgattcagatgcgtcagattctgagatcgaccaggatgacgattcgggccctttggctggggagaatgtcatgaacgtgatcgtggtggctgctgaatgttctccctggtgcaaaacaggcatgtacacgatatatacttcttttttctcttttttgttcttctgatcttgtaaatttgcttcagttactgatatgaacaagtgttgcatttgcacaggtgggcttggagatgttgcaggtgctttacccaaagctttggcgaggagaggacatcgtgttatggtattactccttttttctctccttcatggttggatgtttcttccattcttacagatttgatcatttaattaacgtatattttcagatatataaatttggatcaaatgtaaagcagattagttctcttatgttcttttgtttacataatcatgatggcaaattaaaaaggctactccagctgttagattcaaaatacaaaagtaatattgataaatttgcaaatctgtacttgaaagctaaattgcttactattgttacagaaatgttcatttctaacatgctgttgaaaatatatacactatggcgtagccgcttagatcatcacgtggccatggaaactagtgccaaaagtagttctcttagttacactagttacatacctgtacatgataacggatcaggcccatacaattagggatagattaggagcccgttaacgaactaggcccttataattagggagggacggtagttacttttcgcatatggacatgctgcacgtgttgggaggaggggatggaaggaagacgacttcgcttttaagatagtagagaaatgtagcaattttttttagcaattttagttatggtaataatataaaccacaacgtattcagagatcggaaacggggactctcggtgacttcctgatataaactgataactggcaaatgcatctttcaatcttaggttgtggtaccaaggtacggtgattacgcggaagcccaggatgtaggaatcaggaaatactacaaggctgctggacaggtgtgtgtcaacaatgcaatccaagaagactggcataggagacgcaaattccttagtaattggtttttattttggcctgcaggatctggaagtgaaatatttccatgcatttatcgatggagttgattttgtgttcattgacgctcctctcttccgtcaccgtcaggatgacatctatggggggaacagacaggtgaagcttctatctgtttggtattacattgcattagtaaaacttaagttgcatctcctaggcgtactgatttgaaaatgcttacccattcccattttcattcaggaaatcatgaagcgcatgattctgttttgtaaggctgctgttgaggtattttctccaactccattatcaatcattaatttggttttaggaatgagatgtatttgtttggtttgaggattggtcaaaagcacaaatcattttttctgttgataaatagaagaagtgtattaacttttggactgaagcacacaataagtaggagaaatgaggtcgcagtagatgatttgaatttgatccctcaaacaaacagcccgtaaatgtttctgcaagatttcacagagattcatattcttttttattttaaatatattacacattatcgccaaatacacggatgaactccttcgatacctctagcagcatttcaacctgctaccgttcgtaatatgcaatgctcttgccaatgttgtcatatgttcccctacaaagggctatattttctgtttctgtacaatcggcaggttccttggcacgttccatgcggtggtgtgccctatggggatggcaacttggtgttccttgcaaacgattggcacactgcactcctgcctgtttatctgaaggcatattacagagacaatggcatgatgcagtacactcgctctgtccttgtgatacataatatcgcttaccaggttttgtttttctctcctccctaatgaatcatctttattctatttgtatgcatctcctgctgtttgttagagaaattagttgagtgcacaaattgtgggtcatggtaattattgagcagggacacgataaactcttcttcagtctattactacttttagttcagcaatttctccgtttcatattataatttataagtcgttttttttctaatcaaacatctttacgtttgattaactttatcgaaaaatttaacagcatctataacatcaaattagtttaattaaatataatgtttaatgtaatttgattatatgtttgttttgtattggaaatgttattgtatttttctataaactaattaaatttaaaactgtttaacttaaaaaaatatcaaaacaatttacaatatgaaacgggccggggagtactttttttgtgtgctaaatggttcgtgtaatgtttgtagggccgtggcccagtagatgaattcccctacatggaattgccggagcactacctggatcacttcaagctgtacgaccccgtcggcggcgagcacgccaacatcttcggcgcgggcctgaagatggcggaccgggtggtgaccgtgagccccggctacctctgggagctgaagacgacggagggcggctggggcctccacgacatcatacgggagaacgactggaagatgaacggcatcgtgaacggcatcgactaccgggagtggaacccggaggtggacgtgcacctgcagtccgacggctacgccaactacaccgtggcctcgctggactccagcaagccgcggtgcaaggcggcgctgcagcgcgagctggggctggaggtgcgcgacgacgtgccgctgatcgggttcatcgggcggctcgacgggcagaaaggtgtggacatcatcggcgacgcgatgccgtggatcgccgggcaggacgtgcagctggtgctgctgggctccggccgccgcgacctggaggtgatgctgcagcggttcgaggcgcagcacaacagcaaggtgcgcgggtgggtggggttctcggtgaagatggcgcaccggatcacggcgggcgccgacgtgctggtcatgccgtcgcggttcgagccgtgcggcctcaaccagctctacgccatggcgtacggcaccgtccccgtcgtgcacgccgtcggcgggctgagggacaccatgtcggcgttcgacccgttcgaggacaccggcctcgggtggacgttcgaccgcgccgagccgcacaagctcatcgaggcgctcggccactgcctcgagacgtaccgcaagtacaaggagagctggagggggctccaggtgcgcggcatgtcgcaggacctcagctgggaccacgccgccgagctctacgaggaggtccttgtcaaggccaagtaccaatggtgaagagaccatgtccgcccgcggtctccgcctgcgcgttcggcagctatagctatagcctccctgaagaagcttggcgctgctgtggaggtgcgactcggtggcggtgtggcgccggcgccggcgcttgcaggggaggtgtttgtgctgaccgagctgtgcgttgaggtgcgcaaattagcttccggtttgtgtgttcatggcgaggcatggtggagttgagggagtattaagctttgtttcagatgcatcatgcatgcgtaataggatgttgtatttaataatgtgtttgttatgtccattgatgcgatgttacttcttcatta</dnaseqindica> |
| External Link(s) |
