RiceWiki - User contributions [en]

Os01g0834400

2014-05-31T11:19:15Z

YaliGuo: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:Expression.png|top|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:Phylogenetic_tree_of_HAP3.png|right|thumb|350px| '''Figure 3''''' (from reference <ref name="ref1" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.<references><ref name="ref1"> Kazumaru Miyoshi;Yukihiro Ito;Akiko Serizawa;Nori Kurata, OsHAP3 genes regulate chloroplast biogenesis in rice, The Plant Journal, 2003, 36(4): 532-540.</ref> 
2.<references><ref name="ref2"> Thiruvengadam Thirumurugan,Yukihiro Ito,Takahiko Kubo,Akiko Serizawa,Nori Kurata, Identification, characterization and interaction of HAP family genes in rice, Molecular Genetics and Genomics, 2008, 279(3): 279-289.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os05g0573500

2014-05-31T11:18:53Z

YaliGuo: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, the mRNA level of OsHAP3C was reduced and these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3C is highly similar to OsHAP3A in their amino acid sequence and it can also expressed in roots. SO it may also affect the amyloplast. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:Expression.png|top|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control.Although there are some differences in their gene structure, such as OsHAP3A contains seven exons divided by six introns, and OsHAP3C contains six exons divided by five introns. OsHAP3A,OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:Phylogenetic_tree_of_HAP3.png|right|thumb|350px| '''Figure 3''''' (from reference <ref name="ref1" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade) and 76%(LEC1 clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues. OsHAP3C protein also have the characteristic stretched of glycine amino acid residue.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.<references><ref name="ref1"> Kazumaru Miyoshi;Yukihiro Ito;Akiko Serizawa;Nori Kurata, OsHAP3 genes regulate chloroplast biogenesis in rice, The Plant Journal, 2003, 36(4): 532-540.</ref> 
2.<references><ref name="ref2"> Thiruvengadam Thirumurugan,Yukihiro Ito,Takahiko Kubo,Akiko Serizawa,Nori Kurata, Identification, characterization and interaction of HAP family genes in rice, Molecular Genetics and Genomics, 2008, 279(3): 279-289.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os05g0573500

2014-05-31T11:18:31Z

YaliGuo: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, the mRNA level of OsHAP3C was reduced and these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3C is highly similar to OsHAP3A in their amino acid sequence and it can also expressed in roots. SO it may also affect the amyloplast. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:Expression.png|top|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control.Although there are some differences in their gene structure, such as OsHAP3A contains seven exons divided by six introns, and OsHAP3C contains six exons divided by five introns. OsHAP3A,OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:Phylogenetic_tree_of_HAP3.png|right|thumb|350px| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade) and 76%(LEC1 clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues. OsHAP3C protein also have the characteristic stretched of glycine amino acid residue.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.<references><ref name="ref1"> Kazumaru Miyoshi;Yukihiro Ito;Akiko Serizawa;Nori Kurata, OsHAP3 genes regulate chloroplast biogenesis in rice, The Plant Journal, 2003, 36(4): 532-540.</ref> 
2.<references><ref name="ref2"> Thiruvengadam Thirumurugan,Yukihiro Ito,Takahiko Kubo,Akiko Serizawa,Nori Kurata, Identification, characterization and interaction of HAP family genes in rice, Molecular Genetics and Genomics, 2008, 279(3): 279-289.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os05g0573500

2014-05-31T11:17:09Z

YaliGuo: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, the mRNA level of OsHAP3C was reduced and these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3C is highly similar to OsHAP3A in their amino acid sequence and it can also expressed in roots. SO it may also affect the amyloplast. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:Expression.png|top|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control.Although there are some differences in their gene structure, such as OsHAP3A contains seven exons divided by six introns, and OsHAP3C contains six exons divided by five introns. OsHAP3A,OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:Phylogenetic_tree_of_HAP3.png|right|thumb|350px| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade) and 76%(LEC1 clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues. OsHAP3C protein also have the characteristic stretched of glycine amino acid residue.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os05g0573500

2014-05-31T11:11:54Z

YaliGuo: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, the mRNA level of OsHAP3C was reduced and these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3C is highly similar to OsHAP3A in their amino acid sequence and it can also expressed in roots. SO it may also affect the amyloplast. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:Expression.png|top|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control.Although there are some differences in their gene structure, such as OsHAP3A contains seven exons divided by six introns, and OsHAP3C contains six exons divided by five introns. OsHAP3A,OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

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

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

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os05g0573500

2014-05-31T11:05:30Z

YaliGuo: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, the mRNA level of OsHAP3C was reduced and these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3C is highly similar to OsHAP3A in their amino acid sequence and it can also expressed in roots. SO it may also affect the amyloplast. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:Expression.png|top|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

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

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

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os05g0573500

2014-05-31T11:04:43Z

YaliGuo: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, the mRNA level of OsHAP3C was reduced and these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3C is highly similar to OsHAP3A in their amino acid sequence and it can also expressed in roots. SO it may also affect the amyloplast. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===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==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os05g0573500

2014-05-31T10:57:57Z

YaliGuo: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

===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==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os05g0573500

2014-05-31T10:57:33Z

YaliGuo: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

===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==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os01g0834400

2014-05-31T10:55:23Z

YaliGuo: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:Expression.png|top|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:Phylogenetic_tree_of_HAP3.png|right|thumb|350px| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.<references><ref name="ref1"> Kazumaru Miyoshi;Yukihiro Ito;Akiko Serizawa;Nori Kurata, OsHAP3 genes regulate chloroplast biogenesis in rice, The Plant Journal, 2003, 36(4): 532-540.</ref> 
2.<references><ref name="ref2"> Thiruvengadam Thirumurugan,Yukihiro Ito,Takahiko Kubo,Akiko Serizawa,Nori Kurata, Identification, characterization and interaction of HAP family genes in rice, Molecular Genetics and Genomics, 2008, 279(3): 279-289.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Expression.png

2014-05-31T10:53:23Z

YaliGuo: uploaded a new version of "File:Expression.png"

Os01g0834400

2014-05-31T10:51:50Z

YaliGuo: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:Phylogenetic_tree_of_HAP3.png|right|thumb|350px| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.<references><ref name="ref1"> Kazumaru Miyoshi;Yukihiro Ito;Akiko Serizawa;Nori Kurata, OsHAP3 genes regulate chloroplast biogenesis in rice, The Plant Journal, 2003, 36(4): 532-540.</ref> 
2.<references><ref name="ref2"> Thiruvengadam Thirumurugan,Yukihiro Ito,Takahiko Kubo,Akiko Serizawa,Nori Kurata, Identification, characterization and interaction of HAP family genes in rice, Molecular Genetics and Genomics, 2008, 279(3): 279-289.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Phylogenetic tree of HAP3.png

2014-05-31T10:51:34Z

YaliGuo:

Os01g0834400

2014-05-31T10:43:21Z

YaliGuo: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==
1.<references><ref name="ref1"> Kazumaru Miyoshi;Yukihiro Ito;Akiko Serizawa;Nori Kurata, OsHAP3 genes regulate chloroplast biogenesis in rice, The Plant Journal, 2003, 36(4): 532-540.</ref> 
2.<references><ref name="ref2"> Thiruvengadam Thirumurugan,Yukihiro Ito,Takahiko Kubo,Akiko Serizawa,Nori Kurata, Identification, characterization and interaction of HAP family genes in rice, Molecular Genetics and Genomics, 2008, 279(3): 279-289.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T10:39:03Z

YaliGuo: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]]]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T10:37:27Z

YaliGuo: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref1" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges '']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T10:37:02Z

YaliGuo: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges '']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref2" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T10:36:23Z

YaliGuo: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges '']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref3" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T10:30:49Z

YaliGuo: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges (from reference <ref name="ref2" />)'']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref3" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

==Labs working on this gene==
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

==References==

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os05g0573500

2014-05-31T10:30:18Z

YaliGuo: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
1.Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan. 
2.Department of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.

===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 = Os05g0573500|
Description = HAP3|
Version = NM_001062918.1 GI:115465566 GeneID:4339676|
Length = 2697 bp|
Definition = Oryza sativa Japonica Group Os05g0573500, 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 5|Chromosome 5]]|
AP = Chromosome 5:28654041..28656737|
CDS = 28654226..28654428,28654585..28654714,28655594..28655599,28655680..28655757,28656441..28656455 |
GCID = <gbrowseImage1>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:28654041..28656737
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgaagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggagacggagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcgtttgaaggcatgtag</cdnaseq>|
AA = <aaseq>MSEGFDGTENGGGGGGGGVGKEQDRFLPIANIGRIMRRAVPENG KIAKDSKESVQECVSEFISFITSEASDKCLKEKRKTINGDDLIWSMGTLGFEDYVEPL KLYLRLYRETEGDTKGSRASELPVKKDVVLNGDPGSSFEGM</aaseq>|
DNA = <dnaseqindica>186..388#545..674#1554..1559#1640..1717#2401..2415#gtcgagatccggcggccggtggcgtcctcctccctctccctcctccccaaccaacggcgctgatcccctccgccatctccgtccatctccgcctaaaaaaactaaggtaagccaccaactttcccttgacaccagcagtagtggtagtcgctctccttctcaccgacctctgccatggcccagcgatgtcggaggggttcgacgggacggagaacggcggcggcggcggcggaggcggagtagggaaggagcaggaccggttcctgccgatcgccaacatcggccgcatcatgcgccgggccgtgccggagaacggcaagatcgccaaggactccaaggagtccgtccaggagtgcgtctccgagttcatcagcttcatcaccagcgagtcagtgtcgcctcgcctttgtatttgctgtatatatcggtgccggagcttgcttgatccgatccagttcggagcggcggcggcgcattttgtcgtgcacctgccgtgcagatggcaagggtgactgacggccatctttggcatctttccctgcagagcaagcgacaagtgcctcaaggagaagcgcaagaccatcaatggggacgacctgatctggtcaatgggcacgctcggattcgaggactatgtcgagcctctcaagctctacctcaggctctaccgggaggtattgttcctctcctctctcttccagagtgtttcctagtattgtattgcctagtgatgcatatgttactacgtgggaagtgaaggctggttcacctcgattaggtaggcgtaggcttctatattcgcacacagtttgcctaagcttttgatacacagactgatgctcatacgagctctgcactgattggattgtgcatataccatgaggccatgattcgtgcaaaaggagagagctttcgtgattgtacttatatcaaggctttgacttagtattacttggtctgtcacatgggttgattcactccaaattgatggatggttgatttagttgccaacagtagattgcggaaaggttgaatgtgctgcctgaatgttaagcgcccaatatttctaggtccagggcatgcactgtaaaggtggaattttctttgtacttattggcatgaaccgattcaaaatggccgtagtcttccatctgtaggcgtgctgctggcagagtggccaggttaacatggactgtaattttgttttatgtccataaagctacatatctgatgaacgccaatgcaaacttgcaattgtcagattatgaactacatttatgctgaagacatgtaacatttttgctgaactgacattagtgcctggaccaagattgattttttttcatcagcatatatttttaatttcaatcactagtgagatataaaatacaacaaaaggatgtttcattgtcctccagaaaaagatatttaccgatataatttcctttgttttcttttccatattatacacaaatttttacgtgcactgatagttttttcccctttcttgcatgaataacaacggccgttgattacccttgatggtactgaagacggaggtatttcccatgttgtattacttgttaatctttaagttttgttaatgaaggtttattcaatttacttgttgatcttctagggtgacacaaagggttcaagagcttctgaactgccagtaaagaaagatgttgtacttaatggagatcctggatcatcggtaatatatagttccttgtgccaagttttaataaaacgaaacattgcactaccatctgcctttctttattgtcaagcacacattcacatatttttccctacaacttgctgtattatcttttttgcaagtgctacatcaatatgcacaaaactctcattgttttgaccattcttctattcatgccagtatgccactagctgatgcatcagcagcgtgaaaatgttaactgttttttttagtttctaagattatcgtttgggctgtaaacatattcataacctgttatttctgctgctgcattatgggtctgtgattttgttggagggctgtagtcaggctagcctttgactggttctggtataaaaatggattgaaaagccaaacataaagcctggttttgttttaaggtttcatggaagctggcttactttgtataaacttgttattttcaaaaatcaatcacttctagattgcacattgttgagccatgcattttctttccttttgcttttcaacctttaataccatttctgtatcatgatatatttgttccccttacttttggttttcctgctattcttgatcggtaaccattggtagccatattagtaatattgaaaagttatttttggatgaatataatggtgcaagcaaatctcactggagcattattttcttgacagtttgaaggcatgtaggacgaggagtgtgatagcatctaggaaggagaaccatcgtttttagggaaagaacgctccagcatcctgttatgttgtaagcaggatgcttctaaagttccaataccttgttaccacgaatgttagtcgtcgttctttttgaaatgttcttgtgttagccaggatgtccaaatttgttgtaggttctagttcagtcgtgtgttgtgtggttgtgtctaaccatatttggccgtttccggctgtcctgcatatgctaaattcagaggggtaaagagatctaag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062918.1 RefSeq:Os05g0573500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os01g0834400

2014-05-31T10:23:47Z

YaliGuo: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges (from reference <ref name="ref2" />)'']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref3" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

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

==References==

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T10:21:23Z

YaliGuo: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges (from reference <ref name="ref2" />)'']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref3" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

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

==References==
<references>
<ref name="ref1">Kazumaru Miyoshi, Yukihiro Ito, Akiko Serizawa and Nori Kurata,OsHAP3 genes regulate chloroplast biogenesis in rice,The Plant Journal, 2003, 36(4): 532-540.</ref> 
<ref name="ref2"> Thiruvengadam Thirumurugan,Yukihiro Ito,Takahiko Kubo,Akiko Serizawa;Nori Kurata, Identification, characterization and interaction of HAP family genes in rice, Molecular Genetics and Genomics, 2008, 279(3): 279-289.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T08:49:57Z

YaliGuo: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges (from reference <ref name="ref2" />)'']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===Evolution===
[[File:文件名|right|thumb|Phylogenetic_tree_of_HAP3.png| '''Figure 3''''' (from reference <ref name="ref3" />)'']]
Rice has 11 HAP3 genes in its genome, the newly identified genes were named as OsHAP3D to OsHAP3D A phylogenetic analysis based on the amino acid sequeces of the conserved domain showed that the OsHAP3 proteins were located in several different clades. A comparison of amino acid sequences in the conserved domain showed that OsHAP3 proteins are 96-39% identical to each other and also to the Arabidopsis proteins. Among the proteins in the same clade, the amino acid identities increased to not less than 77(OsHAP3A clade). OsHAP3A，OsHAP3B and OsHAP3C also showed similarity in their C-terminus regions with 67-44% identity in 45-35 amino acid resudues.

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

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T07:56:48Z

YaliGuo: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===Expression===
[[File:文件名|top|thumb|Expression.png| ''expression patterns of OsHAP3 genges (from reference <ref name="ref2" />)'']]
RNAs isolated from indicated organs were analysed by RT-PCR. Actin was used for an internal control. OsHAP3A, OsHAP3B, OsHAP3C showed ubiquitous expression. They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 Days after pollination, and regenerating calli at 0, 2, 4, 6 days after regeneration. The expression wwas also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm.

===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 = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Expression.png

2014-05-31T07:44:59Z

YaliGuo: uploaded a new version of "File:Expression.png"

Os01g0834400

2014-05-31T07:30:20Z

YaliGuo: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size. 
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch. 
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed 
b. Electron-dense fibre-like structure was observed. 
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated. 
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small. 
e. The inside of the chloroplast was almost empty. 
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated. 

===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 = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0834400

2014-05-31T07:28:00Z

YaliGuo: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size.
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch.
a. The chloroplast of the antisense plant #31. A membrane structure of the chloroplasts was not well developed and no accumulation of starch grains was observed
b. Electron-dense fibre-like structure was observed.
c. The amyloplast of the antisense plant #31. The reduced amount of the starch was accumulated.
d. The chloroplast of the antisense plant #56. Almost no membrane structure was observed inside the chloroplast. The chloroplast was small.
e. The inside of the chloroplast was almost empty.
f. The amyloplast of the antisense plant #56. The reduced amount of the starch was accumulated.

===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 = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:1.png

2014-05-31T07:27:36Z

YaliGuo: uploaded a new version of "File:1.png"

Os01g0834400

2014-05-31T07:11:23Z

YaliGuo: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:1.png|right|thumb|350px| '''Figure. 1''' ''(from reference <ref name="ref3" />)'']]
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size.
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch.

===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 = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:1.png

2014-05-31T07:10:03Z

YaliGuo: uploaded a new version of "File:1.png"

Os01g0834400

2014-05-31T06:54:47Z

YaliGuo: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
The CCAAT-box is one of the most common promoter elements found in a large number of genes in plants. The HAP complex, which is also called NF-Y or CBF in animals, binds the CCAAT-box and regulates expression of genes.This complex consists of three distinct subunits: HAP2、HAP3、HAP5，all of which are necessary for DNA binding. Each subunit contains an evolutionary conserved domain that is responsible for DNA binding and protein-protein interaction. 10 genes for HAP2 subunit, 11 genes for HAP3 subunit and 7 genes for HAP5 subunit has been identified. HAP3A、HAP3B、HAP3C are genes encode subunits of HAP3. HAP3 genes regulate chloroplast biogenesis. In the transgenic rice plants with antisense or RNAi construct of OsHAP3A, these plants showed pale green leaves, in which the amount of chlorophyll was reduced and chloroplasts were degenerated. The thylakoid membrane was hardly generated of formed only sightly along the enveolpe, no clear grana or stroma was observed and the accumulation of the starch was not evident. Instead, an electron-dense fibre-like structure was observed in the central portion of the deformed chloroplast. The chloroplast was almost empty and smaller in size.
OsHAP3A was also expressed in roots. In the antisense root, although the amount of accumulated starch was reduced, the accumulation of the starch was still observed in the amyloplasts. Showing that the OsHAP3A can also affect the amyloplast, mainly the accumulation of the starch.

===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==
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==Structured Information==
{{JaponicaGene|
GeneName = Os01g0834400|
Description = Similar to HAP3|
Version = NM_001185707.1 GI:297720548 GeneID:9268285|
Length = 2312 bp|
Definition = Oryza sativa Japonica Group Os01g0834400, 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 1:37512199..37514510|
CDS = 37512340..37512558|
GCID = <gbrowseImage1>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:37512199..37514510
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>aagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataa</cdnaseq>|
AA = <aaseq>KTKALEGCWFRKGVNSWLWRLLHRCKLLHKWFNACFCLYIQSNF HILVVLQSFAFPYMYQVAQIYCKYPSIE</aaseq>|
DNA = <dnaseqindica>1953..2171#aaccgccgtctcctcctccccccactctcgccttcccccctctctctcctctcctctccgcgactccctccacccccgcgcgcgcgcgttttttttttttcgtaaggtacggatccaacgacgctgctcggctgctcctctccccaccaccatctctgatggtttgttgctgtgatgatgatgatggatctagggtttttggagggcggcgcggggatggcggacgcggggcacgacgagagcgggagcccgccgaggagcggcggggtgagggagcaggacaggttcctgcccatcgccaacatcagccgcatcatgaagaaggccgtcccggcgaacggcaagatcgccaaggacgccaaggagaccctgcaggagtgcgtctcggagttcatctccttcgtcaccagcgagtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacagggcgagcgacaaatgtcagaaggagaagcgcaagaccatcaacggggaagatctcctctttgcgatgggtacgcttggctttgaggagtacgttgatccgttgaagatctatttacacaagtacagagaggtaattgtgcgcttcgtactctctgccagtataaatgttaaacctttcgttgttgtatgaatatctgatgtctcttctgtcctcctggcaaatttgcaatacgtggggatgtgcactgttaactgcagatggaggtacaccatctaccattctaccctcctcaaaatccccttttttccccaacaatatgctatggtttcatgtgaattttttttttgtcaacgcaaaaatgtgtcactcttgtaatcctgcttttagaacaatcccacaaaaaattgatatgcaattatgccctttgattagagatagttggtgctcaacatgaaatgtacatatcctactctgaactgtaaggttaacacctgaatcattctttcattcctctgcttcatatacattgaaggaaagctaaccgcatccatttagtatgtcactgttcaatttgcctggaaatatatatttgtgccttagtaatactctaagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagggtgatagtaagctgtcctcaaaggctggtgatggttcagtaaagaaggatacaattggtccgcacagtggcgctagtagctcaagtgcgcaaggggttggtatcagtaacttgtactgctttgttctttctgatgtttgaaaacactgacatactgataatatttttagatggttggggcttacacccaagggatgggttatatgcaacctcaggtaacctagcactagcatagtatcatttgtcagcacaatgctatggttcatccttgaagctaaacaagatataaagtaataatgcacattcaactttttttttctagctgacactgtttatgccattacacgtgcagtatcataatggggacacctaaagatgaggacagtgaaaattttcagtaactggtgtcctctgtgaggtaagatcttttgtacagaaatcatttgccatccttggggcagttttcagttagatgtttttttcactaaaaattgcccgttctgtctcaaggttcacatatactacatctgtatttttttattctttttacatgtgaactctggagatgttgagctgcacatgtgaaaaattctccgagtgcttttatactttttcgcgctcttctagttctgacacaatactcccttttgctgcagttattatccatctgttaaggaagaacccacattagggccatatttattagtagaagactaaagcacttgaagggtgttggtttagaaagggtgttaacagttggctgtggcgattgcttcacagatgtaaattgcttcataagtggtttaatgcttgtttttgcctgtatattcagagcaattttcacatattggtagttctgcaatcttttgcattcccatacatgtatcaggtggcacaaatctattgcaagtaccctagcattgaataatgctggttaacatataattctgtaacgtccgtattgtttcgactgtgatgcttgccgtatgggcaatggcatgtgttctagagggggcattcaatatttaggtatctcaagaatgtaccaaatactcccttcgttcaattc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185707.1 RefSeq:Os01g0834400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]