http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=HamletShaoERiceWiki - User contributions [en]2026-08-28T08:02:50ZUser contributionsMediaWiki 1.30.0https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0174500&diff=172385Os08g01745002014-05-25T13:36:07Z<p>HamletShaoE: /* Function */</p>
<hr />
<div>The rice ''Os08g0174500'' is a major QTL located at chromosome 8 of rice with pleiotropic effects on grain yield, heading date, and plant height<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. It was reported as ''DTH8'', ''Ghd8'' and ''LHD1'' in 2010, 2011 and 2012, espectively<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. <br />
<br />
==Annotated Information==<br />
[[File:OsDTH8_1.jpg|right|thumb|350px|'''Figure 1.''' ''Phenotypes of Asominori and chromosome segment substitution line of ''OsDTH8''(CSSL61). The left is Asominori and right is CSSL61 (from reference<ref name="ref1" />).'']]<br />
<br />
===Function===<br />
* Grain yield, heading date, and plant height have been regarded as the three most important agronomic traits of rice regulated by many quantitative trait loci (QTLs). ''OsDTH8'' is a major QLT encoding a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor which suppress flowering by down-regulating several important floral transition activators, such as ''Ehd1'', ''Hd3a'' and ''RFT1''<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. <br><br><br />
* ''OsDTH8'' can also influence plant height and yield potential by the regulation of stem growth and panicle development <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. It was considerd that ''OsDTH8'' could provide a hard-won opportunity for molecular mechanism exploration of the relationship between grain yield and heading potential<ref name="ref2" />.<br><br><br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003677 GO:0003677], [http://amigo.geneontology.org/amigo/term/GO:0005622 GO:0005622], [http://amigo.geneontology.org/amigo/term/GO:0005634 GO:0005634], [http://amigo.geneontology.org/amigo/term/GO:0043565 GO:0043565]<br />
<br />
===Wild Type & Mutants===<br />
[[File:OsDTH8_2.jpg|left|thumb|210px|'''Figure 2.''' ''Transformants (left) VS. wild-type (right)(from reference<ref name="ref2" />).'']]<br />
<br><br />
* The population genetics analysis made by ''Xiangjin Wei'' et al. in 2010 showed that the chromosome segment substitution lines of ''OsDTH8'' under the Asominori genetic background (''Japonica'') diplayed earlier heading than Asominori. Their plant height, number of grains per panicle, yield, and dry weight per plant decreased significantly in compared with Asominori NLD condition (Figure 1)<ref name="ref1" />.<br><br><br />
* The transgenetic analysis in rice made by ''Wen-Hao Yan'' et al. showed that the positive T1 plants of ''OsDTH8'' could produce more grains. They displayed significantly delayed heading with taller culms compared to the transgenic negative plants. On the whole, a positive T1 plant resulted in an increases 60% in grain yield per plant and grains per panicle compared to the control group<ref name="ref2" />.<br><br><br />
* The transgenetic analysis in Arabidopsis by ''Wen-Hao Yan'' et al. showed that transformants of ''OsDTH8'' can bloom about 10 days earlier than the wild-type under LD conditions, however, no obvious difference was observed between the transformants and wild-type under SD conditions (Figure 2)<ref name="ref2" />.<br><br><br><br />
[[File:OsDTH8_3.jpg|right|thumb|300px|'''Figure 3.''' ''The expression pattern of OsDTH8 (L/leaves, S/leaf sheaths, C/culms, P/young panicles, R/roots) (from reference<ref name="ref1" />).'']]<br />
<br />
===Expression===<br />
* The expression pattern analysis made by ''Xiangjin Wei'' et al. showed that ''OsDTH8'' was expressed in leaves, leaf sheaths, culms, young panicles and roots. However, its expression levels were higher in roots, young panicles, and leaves than those in leaf sheaths and culms (Figure 3)<ref name="ref1" />.<br />
<br />
* ''OsDTH8'' could negatively influence the expression of ''Ehd1'', ''Hd3a'' and ''RFT1'' but not ''Hd1'' and ''Ghd7''<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
===Subcellular Localization ===<br />
* The subcellular localization analysis made by ''Xiangjin Wei'' et al. suggests that ''OsDTH8'' is a nuclear protein<ref name="ref1" />.<br />
<br><br />
===Gene Structure===<br />
[[File:OsDTH8_4.png|center|thumb|727px|'''Figure 4.''' ''Structure of OsDTH (from NCBI BLASTP).'']]<br />
<br />
==Labs working on this gene==<br />
* State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China;<br />
* Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China;<br />
* Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China;<br />
* National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan;<br />
* State Key Laboratory of Plant Physiology and Biochemistry, National Evaluation Centre for Agricultural Wild Plants (Rice), Laboratory of Crop Heterosis and Utilization of the Ministry of Education, Beijing 100193, China;<br />
* Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Wei X, Xu J, Guo H, et al. DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously[J]. Plant Physiology, 2010, 153(4): 1747-1758.<br />
</ref><br />
* <ref name="ref2"><br />
Yan W H, Wang P, Chen H X, et al. A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice[J]. Molecular Plant, 2011, 4(2): 319-330.<br />
</ref><br />
* <ref name="ref3"><br />
Dai X, Ding Y, Tan L, et al. LHD1, an Allele of DTH8/Ghd8, Controls Late Heading Date in Common Wild Rice (Oryza rufipogon) F[J]. Journal of Integrative Plant Biology, 2012, 54(10): 790-799.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os08g0174500|<br />
Description = Similar to HAP3|<br />
Version = NM_001067642.1 GI:115475020 GeneID:4344784|<br />
Length = 1640 bp|<br />
Definition = Oryza sativa Japonica Group Os08g0174500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 8|Chromosome 8]]|<br />
AP = Chromosome 8:4332728..4334367|<br />
CDS = 4332849..4333742|<br />
GCID = <gbrowseImage1><br />
name=NC_008401:4332728..4334367<br />
source=RiceChromosome08<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008401:4332728..4334367<br />
source=RiceChromosome08<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgaagagtaggaagagctatgggcacttgctgagcccggtgggcagcccgccgttggacaacgagtccggcgaggcggcggcggcggctgcggctggcggcggcggctgcgggagcagcgccgggtatgtcgtctacggcggcggcggcggtggggactcgccggcgaaggagcaggacaggttcctgccgatcgcgaacgtgagccgcatcatgaagcggtcgctgccggcgaacgccaagatctccaaggagtcgaaggagacggtgcaggagtgcgtgtcggagttcatcagcttcgttacaggcgaggcctccgacaagtgccagcgcgagaagcggaagaccatcaacggcgacgacctcctctgggccatgaccacgctggggttcgaggcctacgtcggcccgctcaagtcctacctcaaccgctaccgcgaggccgagggcgagaaggccgacgtgctcggcggcgccggcggcgccgccgcggcgcgccacggcgagggcggttgctgcggcggcggcggcggcggcgccgatggcgtcgtcatcgacgggcattacccgctcgccggcggcctgtcacactcacaccatggtcatcagcagcaggacggcggcggcgacgtcgggctcatgatgggcggcggcgacgccggcgtcgggtacaacgccggggccgggtcgacgacgacggcgttctacgcgccggcggcgacggcggcgtcagggaacaaggcgtactgcggcggcgacgggtcgagggtgatggagttcgagggcatcggcggcgaggaggagagcggaggcggcggcggcggcggcgagagggggttcgccggccacctccatggcgtgcaatggtttagactaaagaggaatactaattag</cdnaseq>|<br />
AA = <aaseq>MKSRKSYGHLLSPVGSPPLDNESGEAAAAAAAGGGGCGSSAGYV VYGGGGGGDSPAKEQDRFLPIANVSRIMKRSLPANAKISKESKETVQECVSEFISFVT GEASDKCQREKRKTINGDDLLWAMTTLGFEAYVGPLKSYLNRYREAEGEKADVLGGAG GAAAARHGEGGCCGGGGGGADGVVIDGHYPLAGGLSHSHHGHQQQDGGGDVGLMMGGG DAGVGYNAGAGSTTTAFYAPAATAASGNKAYCGGDGSRVMEFEGIGGEEESGGGGGGG ERGFAGHLHGVQWFRLKRNTN</aaseq>|<br />
DNA = <dnaseqindica>626..1519#tcggtcattagtatatgttagtataaattaaataattaaacaccttaaacaatattttttcgtcgtagtttgatcatcacctaagattttttagtcttttcaaaatgatcatcagctaacaagtgtatctttatttatttgtgcaagaagtaaatgagcatcattgaatgcgctgcacacatgtaatgcaaacaaccaagttaatttttattggtgcaacggcgcgcactatttaaaacgtgacgcaatgcagcgatagagcaccttgatagataagaattaatttcagcatgatgtagattttgttatccttaatctctactcactttgcataggtaataaattaaaccgctgaactattactacatggtttacatgaaaggtgatcgggtagggacgagaatgtcgcgacacacataatatatatagtagcgtccttatgtttgctttgtgtccgcatcgataccgtcttcccactcgcatctcctcacctcctttccttctttaaaaggagagcatcaccactccatcctcaactcccataacctcccccttctctctctctctaactacacactctctctctagctagctagctagctatagctagtgttgttagcttcacatgaagagtaggaagagctatgggcacttgctgagcccggtgggcagcccgccgttggacaacgagtccggcgaggcggcggcggcggctgcggctggcggcggcggctgcgggagcagcgccgggtatgtcgtctacggcggcggcggcggtggggactcgccggcgaaggagcaggacaggttcctgccgatcgcgaacgtgagccgcatcatgaagcggtcgctgccggcgaacgccaagatctccaaggagtcgaaggagacggtgcaggagtgcgtgtcggagttcatcagcttcgttacaggcgaggcctccgacaagtgccagcgcgagaagcggaagaccatcaacggcgacgacctcctctgggccatgaccacgctggggttcgaggcctacgtcggcccgctcaagtcctacctcaaccgctaccgcgaggccgagggcgagaaggccgacgtgctcggcggcgccggcggcgccgccgcggcgcgccacggcgagggcggttgctgcggcggcggcggcggcggcgccgatggcgtcgtcatcgacgggcattacccgctcgccggcggcctgtcacactcacaccatggtcatcagcagcaggacggcggcggcgacgtcgggctcatgatgggcggcggcgacgccggcgtcgggtacaacgccggggccgggtcgacgacgacggcgttctacgcgccggcggcgacggcggcgtcagggaacaaggcgtactgcggcggcgacgggtcgagggtgatggagttcgagggcatcggcggcgaggaggagagcggaggcggcggcggcggcggcgagagggggttcgccggccacctccatggcgtgcaatggtttagactaaagaggaatactaattagctagctaggcacacgcgtagttttattattacttaattaccgcgttaattaattgttgatgctgatgctgtttaaaattgattctccttttgcatgaaatgtttgatggtatggtttaaaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001067642.1 RefSeq:Os08g0174500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0174500&diff=172384Os08g01745002014-05-25T13:35:52Z<p>HamletShaoE: /* Function */</p>
<hr />
<div>The rice ''Os08g0174500'' is a major QTL located at chromosome 8 of rice with pleiotropic effects on grain yield, heading date, and plant height<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. It was reported as ''DTH8'', ''Ghd8'' and ''LHD1'' in 2010, 2011 and 2012, espectively<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. <br />
<br />
==Annotated Information==<br />
[[File:OsDTH8_1.jpg|right|thumb|350px|'''Figure 1.''' ''Phenotypes of Asominori and chromosome segment substitution line of ''OsDTH8''(CSSL61). The left is Asominori and right is CSSL61 (from reference<ref name="ref1" />).'']]<br />
<br />
===Function===<br />
* Grain yield, heading date, and plant height have been regarded as the three most important agronomic traits of rice regulated by many quantitative trait loci (QTLs). ''OsDTH8'' is a major QLT encoding a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor which suppress flowering by down-regulating several important floral transition activators, such as ''Ehd1'', ''Hd3a'' and ''RFT1''<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. <br><br><br />
* ''OsDTH8'' can also influence plant height and yield potential by the regulation of stem growth and panicle development <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. It was considerd that ''OsDTH8'' could provide a hard-won opportunity for molecular mechanism exploration of the relationship between grain yield and heading potential<ref name="ref2" />.<br><br><br />
'''GO assignment(s):''' [[http://amigo.geneontology.org/amigo/term/GO:0003677 GO:0003677], [[http://amigo.geneontology.org/amigo/term/GO:0005622 GO:0005622], [[http://amigo.geneontology.org/amigo/term/GO:0005634 GO:0005634], [[http://amigo.geneontology.org/amigo/term/GO:0043565 GO:0043565]<br />
<br />
===Wild Type & Mutants===<br />
[[File:OsDTH8_2.jpg|left|thumb|210px|'''Figure 2.''' ''Transformants (left) VS. wild-type (right)(from reference<ref name="ref2" />).'']]<br />
<br><br />
* The population genetics analysis made by ''Xiangjin Wei'' et al. in 2010 showed that the chromosome segment substitution lines of ''OsDTH8'' under the Asominori genetic background (''Japonica'') diplayed earlier heading than Asominori. Their plant height, number of grains per panicle, yield, and dry weight per plant decreased significantly in compared with Asominori NLD condition (Figure 1)<ref name="ref1" />.<br><br><br />
* The transgenetic analysis in rice made by ''Wen-Hao Yan'' et al. showed that the positive T1 plants of ''OsDTH8'' could produce more grains. They displayed significantly delayed heading with taller culms compared to the transgenic negative plants. On the whole, a positive T1 plant resulted in an increases 60% in grain yield per plant and grains per panicle compared to the control group<ref name="ref2" />.<br><br><br />
* The transgenetic analysis in Arabidopsis by ''Wen-Hao Yan'' et al. showed that transformants of ''OsDTH8'' can bloom about 10 days earlier than the wild-type under LD conditions, however, no obvious difference was observed between the transformants and wild-type under SD conditions (Figure 2)<ref name="ref2" />.<br><br><br><br />
[[File:OsDTH8_3.jpg|right|thumb|300px|'''Figure 3.''' ''The expression pattern of OsDTH8 (L/leaves, S/leaf sheaths, C/culms, P/young panicles, R/roots) (from reference<ref name="ref1" />).'']]<br />
<br />
===Expression===<br />
* The expression pattern analysis made by ''Xiangjin Wei'' et al. showed that ''OsDTH8'' was expressed in leaves, leaf sheaths, culms, young panicles and roots. However, its expression levels were higher in roots, young panicles, and leaves than those in leaf sheaths and culms (Figure 3)<ref name="ref1" />.<br />
<br />
* ''OsDTH8'' could negatively influence the expression of ''Ehd1'', ''Hd3a'' and ''RFT1'' but not ''Hd1'' and ''Ghd7''<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
===Subcellular Localization ===<br />
* The subcellular localization analysis made by ''Xiangjin Wei'' et al. suggests that ''OsDTH8'' is a nuclear protein<ref name="ref1" />.<br />
<br><br />
===Gene Structure===<br />
[[File:OsDTH8_4.png|center|thumb|727px|'''Figure 4.''' ''Structure of OsDTH (from NCBI BLASTP).'']]<br />
<br />
==Labs working on this gene==<br />
* State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China;<br />
* Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China;<br />
* Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China;<br />
* National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan;<br />
* State Key Laboratory of Plant Physiology and Biochemistry, National Evaluation Centre for Agricultural Wild Plants (Rice), Laboratory of Crop Heterosis and Utilization of the Ministry of Education, Beijing 100193, China;<br />
* Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Wei X, Xu J, Guo H, et al. DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously[J]. Plant Physiology, 2010, 153(4): 1747-1758.<br />
</ref><br />
* <ref name="ref2"><br />
Yan W H, Wang P, Chen H X, et al. A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice[J]. Molecular Plant, 2011, 4(2): 319-330.<br />
</ref><br />
* <ref name="ref3"><br />
Dai X, Ding Y, Tan L, et al. LHD1, an Allele of DTH8/Ghd8, Controls Late Heading Date in Common Wild Rice (Oryza rufipogon) F[J]. Journal of Integrative Plant Biology, 2012, 54(10): 790-799.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os08g0174500|<br />
Description = Similar to HAP3|<br />
Version = NM_001067642.1 GI:115475020 GeneID:4344784|<br />
Length = 1640 bp|<br />
Definition = Oryza sativa Japonica Group Os08g0174500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 8|Chromosome 8]]|<br />
AP = Chromosome 8:4332728..4334367|<br />
CDS = 4332849..4333742|<br />
GCID = <gbrowseImage1><br />
name=NC_008401:4332728..4334367<br />
source=RiceChromosome08<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008401:4332728..4334367<br />
source=RiceChromosome08<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgaagagtaggaagagctatgggcacttgctgagcccggtgggcagcccgccgttggacaacgagtccggcgaggcggcggcggcggctgcggctggcggcggcggctgcgggagcagcgccgggtatgtcgtctacggcggcggcggcggtggggactcgccggcgaaggagcaggacaggttcctgccgatcgcgaacgtgagccgcatcatgaagcggtcgctgccggcgaacgccaagatctccaaggagtcgaaggagacggtgcaggagtgcgtgtcggagttcatcagcttcgttacaggcgaggcctccgacaagtgccagcgcgagaagcggaagaccatcaacggcgacgacctcctctgggccatgaccacgctggggttcgaggcctacgtcggcccgctcaagtcctacctcaaccgctaccgcgaggccgagggcgagaaggccgacgtgctcggcggcgccggcggcgccgccgcggcgcgccacggcgagggcggttgctgcggcggcggcggcggcggcgccgatggcgtcgtcatcgacgggcattacccgctcgccggcggcctgtcacactcacaccatggtcatcagcagcaggacggcggcggcgacgtcgggctcatgatgggcggcggcgacgccggcgtcgggtacaacgccggggccgggtcgacgacgacggcgttctacgcgccggcggcgacggcggcgtcagggaacaaggcgtactgcggcggcgacgggtcgagggtgatggagttcgagggcatcggcggcgaggaggagagcggaggcggcggcggcggcggcgagagggggttcgccggccacctccatggcgtgcaatggtttagactaaagaggaatactaattag</cdnaseq>|<br />
AA = <aaseq>MKSRKSYGHLLSPVGSPPLDNESGEAAAAAAAGGGGCGSSAGYV VYGGGGGGDSPAKEQDRFLPIANVSRIMKRSLPANAKISKESKETVQECVSEFISFVT GEASDKCQREKRKTINGDDLLWAMTTLGFEAYVGPLKSYLNRYREAEGEKADVLGGAG GAAAARHGEGGCCGGGGGGADGVVIDGHYPLAGGLSHSHHGHQQQDGGGDVGLMMGGG DAGVGYNAGAGSTTTAFYAPAATAASGNKAYCGGDGSRVMEFEGIGGEEESGGGGGGG ERGFAGHLHGVQWFRLKRNTN</aaseq>|<br />
DNA = <dnaseqindica>626..1519#tcggtcattagtatatgttagtataaattaaataattaaacaccttaaacaatattttttcgtcgtagtttgatcatcacctaagattttttagtcttttcaaaatgatcatcagctaacaagtgtatctttatttatttgtgcaagaagtaaatgagcatcattgaatgcgctgcacacatgtaatgcaaacaaccaagttaatttttattggtgcaacggcgcgcactatttaaaacgtgacgcaatgcagcgatagagcaccttgatagataagaattaatttcagcatgatgtagattttgttatccttaatctctactcactttgcataggtaataaattaaaccgctgaactattactacatggtttacatgaaaggtgatcgggtagggacgagaatgtcgcgacacacataatatatatagtagcgtccttatgtttgctttgtgtccgcatcgataccgtcttcccactcgcatctcctcacctcctttccttctttaaaaggagagcatcaccactccatcctcaactcccataacctcccccttctctctctctctaactacacactctctctctagctagctagctagctatagctagtgttgttagcttcacatgaagagtaggaagagctatgggcacttgctgagcccggtgggcagcccgccgttggacaacgagtccggcgaggcggcggcggcggctgcggctggcggcggcggctgcgggagcagcgccgggtatgtcgtctacggcggcggcggcggtggggactcgccggcgaaggagcaggacaggttcctgccgatcgcgaacgtgagccgcatcatgaagcggtcgctgccggcgaacgccaagatctccaaggagtcgaaggagacggtgcaggagtgcgtgtcggagttcatcagcttcgttacaggcgaggcctccgacaagtgccagcgcgagaagcggaagaccatcaacggcgacgacctcctctgggccatgaccacgctggggttcgaggcctacgtcggcccgctcaagtcctacctcaaccgctaccgcgaggccgagggcgagaaggccgacgtgctcggcggcgccggcggcgccgccgcggcgcgccacggcgagggcggttgctgcggcggcggcggcggcggcgccgatggcgtcgtcatcgacgggcattacccgctcgccggcggcctgtcacactcacaccatggtcatcagcagcaggacggcggcggcgacgtcgggctcatgatgggcggcggcgacgccggcgtcgggtacaacgccggggccgggtcgacgacgacggcgttctacgcgccggcggcgacggcggcgtcagggaacaaggcgtactgcggcggcgacgggtcgagggtgatggagttcgagggcatcggcggcgaggaggagagcggaggcggcggcggcggcggcgagagggggttcgccggccacctccatggcgtgcaatggtttagactaaagaggaatactaattagctagctaggcacacgcgtagttttattattacttaattaccgcgttaattaattgttgatgctgatgctgtttaaaattgattctccttttgcatgaaatgtttgatggtatggtttaaaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001067642.1 RefSeq:Os08g0174500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0114500&diff=172383Os09g01145002014-05-25T13:35:10Z<p>HamletShaoE: </p>
<hr />
<div>The rice ''Os09g0114500'' was reported as ''Brittle Culm 12('''BC12''')'' and ''gibberellin-deficient dwarf1 ('''gdd1''')'' respectively in 2010 and 2011 by Chinese researchers<ref name="ref1" /><ref name="ref2" />.<br />
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==Annotated Information==<br />
[[File:BC12_1.jpg|right|thumb|320px|'''Figure 1.''' '' '''BC12''' Mutant VS. WT(from reference) <ref name="ref2" />.'']]<br />
===Function===<br />
'''''BC12''''' plays an important role in cell-cycle progression, cellulose microfibril deposition and wall composition in the monocot plant rice<ref name="ref1" />. This gene encodes a kinesin-like protein with transcription regulation activity, which can mediate cell elongation by regulating the expression of the '''''KO2''''' gene in the GA biosynthesis pathway<ref name="ref2" />. It is also likely to be a good subject for exploring the link between cell growth and cell wall formation in rice<ref name="ref1" />.<br><br><br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003777 GO:0003777], [http://amigo.geneontology.org/amigo/term/GO:0005524 GO:0005524], [http://amigo.geneontology.org/amigo/term/GO:0005875 GO:0005875], [http://amigo.geneontology.org/amigo/term/GO:0007018 GO:0007018]<br />
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===Mutation===<br />
* Figure 1 shows the gross morphology of the wild type and mutant plants. The mutant was shorter than the wild type at the three-leaf and heading stages (Figures 1A and 1B). Also, mutant spikes and grains were slightly shorter than those of the wild type (Figure 1C). Nearly every internode of the mutant was shorter than that in the wild type<ref name="ref2" />.<br><br><br />
*The breaking force of '''''bc12''''' mutation culms and leaves was reduced to approximately 25% of that in the wild-type. The cellulose content was not significantly altered, but the lignin content was increased by approximately 50% in mutation. The higher lignin content resulted from a general increase in all three monomers.<ref name="ref1" />.<br />
[[File:BC12_4.jpg|right|thumb|320px|'''Figure 2.''' ''Classification of the genes up- or downregulated fourfold or more in Mutation by whole-genome DNA microarray analysis<ref name="ref2" />'']]<br />
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===Expression===<br />
* '''Expression pattern of ''BC12'' '''<br> Quantitative PCR revealed that '''''BC12''''' is universally expressed in all organs examined, with higher expression in panicles and culms<ref name="ref1" /><ref name="ref2" />. The RT-PCR analyses also shows greater expression of '''''BC12''''' in the tissues enriched in dividing cells than in those enriched in non-dividing cells<ref name="ref1" />.<br><br><br />
* '''Expression Analysis in Mutant'''<br> Affymetrix whole-genomemicroarray chip analyses by ''Juan Li et al.'' shows that 116 downregulated and 125 upregulated genes in the mutant compared with the wild type (more than four fold expression change; Figure 2). Of note, the genes involved in cell wall expansion were significantly altered in expression in the mutant. <br>Those encoding xylanase inhibitor protein and cellulose synthase (CESA6) were greatly upregulated. By contrast, the gene for lignin forming anionic peroxidase was downregulated. That imply '''''BC12''''' might be involved in the regulation of genes associated with cell wall assembly.Of note, the expression of the rice KO gene KO2, a key enzyme in early GA synthesis, was greatly decreased in mutation compared with the wild type<ref name="ref2" />.<br />
[[File:BC12_5.jpg|right|thumb|320px|'''Figure 3.''' ''Phylogenetic tree of '''BC12''' and representative homologs from Arabidopsis and animals.(from reference) <ref name="ref1" />.'']]<br />
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===Localization===<br />
The production of '''''BC12''''' was located at both the nucleus and cytoplasm and associated with microtubule arrays during cell division<ref name="ref1" /><ref name="ref2" />. An NLS with 17 amino acid sequence was found in this gene<ref name="ref1" />.<br />
===Evolution===<br />
Phylogenetic analysis by ''Mu Zhang et al.'' revealed that '''''BC12''''' and motor proteins selected from various kinesin subfamilies are divided into separated clades(Figure 3). Kinesin-4 proteins from several representative species were clustered together but formed different subclades. Among the kinesin-4 proteins, those from rice and Arabidopsis were found to belong to a monophyletic clade with 100% bootstrap support. '''''BC12''''' showed the closest homology to FRA1, which has been reported to be involved in cellulose microfibril deposition<ref name="ref1" />.<br />
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===Knowledge Extension===<br />
* [http://en.wikipedia.org/wiki/Gibberellins Gibberellins (GAs)] are one of the most important endogenous growth regulators in plants<ref name="ref2" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. They are not only required for stem elongation but indeed participate in most stages of plant development<ref name="ref3" />. GAs mediate between certain environmental signals (e.g. light quality and photoperiod) and the inducedphysiological responses <ref name="ref3" />(e.g. stem extension and flowering). GA-deficient mutants are usually much shorter than the wild type, which indicates the corresponding genes such as '''''sd1''''' ('''''[[Os01g0883800]]''''')<ref name="ref6" /> in rice may have a relationship with [http://en.wikipedia.org/wiki/The_Green_Revolution The Green revolution].<br />
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* The biosynthesis of GA in higher plants can be divided into three stages: (1) biosynthesis of ''ent''-kaurene in proplastids;(2) conversion of ''ent''-kaurene to GA12 via microsomal cytochrome P450 monooxygenases;(3) formation of C20- and C19-GAs in the cytoplasm<ref name="ref4" /><ref name="ref2" />. GA biosynthesis is catalyzed by three classes of enzymes: terpene cyclases catalyze the synthesis of ''ent''-kaurene from geranylgeranyl diphosphate; cytochrome P450 monooxygenases catalyze the steps of the pathway from ''ent''-kaurene to GA12; and soluble dioxygenases catalyze the final steps of the pathway<ref name="ref5" />.<br />
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==Labs working on this gene==<br />
* Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China<br />
* State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
* State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, angzhou 310006, China<br />
* Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China<br />
* Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
* State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100094, China<br />
* National Center for Plant Gene Research, Beijing 100093, China<br />
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==References==<br />
<references><br />
* <ref name="ref1"><br />
Zhang M, Zhang B, Qian Q, et al. Brittle Culm 12, a dual‐targeting kinesin‐4 protein, controls cell‐cycle progression and wall properties in rice[J]. The Plant Journal, 2010, 63(2): 312-328.<br />
</ref><br />
* <ref name="ref2"><br />
Li J, Jiang J, Qian Q, et al. Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation[J]. The Plant Cell Online, 2011, 23(2): 628-640.<br />
</ref><br />
* <ref name="ref3"><br />
Hedden P, Phillips A L. Gibberellin metabolism: new insights revealed by the genes[J]. Trends in plant science, 2000, 5(12): 523-530.<br />
</ref><br />
* <ref name="ref4"><br />
Olszewski N, Sun T, Gubler F. Gibberellin signaling biosynthesis, catabolism, and response pathways[J]. The Plant Cell Online, 2002, 14(suppl 1): S61-S80.<br />
</ref><br />
* <ref name="ref5"><br />
Helliwell C A, Chandler P M, Poole A, et al. The CYP88A cytochrome P450, ent-kaurenoic acid oxidase, catalyzes three steps of the gibberellin biosynthesis pathway[J]. Proceedings of the National Academy of Sciences, 2001, 98(4): 2065-2070.<br />
</ref><br />
* <ref name="ref6"><br />
Lina Ma, Zhang Zhang, Gang Wu (2012) Gene: "Os01g0883800" in RiceWiki, available at http://ricewiki.big.ac.cn/index.php?title=Os01g0883800&oldid=166658 (Last update: Aug 23, 2012).<br />
</ref><br />
</references><br />
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==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0114500|<br />
Description = Similar to Kinesin-like protein (Fragment)|<br />
Version = NM_001069115.1 GI:115477969 GeneID:4346402|<br />
Length = 9531 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0114500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:1104794..1114324|<br />
CDS = 1105331..1105453,1106559..1106705,1107046..1107195,1107272..1107531,1107897..1108084<br>,1108187..1108311,1108485..1108521,1108802..1108893,1109023..1109133<br>,1109242..1109352,1109576..1109669,1109830..1109945,1110316..1110411<br>,1110510..1110617,1110698..1110814,1110910..1110990,1111205..1111276<br>,1111553..1111646,1111759..1111787,1111870..1111967,1112065..1112160<br>,1112399..1112620,1113002..1113158,1113472..1113627,1113703..1113930<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:1104794..1114324<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:1104794..1114324<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgacgatggagcacggcgaggattgctgcgtcaaggtggccgtccatgtccgcccgctcatcggcgacgagaagcttcagggctgtaaggactgcgtctccgtcgtctccggcaagccgcaggttcagatcgggagccattccttcaccttcgaccatgtgtacggcagctccggcacgccgtcggcggccatgttcgaggagtgcgtggcgccgctcgtcgacggcctcttccagggctacaacgccaccgtgctcgcatacggccagactgggtcagggaagacctacaccatggggacggcctgcaaggagggctcacacattgggattatcccgcgtgccatggccacgctgttcgacaagatcgacaagctcaagaaccaagtagagttccagctgcgcgtttcgtttattgagattctgaaagaagaggtgagggatttgcttgatcctgctactgctgctgttggcaaacttgagaatggaaatggacatgcaaccaagttgtcggttccaggtaaaccccctgttcagatccgggaggcgtcgaacggggtcataacgttagcaggatcgaccgaagtgcatgtcactacccagaaagaaatgacggcatgccttgagcaaggatctctgagtcgtgcaactggaagtaccaacatgaacaaccaatcaagtcgttcccatgccatcttcacaatcacattggagcagatgcgcaaagcagatcccatcatgactttagatggaatgcctattgaagagatgaatgaagactatctctgtgccaaactccacttagtagatcttgctggatcagaacgtgctaaaagaactggttctgatggccttcggtttaaggaaggtgttcatatcaacagaggacttcttgctcttggcaatgtcatcagtgctctcggtgatgagaaaaagaggaaagaaggcgctcatgttccttaccgggacagcaaactcactcgccttctgcaggactctctaggtggaaacagcaagactgtaatgatagcctgtattagtccagcagatatcaatgctgaagaaacactgaacactttgaaatatgctaaccgcgctcgtaacatccagaataagccaattgtaaatagaaatcctgttgctgatgagatgaaaaggatgcgccagcaaattgaatacttgcaagcagaactcgtttcagctcgaggaggagttgtcttagatgatgttcagggtctcagggaaaggatctcaatgcttgaacagaaaaatgaagacctttgcagggaactgtatgaccttcgcaaccatggttacactgatccttgtgaacctgaactgcaaaaaattggaactggttacactaaaggtgaagggctcaaaagaagcttgcaaagtacagaaccatttgatgtccccatgactgactcagtaagagcaggcagccctaaagatattgatgatgaagtggccaaagaatgggaacacacaatgctgcaggatagcatgggcaaagagttgaatgaattaaacagacaactggagcaaaaggagtctgagatgaaaatgtatggatctgacactgttgcacttaaacaacactttggaaagaaacttttggagcttgaagaagagaaaagagctgtacagcaagaaagggacagattgttagctgaagttgaaagtctaaatgctgatggacaaacacacaagttgcgagatgcccagctgcaaaaattaaaaacccttgaagcacagattctagacctcaagaaaaagcaggagaaccaagttcaacttctgaaggaaaagcaaaagagtgatgaagctgctaagaagttgcaggaagaaattcattctataaaggcacagaaggttcaactacaacataaaatcaaacaagaagcggaacaattccggcaatggaaggctacccgtgaaaaggaactcctgcagttgaggaaagaggggcggcgaaatgagtatgaacgccacaaacttcaagcacttaatcagcggcagaagttggttttgcagaggaagactgaagaagctgcgatggctaccaaaaggctgaaagagttactagaggctcggaaatcatcaggacgtgacaactcaggcatgaatggtacttctcctggctctcatatgactgagaaatcattgcaaaaatggctagagcaagatttggaagtcatggtgcatgttcatgaagttcgaaacgaatatgaaaagcaaagtcaattgcgtgctgcacttggtgaggagcttgccattttaaaacaagaagatgtcatgtctggtgcagctagtccgcccagagggaagaatggaaactctagggcaaatactttgtcaccaaatgcaagacaagctaggatagcatcacttgaaagcatggtgacaatatcttcaaatactctcgttgctatggcttctcaactctcagaagctgaagaaagagagcgtgcattctctgggcgtggtcggtggaatcagttgcgttcaatggcagaggcaaagagtttactgcagtatatatttaacgttgctgcagatgcaagatgccaagtaagggagaaagagatggagatcaaggaaatgaaggagcaaatgacagagcttgtgaccatccttcgacacagcgaatcacgtagaagggaaacggaaaagcagcttaagcaaagagagcaggcagctgtaactgccactacatctccaggaaacggaaatggttcagtgaagcactctgctgatgactccaacacaccattgtcaccagttgcggtgcctgcacagaagcagctgaagtactctgctggaattgtaaatagccccagcaaaggggttcctgcattcaacaaacaacatcttaagatggttcctatggcacagttgcctgttggcaagaaggtttcaatagcagggcaatcaggaaaactttggagatggaaaagaagccaccaccagtggctactgcagttcaagtggaagtggcaaaagccctggaaattgtccgagatgattcgacacagtgacgaaacgatgacaaggactcgacccagaccccagcttcttcctcatagacctcaaagagtgatgtga</cdnaseq>|<br />
AA = <aaseq>MTMEHGEDCCVKVAVHVRPLIGDEKLQGCKDCVSVVSGKPQVQI GSHSFTFDHVYGSSGTPSAAMFEECVAPLVDGLFQGYNATVLAYGQTGSGKTYTMGTA CKEGSHIGIIPRAMATLFDKIDKLKNQVEFQLRVSFIEILKEEVRDLLDPATAAVGKL ENGNGHATKLSVPGKPPVQIREASNGVITLAGSTEVHVTTQKEMTACLEQGSLSRATG STNMNNQSSRSHAIFTITLEQMRKADPIMTLDGMPIEEMNEDYLCAKLHLVDLAGSER AKRTGSDGLRFKEGVHINRGLLALGNVISALGDEKKRKEGAHVPYRDSKLTRLLQDSL GGNSKTVMIACISPADINAEETLNTLKYANRARNIQNKPIVNRNPVADEMKRMRQQIE YLQAELVSARGGVVLDDVQGLRERISMLEQKNEDLCRELYDLRNHGYTDPCEPELQKI GTGYTKGEGLKRSLQSTEPFDVPMTDSVRAGSPKDIDDEVAKEWEHTMLQDSMGKELN ELNRQLEQKESEMKMYGSDTVALKQHFGKKLLELEEEKRAVQQERDRLLAEVESLNAD GQTHKLRDAQLQKLKTLEAQILDLKKKQENQVQLLKEKQKSDEAAKKLQEEIHSIKAQ KVQLQHKIKQEAEQFRQWKATREKELLQLRKEGRRNEYERHKLQALNQRQKLVLQRKT EEAAMATKRLKELLEARKSSGRDNSGMNGTSPGSHMTEKSLQKWLEQDLEVMVHVHEV RNEYEKQSQLRAALGEELAILKQEDVMSGAASPPRGKNGNSRANTLSPNARQARIASL ESMVTISSNTLVAMASQLSEAEERERAFSGRGRWNQLRSMAEAKSLLQYIFNVAADAR CQVREKEMEIKEMKEQMTELVTILRHSESRRRETEKQLKQREQAAVTATTSPGNGNGS VKHSADDSNTPLSPVAVPAQKQLKYSAGIVNSPSKGVPAFNKQHLKMVPMAQLPVGKK VSIAGQSGKLWRWKRSHHQWLLQFKWKWQKPWKLSEMIRHSDETMTRTRPRPQLLPHR PQRVM</aaseq>|<br />
DNA = <dnaseqindica>538..660#1766..1912#2253..2402#2479..2738#3104..3291#3394..3518#3692..3728#4009..4100#4230..4340#4449..4559#4783..4876#5037..5152#5523..5618#5717..5824#5905..6021#6117..6197#6412..6483#6760..6853#6966..6994#7077..7174#7272..7367#7606..7827#8209..8365#8679..8834#8910..9137#accccacctacacactcttcttcctcctcttccttcttcttcttcctcttcttctcctccatttccatttctccacccaccaccaaacatctccggatccttcgctccatcctcctcctaagaagagcccaagaagccagcaagatccaaagatcaagagcagcatttgtagctgcaactgctggtgctggtgctgttgctgttagatcgaggaggattcaacaagtgtgttggtggtggtggaagttgttacagaattgcgggtgagagaagtttcttcaccgcacctcaccaaaatctccatccatccgtctgaatcccaactccacctgcaactgcaactgcacggcgagattgcagtacaacccaagaaaccatgatgaagtggcagcatcagtagcagtagcagcagcaggaggaggaggaggaagagggctcctctttaatccttgcttcactcatcttcatcagaatcctccttattggctccgcctcgcattctgtgctgcatcggctgttgtatggtcggtggcgaagatgacgatggagcacggcgaggattgctgcgtcaaggtggccgtccatgtccgcccgctcatcggcgacgagaagcttcagggctgtaaggactgcgtctccgtcgtctccggcaagccgcaggtattccttctcttctctttttatcactcactcatttggcttcttttttcttgtttatacgtcccaattcagagagactagattgactctcatcctgtcaattgtttctggatttctcttttattttattttttttgggggggacgtgatttcctgggaaaatccaaacaatatgataagttctctgcattgttcttttaagattacctgaaatttttaattaaattcagagattggagacatattttgtccaagtcaagaaagaaaaatctctgactctgtttttctctgttgagtacaagaacagaggagctcagaagaggacttgttgtttcccccaattttggtcctctaattcagaaaaaaaaacttgtcaaaattcatggagaatctagcttgcttccttgttttagctccctatgaaatgatagagatgcccatctgttcgctttccctttctcttagttttgttttcttttccttttgatcatcattaaatgaggctctagagtcttccttctccttttttcttcttcagaataaaattgtatatatttttttcactgtcggcagcgccaaatgttcctcattttttggtgtgaagttgcgtccaatgttgatgacgctaatgctataccctttcttttatctggggctggaattctgtcagcatcacgcaattatcacccaggttttctttctccagttttgtccatccaacactcatccttgttggattcttcccttcccttccttttctttcttccatcaagatttattaagtcattttctcagacaaaacgcagcaagattaattaggttccttaattaatctaatcctccattacacaaactcgaatgatgagatctggcttaggtatcatattcttttggtaagatggtttgctctccataagactgttgtttgttgatctttcttgggttccccaccaatttcatttctttgggagatgatgaaaagttactttctttcattctcccaaatcaatctttttaccggtggtggcggtggtgatgatgggggtgaaaaaaaagggcatatctttctttgttttgttgttgctgatgggttttgttgttgcaggttcagatcgggagccattccttcaccttcgaccatgtgtacggcagctccggcacgccgtcggcggccatgttcgaggagtgcgtggcgccgctcgtcgacggcctcttccagggctacaacgccaccgtgctcgcatacggccaggtccgccattgccattgccatccaatcatatgcttccatctccatccccatgtgccaccatggaccaccatgttggggaagatgcaaaagccagcaccacatcatgtgctcctgctcctgctcctcctgctgctgcctgctaatccccttttcttttcttttccttttcttttcacacttgcttattagttgcttttcttctccagctgtttctgcctcatgatgctagatcattttcttgttttttcacatcctctgtgaacaaaaaaaggaaaagaagagaagagattggaaaaatgctgattgatttggtggttgtttcatctcttcctttttacagactgggtcagggaagacctacaccatggggacggcctgcaaggagggctcacacattgggattatcccgcgtgccatggccacgctgttcgacaagatcgacaagctcaagaaccaagtagagttccagctgcgcgtttcgtttattgaggtaaattacctgttcctggatgaatcaaacatttgtgggattgtagagaatccaattgtgctcgttctcttgatagattctgaaagaagaggtgagggatttgcttgatcctgctactgctgctgttggcaaacttgagaatggaaatggacatgcaaccaagttgtcggttccaggtaaaccccctgttcagatccgggaggcgtcgaacggggtcataacgttagcaggatcgaccgaagtgcatgtcactacccagaaagaaatgacggcatgccttgagcaaggatctctgagtcgtgcaactggaagtaccaacatgaacaaccaatcaaggttagcaaacattatcctaatcattcgtcctttaccttttttagaggaggaagcaggtccattgatcaaccataattgatgacaagaaactagcatcattatggtcagaaactggcaatctttgcaggatacagctgtttgtgatgatttcttgcttctatgtttagtgtaggacctttttgcaggattagtcaatgtattgtcctaccctcaaaagagaaaccaattatttgtctagtttcaagtaattaattctctgctcaagtgctttaggacacattcaatcagattggttacctgatattccgttactaaattctacaaactttaatgaactttatgcttttggtttcggcatgtaatagtcgttcccatgccatcttcacaatcacattggagcagatgcgcaaagcagatcccatcatgactttagatggaatgcctattgaagagatgaatgaagactatctctgtgccaaactccacttagtagatcttgctggatcagaacgtgctaaaagaactggttctgatggccttcggtttaaggaaggtacttggcatgttgcttgttctatctgaatccctaatcaaacatccatcttgtcttgaaacaagatactccgtataatttatttatgtatcatgtcatcaggtgttcatatcaacagaggacttcttgctcttggcaatgtcatcagtgctctcggtgatgagaaaaagaggaaagaaggcgctcatgttccttaccgggacagcaaactcactcgccttctgcaggtattattcttctgacccaagtgcacaggcctttgtacagaagcattgaattcatagctctgttcaagaagtagggccagctcacatttaagcatatataatacttgaatctttgcatttagtttctttcattttactaactaatctgttttatatctattttattattataggactctctaggtggaaacagcaagactgtaatgataggtaattcatttggttggagattgtttaatcatatttttatatgatttaggattttttctaaataatgcttgtcaaagttccagaattggggtttaaaataaaaaaaaataaaacgatgatctattcattttatcttcggtaaaaaaaaatgcatcttgtcatatgatttaatttgttttcataaataagaaaactcggatgtaccttgattttcactaactgttttggttgatattactattacatgcaactgacatggatctatatttttctcctgcagcctgtattagtccagcagatatcaatgctgaagaaacactgaacactttgaaatatgctaaccgcgctcgtaacatccagaataagccaattgtaagttcattaaaatggtctcgtcagaaaagtatctgacatttatctgcgttatgtttctttaattaattggtttggttccgtcaaggtgattatttgacatccctatatttactttcctattttcaggtaaatagaaatcctgttgctgatgagatgaaaaggatgcgccagcaaattgaatacttgcaagcagaactcgtttcagctcgaggaggagttgtcttagatgatgttcaggtaaattcttttctcgtctatcctcagtgtccttgaccatcttgttctataaggcacactcactcacaataacagtatgagtataataacaagtggttccattttcagggtctcagggaaaggatctcaatgcttgaacagaaaaatgaagacctttgcagggaactgtatgaccttcgcaaccatggttacactgatccttgtgaacctgaactgcaagtatgttgatgagttcttctgcaagctttcggagattttacatttgaaaacaagcatacaatttactcttctacggcttctttcatgatagattcccttttctctcaaaggaaataaaagaggggacataacatgacattgtctactatggatt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/>
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069115.1 RefSeq:Os09g0114500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0114500&diff=172382Os09g01145002014-05-25T13:34:48Z<p>HamletShaoE: /* Function */</p>
<hr />
<div>The rice ''Os09g0114500'' was reported as ''Brittle Culm 12('''BC12''')'' and ''gibberellin-deficient dwarf1 ('''gdd1''')'' respectively in 2010 and 2011 by Chinese researchers<ref name="ref1" /><ref name="ref2" />.<br />
<br />
==Annotated Information==<br />
[[File:BC12_1.jpg|right|thumb|320px|'''Figure 1.''' '' '''BC12''' Mutant VS. WT(from reference) <ref name="ref2" />.'']]<br />
===Function===<br />
'''''BC12''''' plays an important role in cell-cycle progression, cellulose microfibril deposition and wall composition in the monocot plant rice<ref name="ref1" />. This gene encodes a kinesin-like protein with transcription regulation activity, which can mediate cell elongation by regulating the expression of the '''''KO2''''' gene in the GA biosynthesis pathway<ref name="ref2" />. It is also likely to be a good subject for exploring the link between cell growth and cell wall formation in rice<ref name="ref1" />.<br><br><br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003777 GO:0003777, [http://amigo.geneontology.org/amigo/term/GO:0005524 GO:0005524], [http://amigo.geneontology.org/amigo/term/GO:0005875 GO:0005875], [http://amigo.geneontology.org/amigo/term/GO:0007018 GO:0007018]<br />
<br />
===Mutation===<br />
* Figure 1 shows the gross morphology of the wild type and mutant plants. The mutant was shorter than the wild type at the three-leaf and heading stages (Figures 1A and 1B). Also, mutant spikes and grains were slightly shorter than those of the wild type (Figure 1C). Nearly every internode of the mutant was shorter than that in the wild type<ref name="ref2" />.<br><br><br />
*The breaking force of '''''bc12''''' mutation culms and leaves was reduced to approximately 25% of that in the wild-type. The cellulose content was not significantly altered, but the lignin content was increased by approximately 50% in mutation. The higher lignin content resulted from a general increase in all three monomers.<ref name="ref1" />.<br />
[[File:BC12_4.jpg|right|thumb|320px|'''Figure 2.''' ''Classification of the genes up- or downregulated fourfold or more in Mutation by whole-genome DNA microarray analysis<ref name="ref2" />'']]<br />
<br />
===Expression===<br />
* '''Expression pattern of ''BC12'' '''<br> Quantitative PCR revealed that '''''BC12''''' is universally expressed in all organs examined, with higher expression in panicles and culms<ref name="ref1" /><ref name="ref2" />. The RT-PCR analyses also shows greater expression of '''''BC12''''' in the tissues enriched in dividing cells than in those enriched in non-dividing cells<ref name="ref1" />.<br><br><br />
* '''Expression Analysis in Mutant'''<br> Affymetrix whole-genomemicroarray chip analyses by ''Juan Li et al.'' shows that 116 downregulated and 125 upregulated genes in the mutant compared with the wild type (more than four fold expression change; Figure 2). Of note, the genes involved in cell wall expansion were significantly altered in expression in the mutant. <br>Those encoding xylanase inhibitor protein and cellulose synthase (CESA6) were greatly upregulated. By contrast, the gene for lignin forming anionic peroxidase was downregulated. That imply '''''BC12''''' might be involved in the regulation of genes associated with cell wall assembly.Of note, the expression of the rice KO gene KO2, a key enzyme in early GA synthesis, was greatly decreased in mutation compared with the wild type<ref name="ref2" />.<br />
[[File:BC12_5.jpg|right|thumb|320px|'''Figure 3.''' ''Phylogenetic tree of '''BC12''' and representative homologs from Arabidopsis and animals.(from reference) <ref name="ref1" />.'']]<br />
<br />
===Localization===<br />
The production of '''''BC12''''' was located at both the nucleus and cytoplasm and associated with microtubule arrays during cell division<ref name="ref1" /><ref name="ref2" />. An NLS with 17 amino acid sequence was found in this gene<ref name="ref1" />.<br />
===Evolution===<br />
Phylogenetic analysis by ''Mu Zhang et al.'' revealed that '''''BC12''''' and motor proteins selected from various kinesin subfamilies are divided into separated clades(Figure 3). Kinesin-4 proteins from several representative species were clustered together but formed different subclades. Among the kinesin-4 proteins, those from rice and Arabidopsis were found to belong to a monophyletic clade with 100% bootstrap support. '''''BC12''''' showed the closest homology to FRA1, which has been reported to be involved in cellulose microfibril deposition<ref name="ref1" />.<br />
<br><br />
<br />
===Knowledge Extension===<br />
* [http://en.wikipedia.org/wiki/Gibberellins Gibberellins (GAs)] are one of the most important endogenous growth regulators in plants<ref name="ref2" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. They are not only required for stem elongation but indeed participate in most stages of plant development<ref name="ref3" />. GAs mediate between certain environmental signals (e.g. light quality and photoperiod) and the inducedphysiological responses <ref name="ref3" />(e.g. stem extension and flowering). GA-deficient mutants are usually much shorter than the wild type, which indicates the corresponding genes such as '''''sd1''''' ('''''[[Os01g0883800]]''''')<ref name="ref6" /> in rice may have a relationship with [http://en.wikipedia.org/wiki/The_Green_Revolution The Green revolution].<br />
<br />
* The biosynthesis of GA in higher plants can be divided into three stages: (1) biosynthesis of ''ent''-kaurene in proplastids;(2) conversion of ''ent''-kaurene to GA12 via microsomal cytochrome P450 monooxygenases;(3) formation of C20- and C19-GAs in the cytoplasm<ref name="ref4" /><ref name="ref2" />. GA biosynthesis is catalyzed by three classes of enzymes: terpene cyclases catalyze the synthesis of ''ent''-kaurene from geranylgeranyl diphosphate; cytochrome P450 monooxygenases catalyze the steps of the pathway from ''ent''-kaurene to GA12; and soluble dioxygenases catalyze the final steps of the pathway<ref name="ref5" />.<br />
<br />
==Labs working on this gene==<br />
* Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China<br />
* State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
* State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, angzhou 310006, China<br />
* Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China<br />
* Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
* State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100094, China<br />
* National Center for Plant Gene Research, Beijing 100093, China<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Zhang M, Zhang B, Qian Q, et al. Brittle Culm 12, a dual‐targeting kinesin‐4 protein, controls cell‐cycle progression and wall properties in rice[J]. The Plant Journal, 2010, 63(2): 312-328.<br />
</ref><br />
* <ref name="ref2"><br />
Li J, Jiang J, Qian Q, et al. Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation[J]. The Plant Cell Online, 2011, 23(2): 628-640.<br />
</ref><br />
* <ref name="ref3"><br />
Hedden P, Phillips A L. Gibberellin metabolism: new insights revealed by the genes[J]. Trends in plant science, 2000, 5(12): 523-530.<br />
</ref><br />
* <ref name="ref4"><br />
Olszewski N, Sun T, Gubler F. Gibberellin signaling biosynthesis, catabolism, and response pathways[J]. The Plant Cell Online, 2002, 14(suppl 1): S61-S80.<br />
</ref><br />
* <ref name="ref5"><br />
Helliwell C A, Chandler P M, Poole A, et al. The CYP88A cytochrome P450, ent-kaurenoic acid oxidase, catalyzes three steps of the gibberellin biosynthesis pathway[J]. Proceedings of the National Academy of Sciences, 2001, 98(4): 2065-2070.<br />
</ref><br />
* <ref name="ref6"><br />
Lina Ma, Zhang Zhang, Gang Wu (2012) Gene: "Os01g0883800" in RiceWiki, available at http://ricewiki.big.ac.cn/index.php?title=Os01g0883800&oldid=166658 (Last update: Aug 23, 2012).<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0114500|<br />
Description = Similar to Kinesin-like protein (Fragment)|<br />
Version = NM_001069115.1 GI:115477969 GeneID:4346402|<br />
Length = 9531 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0114500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:1104794..1114324|<br />
CDS = 1105331..1105453,1106559..1106705,1107046..1107195,1107272..1107531,1107897..1108084<br>,1108187..1108311,1108485..1108521,1108802..1108893,1109023..1109133<br>,1109242..1109352,1109576..1109669,1109830..1109945,1110316..1110411<br>,1110510..1110617,1110698..1110814,1110910..1110990,1111205..1111276<br>,1111553..1111646,1111759..1111787,1111870..1111967,1112065..1112160<br>,1112399..1112620,1113002..1113158,1113472..1113627,1113703..1113930<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:1104794..1114324<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:1104794..1114324<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgacgatggagcacggcgaggattgctgcgtcaaggtggccgtccatgtccgcccgctcatcggcgacgagaagcttcagggctgtaaggactgcgtctccgtcgtctccggcaagccgcaggttcagatcgggagccattccttcaccttcgaccatgtgtacggcagctccggcacgccgtcggcggccatgttcgaggagtgcgtggcgccgctcgtcgacggcctcttccagggctacaacgccaccgtgctcgcatacggccagactgggtcagggaagacctacaccatggggacggcctgcaaggagggctcacacattgggattatcccgcgtgccatggccacgctgttcgacaagatcgacaagctcaagaaccaagtagagttccagctgcgcgtttcgtttattgagattctgaaagaagaggtgagggatttgcttgatcctgctactgctgctgttggcaaacttgagaatggaaatggacatgcaaccaagttgtcggttccaggtaaaccccctgttcagatccgggaggcgtcgaacggggtcataacgttagcaggatcgaccgaagtgcatgtcactacccagaaagaaatgacggcatgccttgagcaaggatctctgagtcgtgcaactggaagtaccaacatgaacaaccaatcaagtcgttcccatgccatcttcacaatcacattggagcagatgcgcaaagcagatcccatcatgactttagatggaatgcctattgaagagatgaatgaagactatctctgtgccaaactccacttagtagatcttgctggatcagaacgtgctaaaagaactggttctgatggccttcggtttaaggaaggtgttcatatcaacagaggacttcttgctcttggcaatgtcatcagtgctctcggtgatgagaaaaagaggaaagaaggcgctcatgttccttaccgggacagcaaactcactcgccttctgcaggactctctaggtggaaacagcaagactgtaatgatagcctgtattagtccagcagatatcaatgctgaagaaacactgaacactttgaaatatgctaaccgcgctcgtaacatccagaataagccaattgtaaatagaaatcctgttgctgatgagatgaaaaggatgcgccagcaaattgaatacttgcaagcagaactcgtttcagctcgaggaggagttgtcttagatgatgttcagggtctcagggaaaggatctcaatgcttgaacagaaaaatgaagacctttgcagggaactgtatgaccttcgcaaccatggttacactgatccttgtgaacctgaactgcaaaaaattggaactggttacactaaaggtgaagggctcaaaagaagcttgcaaagtacagaaccatttgatgtccccatgactgactcagtaagagcaggcagccctaaagatattgatgatgaagtggccaaagaatgggaacacacaatgctgcaggatagcatgggcaaagagttgaatgaattaaacagacaactggagcaaaaggagtctgagatgaaaatgtatggatctgacactgttgcacttaaacaacactttggaaagaaacttttggagcttgaagaagagaaaagagctgtacagcaagaaagggacagattgttagctgaagttgaaagtctaaatgctgatggacaaacacacaagttgcgagatgcccagctgcaaaaattaaaaacccttgaagcacagattctagacctcaagaaaaagcaggagaaccaagttcaacttctgaaggaaaagcaaaagagtgatgaagctgctaagaagttgcaggaagaaattcattctataaaggcacagaaggttcaactacaacataaaatcaaacaagaagcggaacaattccggcaatggaaggctacccgtgaaaaggaactcctgcagttgaggaaagaggggcggcgaaatgagtatgaacgccacaaacttcaagcacttaatcagcggcagaagttggttttgcagaggaagactgaagaagctgcgatggctaccaaaaggctgaaagagttactagaggctcggaaatcatcaggacgtgacaactcaggcatgaatggtacttctcctggctctcatatgactgagaaatcattgcaaaaatggctagagcaagatttggaagtcatggtgcatgttcatgaagttcgaaacgaatatgaaaagcaaagtcaattgcgtgctgcacttggtgaggagcttgccattttaaaacaagaagatgtcatgtctggtgcagctagtccgcccagagggaagaatggaaactctagggcaaatactttgtcaccaaatgcaagacaagctaggatagcatcacttgaaagcatggtgacaatatcttcaaatactctcgttgctatggcttctcaactctcagaagctgaagaaagagagcgtgcattctctgggcgtggtcggtggaatcagttgcgttcaatggcagaggcaaagagtttactgcagtatatatttaacgttgctgcagatgcaagatgccaagtaagggagaaagagatggagatcaaggaaatgaaggagcaaatgacagagcttgtgaccatccttcgacacagcgaatcacgtagaagggaaacggaaaagcagcttaagcaaagagagcaggcagctgtaactgccactacatctccaggaaacggaaatggttcagtgaagcactctgctgatgactccaacacaccattgtcaccagttgcggtgcctgcacagaagcagctgaagtactctgctggaattgtaaatagccccagcaaaggggttcctgcattcaacaaacaacatcttaagatggttcctatggcacagttgcctgttggcaagaaggtttcaatagcagggcaatcaggaaaactttggagatggaaaagaagccaccaccagtggctactgcagttcaagtggaagtggcaaaagccctggaaattgtccgagatgattcgacacagtgacgaaacgatgacaaggactcgacccagaccccagcttcttcctcatagacctcaaagagtgatgtga</cdnaseq>|<br />
AA = <aaseq>MTMEHGEDCCVKVAVHVRPLIGDEKLQGCKDCVSVVSGKPQVQI GSHSFTFDHVYGSSGTPSAAMFEECVAPLVDGLFQGYNATVLAYGQTGSGKTYTMGTA CKEGSHIGIIPRAMATLFDKIDKLKNQVEFQLRVSFIEILKEEVRDLLDPATAAVGKL ENGNGHATKLSVPGKPPVQIREASNGVITLAGSTEVHVTTQKEMTACLEQGSLSRATG STNMNNQSSRSHAIFTITLEQMRKADPIMTLDGMPIEEMNEDYLCAKLHLVDLAGSER AKRTGSDGLRFKEGVHINRGLLALGNVISALGDEKKRKEGAHVPYRDSKLTRLLQDSL GGNSKTVMIACISPADINAEETLNTLKYANRARNIQNKPIVNRNPVADEMKRMRQQIE YLQAELVSARGGVVLDDVQGLRERISMLEQKNEDLCRELYDLRNHGYTDPCEPELQKI GTGYTKGEGLKRSLQSTEPFDVPMTDSVRAGSPKDIDDEVAKEWEHTMLQDSMGKELN ELNRQLEQKESEMKMYGSDTVALKQHFGKKLLELEEEKRAVQQERDRLLAEVESLNAD GQTHKLRDAQLQKLKTLEAQILDLKKKQENQVQLLKEKQKSDEAAKKLQEEIHSIKAQ KVQLQHKIKQEAEQFRQWKATREKELLQLRKEGRRNEYERHKLQALNQRQKLVLQRKT EEAAMATKRLKELLEARKSSGRDNSGMNGTSPGSHMTEKSLQKWLEQDLEVMVHVHEV RNEYEKQSQLRAALGEELAILKQEDVMSGAASPPRGKNGNSRANTLSPNARQARIASL ESMVTISSNTLVAMASQLSEAEERERAFSGRGRWNQLRSMAEAKSLLQYIFNVAADAR CQVREKEMEIKEMKEQMTELVTILRHSESRRRETEKQLKQREQAAVTATTSPGNGNGS VKHSADDSNTPLSPVAVPAQKQLKYSAGIVNSPSKGVPAFNKQHLKMVPMAQLPVGKK VSIAGQSGKLWRWKRSHHQWLLQFKWKWQKPWKLSEMIRHSDETMTRTRPRPQLLPHR PQRVM</aaseq>|<br />
DNA = <dnaseqindica>538..660#1766..1912#2253..2402#2479..2738#3104..3291#3394..3518#3692..3728#4009..4100#4230..4340#4449..4559#4783..4876#5037..5152#5523..5618#5717..5824#5905..6021#6117..6197#6412..6483#6760..6853#6966..6994#7077..7174#7272..7367#7606..7827#8209..8365#8679..8834#8910..9137#accccacctacacactcttcttcctcctcttccttcttcttcttcctcttcttctcctccatttccatttctccacccaccaccaaacatctccggatccttcgctccatcctcctcctaagaagagcccaagaagccagcaagatccaaagatcaagagcagcatttgtagctgcaactgctggtgctggtgctgttgctgttagatcgaggaggattcaacaagtgtgttggtggtggtggaagttgttacagaattgcgggtgagagaagtttcttcaccgcacctcaccaaaatctccatccatccgtctgaatcccaactccacctgcaactgcaactgcacggcgagattgcagtacaacccaagaaaccatgatgaagtggcagcatcagtagcagtagcagcagcaggaggaggaggaggaagagggctcctctttaatccttgcttcactcatcttcatcagaatcctccttattggctccgcctcgcattctgtgctgcatcggctgttgtatggtcggtggcgaagatgacgatggagcacggcgaggattgctgcgtcaaggtggccgtccatgtccgcccgctcatcggcgacgagaagcttcagggctgtaaggactgcgtctccgtcgtctccggcaagccgcaggtattccttctcttctctttttatcactcactcatttggcttcttttttcttgtttatacgtcccaattcagagagactagattgactctcatcctgtcaattgtttctggatttctcttttattttattttttttgggggggacgtgatttcctgggaaaatccaaacaatatgataagttctctgcattgttcttttaagattacctgaaatttttaattaaattcagagattggagacatattttgtccaagtcaagaaagaaaaatctctgactctgtttttctctgttgagtacaagaacagaggagctcagaagaggacttgttgtttcccccaattttggtcctctaattcagaaaaaaaaacttgtcaaaattcatggagaatctagcttgcttccttgttttagctccctatgaaatgatagagatgcccatctgttcgctttccctttctcttagttttgttttcttttccttttgatcatcattaaatgaggctctagagtcttccttctccttttttcttcttcagaataaaattgtatatatttttttcactgtcggcagcgccaaatgttcctcattttttggtgtgaagttgcgtccaatgttgatgacgctaatgctataccctttcttttatctggggctggaattctgtcagcatcacgcaattatcacccaggttttctttctccagttttgtccatccaacactcatccttgttggattcttcccttcccttccttttctttcttccatcaagatttattaagtcattttctcagacaaaacgcagcaagattaattaggttccttaattaatctaatcctccattacacaaactcgaatgatgagatctggcttaggtatcatattcttttggtaagatggtttgctctccataagactgttgtttgttgatctttcttgggttccccaccaatttcatttctttgggagatgatgaaaagttactttctttcattctcccaaatcaatctttttaccggtggtggcggtggtgatgatgggggtgaaaaaaaagggcatatctttctttgttttgttgttgctgatgggttttgttgttgcaggttcagatcgggagccattccttcaccttcgaccatgtgtacggcagctccggcacgccgtcggcggccatgttcgaggagtgcgtggcgccgctcgtcgacggcctcttccagggctacaacgccaccgtgctcgcatacggccaggtccgccattgccattgccatccaatcatatgcttccatctccatccccatgtgccaccatggaccaccatgttggggaagatgcaaaagccagcaccacatcatgtgctcctgctcctgctcctcctgctgctgcctgctaatccccttttcttttcttttccttttcttttcacacttgcttattagttgcttttcttctccagctgtttctgcctcatgatgctagatcattttcttgttttttcacatcctctgtgaacaaaaaaaggaaaagaagagaagagattggaaaaatgctgattgatttggtggttgtttcatctcttcctttttacagactgggtcagggaagacctacaccatggggacggcctgcaaggagggctcacacattgggattatcccgcgtgccatggccacgctgttcgacaagatcgacaagctcaagaaccaagtagagttccagctgcgcgtttcgtttattgaggtaaattacctgttcctggatgaatcaaacatttgtgggattgtagagaatccaattgtgctcgttctcttgatagattctgaaagaagaggtgagggatttgcttgatcctgctactgctgctgttggcaaacttgagaatggaaatggacatgcaaccaagttgtcggttccaggtaaaccccctgttcagatccgggaggcgtcgaacggggtcataacgttagcaggatcgaccgaagtgcatgtcactacccagaaagaaatgacggcatgccttgagcaaggatctctgagtcgtgcaactggaagtaccaacatgaacaaccaatcaaggttagcaaacattatcctaatcattcgtcctttaccttttttagaggaggaagcaggtccattgatcaaccataattgatgacaagaaactagcatcattatggtcagaaactggcaatctttgcaggatacagctgtttgtgatgatttcttgcttctatgtttagtgtaggacctttttgcaggattagtcaatgtattgtcctaccctcaaaagagaaaccaattatttgtctagtttcaagtaattaattctctgctcaagtgctttaggacacattcaatcagattggttacctgatattccgttactaaattctacaaactttaatgaactttatgcttttggtttcggcatgtaatagtcgttcccatgccatcttcacaatcacattggagcagatgcgcaaagcagatcccatcatgactttagatggaatgcctattgaagagatgaatgaagactatctctgtgccaaactccacttagtagatcttgctggatcagaacgtgctaaaagaactggttctgatggccttcggtttaaggaaggtacttggcatgttgcttgttctatctgaatccctaatcaaacatccatcttgtcttgaaacaagatactccgtataatttatttatgtatcatgtcatcaggtgttcatatcaacagaggacttcttgctcttggcaatgtcatcagtgctctcggtgatgagaaaaagaggaaagaaggcgctcatgttccttaccgggacagcaaactcactcgccttctgcaggtattattcttctgacccaagtgcacaggcctttgtacagaagcattgaattcatagctctgttcaagaagtagggccagctcacatttaagcatatataatacttgaatctttgcatttagtttctttcattttactaactaatctgttttatatctattttattattataggactctctaggtggaaacagcaagactgtaatgataggtaattcatttggttggagattgtttaatcatatttttatatgatttaggattttttctaaataatgcttgtcaaagttccagaattggggtttaaaataaaaaaaaataaaacgatgatctattcattttatcttcggtaaaaaaaaatgcatcttgtcatatgatttaatttgttttcataaataagaaaactcggatgtaccttgattttcactaactgttttggttgatattactattacatgcaactgacatggatctatatttttctcctgcagcctgtattagtccagcagatatcaatgctgaagaaacactgaacactttgaaatatgctaaccgcgctcgtaacatccagaataagccaattgtaagttcattaaaatggtctcgtcagaaaagtatctgacatttatctgcgttatgtttctttaattaattggtttggttccgtcaaggtgattatttgacatccctatatttactttcctattttcaggtaaatagaaatcctgttgctgatgagatgaaaaggatgcgccagcaaattgaatacttgcaagcagaactcgtttcagctcgaggaggagttgtcttagatgatgttcaggtaaattcttttctcgtctatcctcagtgtccttgaccatcttgttctataaggcacactcactcacaataacagtatgagtataataacaagtggttccattttcagggtctcagggaaaggatctcaatgcttgaacagaaaaatgaagacctttgcagggaactgtatgaccttcgcaaccatggttacactgatccttgtgaacctgaactgcaagtatgttgatgagttcttctgcaagctttcggagattttacatttgaaaacaagcatacaatttactcttctacggcttctttcatgatagattcccttttctctcaaaggaaataaaagaggggacataacatgacattgtctactatggattgttttcatgcaattgcgcttgaaatggtatatgataaaccatgcatataactatttttatctctttcagaaaattggaactggttacactaaaggtgaagggctcaaaagaagcttgcaaagtacagaaccatttgatgtccccatgactgactcagtaagaggtaatctattagcaccttcattatttcatctcgttggcattcagaaattttattcagtcccatcttaagccatgactaagcagtgaacatggtggactactattttcattttatttttccttgataatttccttattctgcgataattctggacctccagcaggcagccctaaagatattgatgatgaagtggccaaagaatgggaacacacaatgctgcaggatagcatgggcaaagagttgaatgaattaaacagacaactggagcaaaaggaggtaatacagaaaacgtttaaataaatcaatgtgttttaatcttctaggggtgattaaacaaatacacgagctaatgttcgttcctggatgatatatgattgtacatatctcaatcaagcttcttgtgcaacttcatttttctggatactcaattcatctccatatgttgtatcatggtgacagttaaacgtgttgtcaaagaagttacaaggatcattggttgtaccatttttaatttcaatatgatggaagtgtggatatgaacattatttttaatggttcactgaatgtacatgcagtgacatgctactcttgttaatctgctcatgcttgccaagacctaccttaaattttctcaatttctttgcagtctgagatgaaaatgtatggatctgacactgttgcacttaaacaacactttggaaagaaacttttggagcttgaagaagagaaaagagctgtacaggtttgttttaaaaaaaaatcttcccattagcatattcactcatccaacagttgtgttttcctaacctttgctaacgagaaagttctgaacaatttcagcaagaaagggacagattgttagctgaagttgaaagtctaaatgctgatggacaaacacacaagttgcgagatgcccagctgcaaaaattaaaaacccttgaagcacaggtgaataaacctttataatttgtttgaatgcagttcgtgttgttcagtacatgttggtcatacaagacttggacctgcagattctagacctcaagaaaaagcaggagaaccaagttcaacttctgaaggaaaagcaaaagagtgatgaagctgctaagaagttgcaggaagaaattcattctataaaggcacagaaggttgtcttccctttctcatcatgtcaagttctaatgcatcacattttacactatcgtaagtcataacaattttgccaaccttgttccattatcaggttcaactacaacataaaatcaaacaagaagcggaacaattccggcaatggaaggctacccgtgaaaaggaactcctgcaggtatgaataatttaatatgcagttaaagcaaataactgcaaaattgctatgtcattaaattaaattcatatagaacaaggaacgggtaaaaatgatgtgaccgtatctacttagagattcatctctaacccctttttatgtaatgtttctgttgtactatttttgtggtaagcattatgagaagtaaacctcacttactgtttcctgaatgcagttgaggaaagaggggcggcgaaatgagtatgaacgccacaaacttcaagcacttaatcagcggcagaagttggtaagcttcttatgtagaattgtatttcaaagaaaagaaagtgtcaatgtgaaagtttggaaaaattataagtttattgtaggcattatccaaactatcattatttggactatcttaaaatactaagcttcactttatgtgtaactagctgccctgacatagttttcgtcaaagttcatatcttacttagctatataattacgtgtaagtttttccctcatattatcatgtctatttataaaatattaaatatcaaagttttgcatctttatgcaggttttgcagaggaagactgaagaagctgcgatggctaccaaaaggctgaaagagttactagaggctcggaaatcatcaggacgtgacaactcaggtatctctctccgcattgcgaccatttttcgcattataattaatactcccaatctaacagctcttccttctttttctttttttttttttttgctttcttccaaacacatcaggcatgaatggtacttctcctggctctcatgtaagttattttccatacttaaagaaaaagatcagttgcttatttggaaatatccttgagaatacttttttttgtaatgcagatgactgagaaatcattgcaaaaatggctagagcaagatttggaagtcatggtgcatgttcatgaagttcgaaacgaatatgaaaagcaaagtcaattgtatgtgattcattttatttccttcccaaatgtaaattatagagatcattcctcatgtaatgcatgattatgatgactaatttaaatggttttaaaggcgtgctgcacttggtgaggagcttgccattttaaaacaagaagatgtcatgtctggtgcagctagtccgcccagagggaagaatggaaactctaggtaactgttatccccatagttctattttgtagttcaggtacctttaagctggacagtatctttaatccatatattatcacaaactgtttaagaaatataagagcaccgtttaatatgtccttgtctgtaatctggttgttatatttgggtccgtattttatatttctcatattttctcaaaatgtgcaatcagcacatccaaatatttatgcttgtattgctgcattttgtttctcagggcaaatactttgtcaccaaatgcaagacaagctaggatagcatcacttgaaagcatggtgacaatatcttcaaatactctcgttgctatggcttctcaactctcagaagctgaagaaagagagcgtgcattctctgggcgtggtcggtggaatcagttgcgttcaatggcagaggcaaagagtttactgcagtatatatttaacgttgctgcagatgcaaggttggtatttattcttttggcttcattatttaatagtatggtagcatccatccttgtaggacttctcaatttgcagaacctggaaacaaattatttttactaaagagctaaaaatctcactttttctttctaaatagttgaaaatctgtaagtgttattttgctaagaatatggcactgattcgaataaaagagtgtggtactgatttgaaaataggaataacaaaaaaaaaattctgaactcaaagggcaactttatttcttcctgaaagcatgacaacaatgtgaatggaagaacaatgcaaagccgtttttatgatactctgtaaaaatgatcatttgtacaaaagtatggaactaaccttcactgttgaaatatcagatgccaagtaagggagaaagagatggagatcaaggaaatgaaggagcaaatgacagagcttgtgaccatccttcgacacagcgaatcacgtagaagggaaacggaaaagcagcttaagcaaagagagcaggcagctgtaactgccactacatctccagtatggtttctatgagctcacagcaattacccctcagtagaaaaaaatgttgaatgatgaaaggattacctaaacatctaaaacaaatatctggtggtgaggagggtatttaacatctccattacccatgttcaaattctctcgtacgccctgcttgaaagggcgaaaagaagaaaacatatcatagggtatagtagatggaactgacaaaaaaacattgagtcacttgaatccctaactgatagtcacaagagtacaagatattcaacaaatatcgtgatagttcttaatggaaattttatgcatcttacagggaaacggaaatggttcagtgaagcactctgctgatgactccaacacaccattgtcaccagttgcggtgcctgcacagaagcagctgaagtactctgctggaattgtaaatagccccagcaaaggggttcctgcattcaacaaacaacatcttaaggtatctctacccccctgaaatactctttgttctatctccctctctcgtatttaaaattggtgacgtacaatgcagatggttcctatggcacagttgcctgttggcaagaaggtttcaatagcagggcaatcaggaaaactttggagatggaaaagaagccaccaccagtggctactgcagttcaagtggaagtggcaaaagccctggaaattgtccgagatgattcgacacagtgacgaaacgatgacaaggactcgacccagaccccagcttcttcctcatagacctcaaagagtgatgtgaaaaaggcttttcttttcttttttttcttcgtctccacatggactgacacggtttacacagctaactacctccacaagggtaacaatgcagctaaaagctccaggagatctccttcgtgcttcgattttacttagccacgggatcgaaaaaaaaaaagtatatgttcatagggtgactgtctttggatgtaaatttcttgtgcctatatagtgagtgtgaatgttagagatgaaaatttagcgagtgagcgagggagggagtggccgttcttcgcgaaagcactgactgagcacaatgcttcatgtttcagcactcatcaactggtgagatgtcatacttgttgtccttctgcatataaggaaaaatctgtcgaaggatggcgtcttgtaaagtc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069115.1 RefSeq:Os09g0114500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os02g0682200&diff=172381Os02g06822002014-05-25T13:33:56Z<p>HamletShaoE: /* Function */</p>
<hr />
<div>The rice ''Os02g0682200'' has been reported as ''MADS6'' or ''MFO1'' more than four times since the year 2009. As a member of MADS-box gene family, ''MADS6'' draws attention of plant molecular biologists for its special functions in the regulation of rice flowers development<ref name="ref1" /><ref name="ref2" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />.<br />
==Annotated Information==<br />
[[File:OsMADS6_1_Mutation.jpg|right|thumb|400px|'''Figure 1.''' ''osmads6 mutant VS. WT( from reference <ref name="ref2" />).'']]<br />
===Function===<br />
''OsMADS6'', the ''AGL6''-like gene in rice, plays an essential role in specifying floral organ, meristem identities and endosperm nutrient accumulation in rice<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. It is also an important epigenetic regulator in rice<ref name="ref3" />. The study by ''Shinnosuke Ohmori'' et al. in 2009 showed that the loss of ''OsMADS6'' function in rice resulted in aberrant floral morphology<ref name="ref1" />. The study by ''Dabing Zhanga'' et al. in 2011 further explained how ''OsMADS6'' worked with ''OsMADS3'', ''OsMADS16'', ''OsMADS13'' and ''OsMADS58'' et al. and showed that ''OsMADS6'' is a key player in specifying flower development via interacting with other floral homeotic genes in rice<ref name="ref4" />.<br />
<br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003700 GO:0003700], [http://amigo.geneontology.org/amigo/term/GO:0005634 GO:0005634], [http://amigo.geneontology.org/amigo/term/GO:0043565 GO:0043565]<br />
<br />
===Wild Type VS. Mutant===<br />
<br />
* In the research reported by ''Dabing Zhang'' et al. in 2010, a ''osmads6'' mutant line with flower morphological defects was isolated from ''Japonica'' subspecies 9522 background treated with 60-Co γ-ray (280 Gy)<ref name="ref2" />. No significant differences were observed when compared with the vegetative development stages, flowering time or inflorescene morphology of Wild-Type and the ''osmads6'' mutant (Figure 1A and 1B). <br><br />
<br />
* However, when compared with the morphology of flower organs, a defection of floral development could be found in ''osmads6'' mutant. The spikelets of ''osmads6-1'' at stage In9 showed somewhat larger palea than Wild-Type (Figure 1C and 1D). The wellinterlocked lemma/palea structure was destroyed in the ''osmads6-1'' mutant flower because of the altered marginal tissue (Figure 1F). Ectopic indeterminate glume-like structures enclosed the stamen filament in ''osmads6-1'' mutant flowers (Figure 1G).<br><br><br />
<br />
[[File:OsMADS6_2_Mutation.jpg|center|thumb|680px|'''Figure 2.''' ''mfo1-1 mutant VS. WT (from reference<ref name="ref1" />).'']]<br />
<br />
* In the research reproted by ''Shinnosuke Ohmori'' et al. in 2009, another ''MADS6'' mutant ''mfo1-1'' was described<ref name="ref1" />. There is also no obvious abnormalities between ''mfo1-1'' and Wild-Type in the vegetative stage, however, abnormal flower morphological was observed in ''mfo1-1''. A slightly enlarged palea and were half open was found in the florets of ''mfo1-1'' (Figure 2A and 2B). <br><br />
<br />
* Compared with Wild-Type, ''Mfo1-1'' is in defect of interlocking between the lemma and palea (Figure 2C and 2D). The ''mfo1-1'' palea also lacked the membranous marginal region of palea which is found in Wild-Type and its surface is relatively rougher than that of the Wild-Type lemma (Figures 2E and 2F).<br />
<br />
===Expression Pattern===<br />
[[File:OsMADS6_EP.jpg|right|thumb|374px|'''Figure 3.''' ''Expression analyses of OsMADS6 (from reference <ref name="ref3" />).'']]<br />
* The microarray studies by ''Jian Zhang'' et al. showed that ''OsMADS6'' was highly expressed in the endosperm, compared with other vegetative tissues. Their further RT-PCR and RNA ''in-situ'' hybridization analyses showed that ''OsMADS6'' was expressed in flower and developing seeds, but was not detectable in root, leaf and suspension cells (Figure 3)<ref name="ref3" />.<br><br />
<br />
* The gene expression analysis by ''Dabing Zhang'' et al. in 2010 showed that ''OsMADS6'' was strongly expressed in the floral meristem at early stages. Its transcripts could also be detected in paleas, lodicules, carpels and the integument of ovule. In conclusion, ''OsMADS6'' expression was associated with the specification of floral organ as well as meristem identity<ref name="ref2" />.<br />
<br />
===Evolution===<br />
* The phylogenetic analyses made by ''Dabing Zhang'' et al. ''OsMADS6'' belonged to an ancient and conserved ''AGL6'' family. Both gymnosperms and angiosperms shared one common ancestor of ''AGL6-like'' genes. And the ''AGL6-like'' genes from grasses form two paralogous clades: the ''OsMADS17''-clade contains ''OsMADS17'' gene with an ortholog from Sorghum and the other genes, namely, ''OsMADS6''-clades <ref name="ref2" />.<br />
<br />
==Labs working on this gene==<br />
* Rice Biotechnology Research Subteam (Hokuriku Region), National Agricultural Research Center, National Agriculture and Food Research Organization, Niigata 943-0193, Japan;<br />
* Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Ibaraki 305-8602, Japan;<br />
* School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China;<br />
* Department of Biochemistry and Molecular Biology, Mississippi State University, MS 39762, USA;<br />
* Institute of Plant Science, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;<br />
* Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita` degli Studi di Milano, 20133 Milan, Italy;<br />
* Bio-X Center, Key Laboratory of Genetics and Development and Neuropsychiatric Diseases, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China;<br />
* Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India;<br />
* Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai-625 021, Tamil Nadu, India;<br />
* Institute of Biotechnology, Viikinkaari 1, FI-00790, University of Helsinki, Finland<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"><br />
Ohmori S, Kimizu M, Sugita M, et al. MOSAIC FLORAL ORGANS1, an AGL6-like MADS box gene, regulates floral organ identity and meristem fate in rice[J]. The Plant Cell Online, 2009, 21(10): 3008-3025. </ref><br />
<ref name="ref2">Li H, Liang W, Jia R, et al. The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice[J]. Cell research, 2009, 20(3): 299-313.</ref><br />
<ref name="ref3"><br />
Zhang J, Nallamilli B R, Mujahid H, et al. OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa)[J]. The Plant Journal, 2010, 64(4): 604-617. </ref><br />
<ref name="ref4"><br />
Li H, Liang W, Hu Y, et al. Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate[J]. The Plant Cell Online, 2011, 23(7): 2536-2552. </ref><br />
<ref name="ref5"><br />
Yadav S R, Khanday I, Majhi B B, et al. Auxin-responsive OsMGH3, a common downstream target of OsMADS1 and OsMADS6, controls rice floret fertility[J]. Plant and Cell Physiology, 2011, 52(12): 2123-2135. </ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os02g0682200|<br />
Description = Similar to MADS box protein|<br />
Version = NM_001054284.1 GI:115447938 GeneID:4330328|<br />
Length = 7968 bp|<br />
Definition = Oryza sativa Japonica Group Os02g0682200, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 2|Chromosome 2]]|<br />
AP = Chromosome 2:28762840..28770807|<br />
CDS = 28762972..28763153,28765912..28765990,28767927..28767988,28768220..28768319,28769648..28769689<br>,28769999..28770040,28770138..28770283,28770460..28770559|<br />
GCID = <gbrowseImage1><br />
name=NC_008395:28762840..28770807<br />
source=RiceChromosome02<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008395:28762840..28770807<br />
source=RiceChromosome02<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggggaggggaagagttgagctgaagcgcatcgagaacaagatcaacaggcaggtcaccttctccaagcgccgcaacggcctcctcaagaaggcctacgagctgtccgttctctgcgacgccgaggtcgcgctcatcatcttctccagccgcggcaagctctacgagttcggcagcgccggcataacaaagactttagaaaggtaccaacattgttgctacaatgctcaagattccaacaatgcactttctgaaacccagagttggtaccatgaaatgtcaaagttgaaagcaaaatttgaagctttgcagcgcactcaaaggcacttgcttggggaggatcttggaccactcagcgtcaaagaattgcagcagctggagaaacagcttgaatgtgcactatcacaggcgagacagagaaagacgcaactgatgatggaacaagtggaggaacttcgcagaaaggagcgtcagctgggtgaaattaataggcaactcaagcacaagctcgaggttgaaggttccaccagcaactacagagccatgcagcaagcctcctgggctcagggcgccgtggtggagaatggcgccgcatacgtgcagccgccgccacactccgcggccatggactctgaacccaccttgcaaattgggtatcctcatcaatttgtgcctgctgaagcaaacactattcagaggagcactgcccctgcaggtgcagagaacaacttcatgctgggatgggttctttga</cdnaseq>|<br />
AA = <aaseq>MGRGRVELKRIENKINRQVTFSKRRNGLLKKAYELSVLCDAEVA LIIFSSRGKLYEFGSAGITKTLERYQHCCYNAQDSNNALSETQSWYHEMSKLKAKFEA LQRTQRHLLGEDLGPLSVKELQQLEKQLECALSQARQRKTQLMMEQVEELRRKERQLG EINRQLKHKLEVEGSTSNYRAMQQASWAQGAVVENGAAYVQPPPHSAAMDSEPTLQIG YPHQFVPAEANTIQRSTAPAGAENNFMLGWVL</aaseq>|<br />
DNA = <dnaseqindica>133..314#3073..3151#5088..5149#5381..5480#6809..6850#7160..7201#7299..7444#7621..7720#atattctcgtcatcattggaggctttagcaagcaagaagagaggcagtggtggtggtggtggaggaggagctagctagcctgtgcttgctgatcggtgctgagctgaggaatcgttcgatcgatcgggcgagatggggaggggaagagttgagctgaagcgcatcgagaacaagatcaacaggcaggtcaccttctccaagcgccgcaacggcctcctcaagaaggcctacgagctgtccgttctctgcgacgccgaggtcgcgctcatcatcttctccagccgcggcaagctctacgagttcggcagcgccgggtataattaatacagacacaacaacacacacaaccaacaaaccagcatcaatttgaacctgcagatctgctgttttctctgatcaattgcttctttttttttgttcttttttgtttcttttatctgctgcaacggcgtcctgctcctctggggtttctcgttttctttttcatttatttttagcaggtgccaagtagccgagctactatacttacctggccatgttaattattttattccgtctgtctgtgtgtgtctgtgcatactactatagggacatggcgcggtgttcttataaaccgggaggccggatccctaactagcatgggaggatatcttttcagcggatctatacaaaccctactcctgctgacctctttcttccagtttctccgggtcttccttggattattattgcccatcttccgggttgtgcgtgtgtcagagacagctcgaacgataaatttctcaaaaccagtactagagagggtgtgttgtgtgtgagaactgagtggagagttagcatgaaggctgcaaactagaaaggaaggtatgttctttcctttttgatccatcaggggagccccttctggtattaagatctttccggcacattgattttcatactttgtgatgaccctggaagaatcggcgtagcagcgtagcaccgctccattttggtcttaccctcacctccccatgctatgaactgatcaatttcattgttcttcatcacccttctcctagctttccacttccttcggatctcatgccatgtttctcagcatgaatcaaatttaattcgtgttttctacttccatatatactggaagaaatttaattagatctatttttgctcgggaggtcttcatactttgagttctgatgccatcaccttatttcccccccccccttctcttgttctatcttcttcctcatcttggcttgatcattttgatctgtcagttatagcatgatgcattctcaatttgactgtatgtaagttcaaccggaaatatgttgaatggattttctatatatcaacacttgatgtcaggcctgcatctgtttcgcttgtggtggtgtggccaaaattgtctatatttgatctttgctcttctttctcctcatttcatgacgattcctactacggcttaaaccattctttattctttactaatcatggatgttgcttgactcctagttgtttcgtactagctcaacttggagatcttttcattatttgcctagttggtgggtacgtttgtgacagatctaaaatggtgcacgaaaagttttacttattatgaaaaaagggagcttaacagggtaatttctctatttattcgtgatgacattttttccttgataagggggattttttataatctgcactcacatgtttatatgtaaaatctagctcttttgttttgtttttggcatatttcccgctaagtatagagtttatgtggataacattataacttttcaagatccaatccacatctttgattgtgaaaatcatacaatagggaaaatcaactgaagggttaattagatgctatatgcatatatatatatatgtgcgcgcgcgcgcgcctgaatttaactatgtatgcatccaactgtttcattgaaaaagatttgatatttttcagtctattctttttcgagtatatatttaatatgtttcaatctgttttgaccattataagataaagcctatattcaccaggcatttgagatgatcttttcatgcatgaaaaagctgttgttatcacttcaactaaccagacgatctaacatgtatttgtataagaaacagaccttgatttccttctgtaaaatcatgcatgtgttcgttttgaattggagtcggcgcgcctgtgttttgaccgtcaggaaagtcttttttttccctgaatagtcaagggtctatacttcttgaagcaattgggacactaatcaattattgtttatacctcggaccatcttttccttcttcacaccactaatcagtttatgccttggaccattaattgtgttgttcacaagcttcttgtttatggtttacaaagcattcgcctagatttgtgtgtgtctctacacatcgatcacttttaaatacttgtcgctttcagttattcttttaacgtttggttatttatcttatttaaaaaaattatcgtattattatttattttgtttgtgatttactttattatcaaaagtatttcaaatatgacttatctttttttataagtgcactaatttttcaaataagatgaatggtcaaatgttacaagaaaaagttaaagcaaccactaatttagggcggaggtagtaaaacctagttattgtaaccaataattttatcaatctataaatgcaacacaaagtcacttcgtgatatctcacacaaagccacttcaacgatgaaagctgactgcatgttttatcaaaacacatgtgatcagtttgttggatgaaaaaaattatctatgtcataaatcaagagttataatataagcttctggctctacaagtaacatttctatgttttttttttacgttcttacatactatgttttgccaaaaaaaacatgatcattttgttggacgaaaagaaatagtaaatatagagtgacctttgatatcattataatataagcttctgcctctataaataacatctatgcactttttacgtcgtagtaatttgatatatgagaaatttacatataacatttttgtgcagcataacaaagactttagaaaggtaccaacattgttgctacaatgctcaagattccaacaatgcactttctgaaacccaggtatatatatctgcatgaactggtcatgaatttctgctgttggttttggtttcaaaatgggtcttgtttttttactatatatatttttgtatgaatatgcaattatcaatgtcctgacattgaaattagctacagtataaacctagctaggtattttcatcgtattgtgagattacattcaataaaaagtacacagattagcataactgtgttaatttgatgatgtatcccaaagctaatttgcagtgacttaaaatattttacttgacacagctactaaatcggatgttcttttcgtaaaagcattctaaagaatggcaaagtttagaagaattaaactagtagaatttcaacaccggcatgcattaaccatattttatgtaataaatgaagtttttattgacatgtcaaaggaggacaacaaagacaatcccttcttcctatatagttggtacccactacaagcattaacactataaagaagcatccaggttaagccacatcatcgataatcaatagccgtcggatcaaatgcatctttgtttgtttaactgtgcatgccttaagtaaggaaactgccatgggtaattaggcacatcaatggatgacccacttaagtgctcctggtcatgcattacatgcatcccccatattaagccactgctatatcccttaaccatctaccactcaaatgccaactttacactttattattttagaatgtttacttttgatatttcaattcttcaattctgtttgtaagcacatatttacaaagttgtttatcatcaccataaaatcccgtagcaacgcgcggggtatcaaactagttgtttgttataattataccatattacaatgcaagatcgtgctgtttacggcgtatatgtattcagaaatgttgcacctagtataggtttttaccagcatagaatatacaaatagctagtctaaatgactttttgtgcccctagctccctagtgtaaccttacatgaagtattccctgcatcgaatatgaagtatatattccctgcatcgacgaatatacaaatatactcctagctaggctaaaatacagccaccagtatgaagtaaattagtcgatgtagttcaatatttaaatatagatggtgattgaatgtacaacaatagtgcacatcccaaaaaaataagggtgtacctctgtgaccagatagtactccctcagtcagggtacgtccagattcattggactaggatatgtcacatccagtactagggccctgtttagattccaatttttttttcaaacttttaacttttccgtcacatcgaactttcctacatacaaacttccaacttttccgtcacatcgttccaatatcttcaaacttccaattttggcgtggaactaaacacagcctaggttggtttttcgtgggacggagggagtactctttatggtgattctaaatttcagtcaatcaattagagtacgtcctcataacatttcaaacaaaaacatagatgcccttgtgcataatttcaaaagtcatgagatcaaattgaaattcttgagaacttaccaaccgcaaaatatctaaggagttatgtcacttggttatatttatatcattgacatcctgcaacttatttgcccaataatcagtatatatagtttgctagctgtatcattaatagcatgtttcacaaaattttaaaaaaagaataagcccaacgtatatgtacaaggaggccatgtgacata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/>
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001054284.1 RefSeq:Os02g0682200]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 2]]<br />
[[Category:Chromosome 2]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os11g0523800&diff=172380Os11g05238002014-05-25T13:33:04Z<p>HamletShaoE: /* Function */</p>
<hr />
<div>The rice ''Os11g0523800'' was reported as '''''OsARF1''''' in 2002 and 2008 by researchers from Japan and Egypt respectively<ref name="ref1" /><ref name="ref2" />.<br />
<br />
==Annotated Information==<br />
[[File:OsARF1.jpg|right|thumb|280px|'''Figure 1.''' ''Mutant VS. WT(from reference) <ref name="ref2" />.'']]<br />
[[File:OsARF2.jpg|right|thumb|280px|'''Figure 2.''' ''Transcript abundance of OsARF1 in wild type rice from <ref name="ref2" />.'']]<br />
[[File:OsARF3.jpg|right|thumb|280px|'''Figure 3.''' Auxin concentration dependence of ''OsARF1'' expression.<ref name="ref1" />.'']]<br />
===Function===<br />
'''''OsARF1''''' is the first full-length member of auxin response factor (ARF) gene family to be cloned from monocot plant<ref name="ref1" />. It was shown to be essential for developmental growth stages of the life cycle of rice. The knock down of '''''OsARF1''''' turned off some key switches for transformation from vegetative stage to the reproductive stage<ref name="ref2" />. As an early response gene in auxin signaling, '''''OsARF1''''' could be associated with embryogenesis and may play a key role in fertility and regulate quite a few downstream genes associated with growth and reproduction<ref name="ref1" /><ref name="ref2" />. Further elucidation of the downstream targets of '''''Os-ARF1''''' will help to understand the regulation of plant growth by auxin-mediated gene expression<ref name="ref2" />.<br />
<br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003677 GO:0003677], [http://amigo.geneontology.org/amigo/term/GO:0005634 GO:0005634], [http://amigo.geneontology.org/amigo/term/GO:0006445 GO:0006445], [http://amigo.geneontology.org/amigo/term/GO:0009725 GO:0009725], [http://amigo.geneontology.org/amigo/term/GO:0045449 GO:0045449], [http://amigo.geneontology.org/amigo/term/GO:0046983 GO:0046983]<br />
<br />
===Wild Type VS. Mutant===<br />
An antisense '''''OsARF1''''' recombinant plasmid was transformed into rice embryogenic calli through Agrobacterium-mediated transformation by ''Attia et al'' and they found that the growth of transgenic rice was inhibited<ref name="ref2" />.<br />
* The '''''AS-OsARF1''''' transformed plants showed significantly lower growth and vigor that included smaller leaves and shorter heights, compared to nontransformed plants. Interestingly, the length of the tillering node didn’t change significantly in transgenic plants (Figure 1). Also, the leaves curled across the width<ref name="ref2" />. <br><br><br />
* Eight of 11 transgenic plants failed to head and the remaining three were sterile, although they were able to develop to the heading stage 13–15 days later than the non-transformed plants. Hence, no F2 progeny was obtained<ref name="ref2" />.<br />
<br />
===Expression===<br />
* RT-PCR Analyses by ''Attia et al.'' showed that '''''OsARF1''''' was transcript accumulated in callus and young panicle at much higher amount than in leaf and root(Figure 2). This indicates that '''''OsARF1''''' may be associated with embryogenesis, because of the higher transcript abundance in young panicles and calli, which both are embryonic tissues<ref name="ref2" />.(1.embryogenic callus; 2. differentiating callus; 3. young panicles; 4. leaves;5. roots. Lower lanes: Actin mRNAas a control.)<br><br><br />
* The study by ''Frank Waller et al.'' showed that '''''OsARF1''''' mRNA levels are rapidly induced by auxin<ref name="ref1" />. They extracted total RNA from coleoptile segments which had been incubated in different auxin concentrations after depletion of internal auxin. Then they measured the abundance of '''''OsARF1''''' mRNA in northern blot experiments and found that the highest level of '''''OsARF1 '''''transcript was detected after incubation with either 1 or 3 μM auxin, whereas incubation in 100 μM auxin produced low '''''OsARF1''''' transcript levels<ref name="ref1" />. '''''OsARF1''''' mRNA steady-state levels therefore follow an optimum curve with a maximum of between 1 and 3 μM auxin<ref name="ref1" />.<br><br><br />
* Microarray analysis of the transgenic plants by ''Attia et al.'' showed that 435 genes were differently expressed, 255 of them were down regulated and 180 were up regulated. The annotated genes were located in 9 sub-categories of molecular functions in gene ontology. Most of the differently expressed genes were categorized among those encoding proteins with catalytic activity<ref name="ref2" />.<br />
<br />
===Localization===<br />
The study by ''Frank Waller et al.'' showed that '''''OsARF1''''' was localized to the nucleus in vivo<ref name="ref1" />.<br />
<br />
===Knowledge Extension===<br />
[[File:OsARF4.jpg|left|thumb|400px|'''Figure 4.''' ''The modular structure of the OsARF family.(from reference) <ref name="ref3" />.'']]<br />
* Auxin signaling plays a vital role in plant growth and development processes like, in apical dominance, tropic responses, lateral root formation, vascular differentiation, embryo patterning and shoot elongation<ref name="ref1" /><ref name="ref2" /><ref name="ref3" /><ref name="ref4" />. The auxin response factor (ARF) and auxin/indole acetic acid (Aux/IAA) protein families are required for transcriptional regulation of auxin response genes, and they are very important in auxin signalling and plant development<ref name="ref3" />.<br><br><br />
* An ARF protein contains a DNA-binding domain (DBD) in the N-terminal region, a middle region that functions as an activation domain (AD) or repression domain (RD), and a carboxyl-terminal dimerization domain (CTD) that are similar to those found in the C terminus of Aux/IAAs, which is a protein-protein interaction domain that mediates the homo- and heterodimerization of ARFs and also the hetero-dimerization of ARF and Aux/IAA proteins (Figure 4).<ref name="ref3" /><ref name="ref4" /> <br><br><br />
* The ARF proteins are encoded by a large gene family, with 23, 25 and 31 members in Arabidopsis, Rice and Maize respectively. Genetic divergence between Arabidopsis and rice ARF gene family investigated by genome-wide analysis revealed that most of the rice '''''OsARFs''''' and maize '''''ZmARFs''''' are related to Arabidopsis ARFs and fall into sister pairs as in Arabidopsis<ref name="ref4" />.<br />
<br />
==Labs working on this gene==<br />
* Institut für Biologie II, Albert-Ludwigs-Universität, Schänzlestrasse 1, 79104 Freiburg<br />
* Hitachi Advanced Research Laboratory, Hatoyama, Saitama 350-0395<br />
* Present address: Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan<br />
* Rice Biotechnology Lab., Rice Research & Training Center, Sakha, Kafr EL-Sheikh, 33717, Egypt<br />
* Institute of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200433, China<br />
* Plant Biotechnology and Genomics Core-Facility, Department of Plant, Soil, and Agricultural Systems,Southern Illinois University, Carbondale, IL 62901–4415, USA<br />
* Department of Genetics, Faculty of Agriculture, Alexandria University, Alexandria, Egypt<br />
* Faculty of Agriculture Research Park (FARP) and Biochemistry Department, Faculty of Agriculture, Cairo University,12613 Giza, Egypt<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Waller F, Furuya M, Nick P. OsARF1, an auxin response factor from rice, is auxin-regulated and classifies as a primary auxin responsive gene[J]. Plant molecular biology, 2002, 50(3): 415-425.<br />
</ref><br />
* <ref name="ref2"><br />
Attia K A, Abdelkhalik A F, Ammar M H, et al. Antisense phenotypes reveal a functional expression of OsARF1, an auxin response factor, in transgenic rice[J]. Current issues in molecular biology, 2009, 11(1): I29.<br />
</ref><br />
* <ref name="ref3"><br />
Shen C J, Wang S K, Bai Y H, et al. Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L.)[J]. Journal of experimental botany, 2010, 61(14): 3971-3981.<br />
</ref><br />
* <ref name="ref4"><br />
Xing H, Pudake R, Guo G, et al. Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize[J]. BMC genomics, 2011, 12(1): 178.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os11g0523800|<br />
Description = Transcriptional factor B3 family protein|<br />
Version = NM_001074520.1 GI:115485688 GeneID:4350610|<br />
Length = 6288 bp|<br />
Definition = Oryza sativa Japonica Group Os11g0523800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 11|Chromosome 11]]|<br />
AP = Chromosome 11:20763199..20769486|<br />
CDS = 20763767..20763950,20764042..20764232,20764784..20765727,20765806..20765977,20766055..20766130<br>,20766221..20766340,20766518..20766682,20766771..20766861,20767396..20767480<br>,20767596..20767766,20767874..20767930,20768013..20768108,20768946..20769085<br>,20769187..20769253|<br />
GCID = <gbrowseImage1><br />
name=NC_008404:20763199..20769486<br />
source=RiceChromosome11<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008404:20763199..20769486<br />
source=RiceChromosome11<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcgacggcggaggtcggcggcggcggcggtgagggggatgctgctgccgcggcggtggcgcgaggcggcggcggcggaggaggaggaggaggaggggaggacgcgctgttcacggagctgtggagcgcgtgcgcggggccgctggtgacggtgccgagggttggggagaaggtgttctacttcccgcaggggcacatcgagcaggtggaggcctcgaccaaccaggtaggcgagcagcggatgcagttgtacaatctcccatggaagatcctgtgtgaggttatgaacgttgagctgaaggccgagccagacaccgacgaggtttatgctcagctcactctgcttcctgaatcgaagcaacaagaagataacggctctactgaggaggaggtgccttctgctccagcagctgggcatgttaggccacgggtgcactcattctgcaagacattgaccgcctcggacacgagcacacatggcggcttctcggtgctgcgacgccacgcggacgaatgcctcccaccactggatatgagccgtcagcctccaacacaagagctggtggccaaggatctgcacggtgtggaatggcgctttcgtcacatattcagaggtcaaccacgaagacaccttttgcagagtggctggagtgtgtttgttagtgccaaacggcttgttgctggggatgcctttatctttctcagaggtgagaacggggaactgcgtgttggagtcaggcgtgcaatgaggcagcaaactaatgttccatcttcagtgatatcaagccacagcatgcatcttggggttcttgccacagcatggcatgctgttaacacagggaccatgttcactgtctactacaagcctaggacaagtccagccgagtttgtggtcccttacgatcgctatatggaatcactgaaacaaaattactccattgggatgagatttaagatgaggtttgaaggtgaagaggctccagagcaaagattcactgggactattgtcggaatgggggattctgatccagctggctggcctgaatcaaaatggcgctcccttaaggtgagatgggatgaagcttcttccatacctcgccctgaaagagtttctccctggcaaatagaacctgctgtaagccctcctcctgtcaacccactaccagttccaagaaccaagaggcttcgtccgaatgctaccgctttgccggctgactcttctgctatagcaaaagaagctgctacgaaagttgtggtcgagtctgaaccaaatggtacgcaaaggaccttccagacacaagagaatgcaaccccaaaaagtggtttcggcaatagcagcgagttagaaagtgctcagaaatcaatcatgcgtccatctggatttgatcgtgagaaaaataacactcccatacagtggaagctaggttcagatggtcggatgcagatgagcaagcctgagagttacagtgagatgctatctggatttcagccacctaaagatgtacaaatcccacagggtttctgttctttacctgagcagattactgcaggccattctaacttctggcacacagtaaatgctcagtatcaagatcaacagagcaatcacaatatgttccccagctcatggtccttcatgcctccaaatactcgccttggattaaacaaacagaactattcaatgattcaggaagctggtgtgttgtctcaaaggcctggaaatacaaagtttgggaatggagtttatgctgcactgccaggccgaggtactgagcaatactcagggggttggtttggccatatgatgccaaattcccacatggatgatacacagccacgcctgatcaagcctaaacctctggttgttgcccatggtgatgttcagaaagctaaaggtgcttcatgcaaactatttggaattcaccttgacagcccagcgaaatctgaacctttgaaatctccatcaagtgttgtatatgatgggacgccacaaacaccaggtgctactgaatggcgccgaccagatgtaactgaagtagagaaatgttctgatccttctaaggccatgaagccacttgatactccgcaaccagactctgttcctgagaagccttcttctcagcaagcttcacgaaacatgtcgtgcaaatcacaaggtgtatcaactagaagctgcaagaaggtccacaagcaaggcattgcacttggcaggtctgtggaccttacaaagtttaatggctatgaagagttgattgctgagctggatgacatgtttgatttcaatggtgaactgaagggtcctaagaaggagtggatggttgtctacactgacaacgaaggtgacatgatgctagttggggatgatccctggattgaattctgcgacatggttcacaagatcttcatctacacaagagaagaggttcagcggatgaatccgggaaccctgaactcaagatcagaagatagtcatgctaattcaatggaaaggggctcagtcggcagagaaatgcgaggctgcttgtcaacctcgtctcttaattctgagaactgctaa</cdnaseq>|<br />
AA = <aaseq>MATAEVGGGGGEGDAAAAAVARGGGGGGGGGGGEDALFTELWSA CAGPLVTVPRVGEKVFYFPQGHIEQVEASTNQVGEQRMQLYNLPWKILCEVMNVELKA EPDTDEVYAQLTLLPESKQQEDNGSTEEEVPSAPAAGHVRPRVHSFCKTLTASDTSTH GGFSVLRRHADECLPPLDMSRQPPTQELVAKDLHGVEWRFRHIFRGQPRRHLLQSGWS VFVSAKRLVAGDAFIFLRGENGELRVGVRRAMRQQTNVPSSVISSHSMHLGVLATAWH AVNTGTMFTVYYKPRTSPAEFVVPYDRYMESLKQNYSIGMRFKMRFEGEEAPEQRFTG TIVGMGDSDPAGWPESKWRSLKVRWDEASSIPRPERVSPWQIEPAVSPPPVNPLPVPR TKRLRPNATALPADSSAIAKEAATKVVVESEPNGTQRTFQTQENATPKSGFGNSSELE SAQKSIMRPSGFDREKNNTPIQWKLGSDGRMQMSKPESYSEMLSGFQPPKDVQIPQGF CSLPEQITAGHSNFWHTVNAQYQDQQSNHNMFPSSWSFMPPNTRLGLNKQNYSMIQEA GVLSQRPGNTKFGNGVYAALPGRGTEQYSGGWFGHMMPNSHMDDTQPRLIKPKPLVVA HGDVQKAKGASCKLFGIHLDSPAKSEPLKSPSSVVYDGTPQTPGATEWRRPDVTEVEK CSDPSKAMKPLDTPQPDSVPEKPSSQQASRNMSCKSQGVSTRSCKKVHKQGIALGRSV DLTKFNGYEELIAELDDMFDFNGELKGPKKEWMVVYTDNEGDMMLVGDDPWIEFCDMV HKIFIYTREEVQRMNPGTLNSRSEDSHANSMERGSVGREMRGCLSTSSLNSENC</aaseq>|<br />
DNA = <dnaseqindica>5537..5720#5255..5445#3760..4703#3510..3681#3357..3432#3147..3266#2805..2969#2626..2716#2007..2091#1721..1891#1557..1613#1379..1474#402..541#234..300#gttttttttttcttcttttttctcgcttaaattcacccagtaaaaaaaaaatttaaaacaaaagagaggagaggagaggaagaagaggaggtggtggaggaggaggaggagaagctgcttgtgctgctgctgcgaatcggaggggaattcgagggggcggggggcgcgaatccggcgggggaattcgcgcgattcgggcgtggccgcgggggatgtgaagatctggtggggtgatggcgacggcggaggtcggcggcggcggcggtgagggggatgctgctgccgcggcggtggcgcgaggtgagctcctctcggtggtgggtgggcgtgtgtgggtttgcgcgtgggttttttgtgggctggcttgtgatgccggcttttgggctttgggcttgcagcaggcggcggcggcggaggaggaggaggaggaggggaggacgcgctgttcacggagctgtggagcgcgtgcgcggggccgctggtgacggtgccgagggttggggagaaggtgttctacttcccgcaggggcacatcgagcaggtgagtccgagtccgagctcgaggtcgagcagagcgcgcgccgcccaattcgggcgcggggtggtggcggtggcggcggccgcctttctcgcctctccgcgattccccgctttttattagagagtttattagttccatttcgatttctcttcctggtccttttccgccgtttgattttgagagtttttttggttttcaactctcttttctctctcttcgtgtttctgttgatccgagtggcgtcttcgggtttgagctgttttgaagccactcgttttttttcttcttgacttgttcaaatgcttgaggttttggtgtttatgcgtcctagcggcgatgggaatcttttaagataaattttggggggaatttgtctgtgccgttggcgaatttcgctttcttgagtttgtgtcgtggaattttggcgggttttgagcatttttggtgatgcggttttggggtttacgttttgcctctctaaaattcgaagttttttccaagttttttcggttatactgtatgcaattctctggttcgaactaagtttccgagttgtcgcagttgctgagtgtgagattggaactatttgaatggggaattctgtagtttttgtgccggatcgcttcgcctatgagtcgaattcggcttcttggttgccaaaattcggaattctgtgttttacttcgcaaaagaaaaaaaaactggggattttcgtgcttggtactgaactagtgataatttgttcttcctgcattcttgcaaatgtattttttttcttggctggaatcagtgtttcggtggctgattttggaattctttgcctctgtccattttcaggtggaggcctcgaccaaccaggtaggcgagcagcggatgcagttgtacaatctcccatggaagatcctgtgtgaggttatgaacgttgagctgaaggtacttgctttgtgtttcttgtgaattctgagagctttcattcttggttgtatgtgtggttgacatatagctctgtttgtaggccgagccagacaccgacgaggtttatgctcagctcactctgcttcctgaatcgaaggtaaaaaaaaaaatgtctccagtttgcacgctgtcactgcttcatacattccgggatagaagttttgagcgttttgaaaggaaaaaaaatgttggtctgttgtgtagcaacaagaagataacggctctactgaggaggaggtgccttctgctccagcagctgggcatgttaggccacgggtgcactcattctgcaagacattgaccgcctcggacacgagcacacatggcggcttctcggtgctgcgacgccacgcggacgaatgcctcccaccactggttcgtcccactggttctttgacttgatgttgttttcagtgatgtacttgtagtcctaggtcttactaggatgcttgagttgtagtgatgatctttgctttggcttcttgatcaggatatgagccgtcagcctccaacacaagagctggtggccaaggatctgcacggtgtggaatggcgctttcgtcacatattcagaggtgatcactcttccaacatcgtacttatttctctattttctgaaggacgtgtgatgctcactgctctttgctaatgaacacaagtttccatgatatcatgactaggagacatctttacactgctcttgggttgatcgtatagtgtaagaacagttcttgcatttgactaaccccttcatttataatattggtattaaatgcacttttttggtacgatgcctatcccgtattatcttgatggctttattagagggaccagtttgtgcttcccacaatttcttgtgcatttttgttctttgcatgggcctacacttgatggagtatggataactacaacttttgttggttgatgctgcagtggtcgtgctctagtttcttaggacaagtagtttatgctttcatatgcccttgtgatgtaagagttgtgctaattgattatgttgtcctgcccgagtttcgattgcacctaggttagaaggaagttaattttttgcttcaactcttcttgagctatatctttttgatcaacatcaggtcaaccacgaagacaccttttgcagagtggctggagtgtgtttgttagtgccaaacggcttgttgctggggatgcctttatctttctcaggtttgataatttgacacagtgtttgctttgtctacctgtgctttcccctgtactgcttaataaatatccccctatatgatctgcacagaggtgagaacggggaactgcgtgttggagtcaggcgtgcaatgaggcagcaaactaatgttccatcttcagtgatatcaagccacagcatgcatcttggggttcttgccacagcatggcatgctgttaacacagggaccatgttcactgtctactacaagcctaggtttgttgtgaagtttttctggattttatgcacatgattttatttatgcactttgggagcattgtctgtttacttgtcacctgaattctgaactgatcttgctatgtgatagaattaaatttgtccgattgtgctagcacttaaacgctatcgctgaaatcttctatttttcatcaggacaagtccagccgagtttgtggtcccttacgatcgctatatggaatcactgaaacaaaattactccattgggatgagatttaagatgaggtttgaaggtgaagaggctccagagcaaaggtagcacttagatggatatgcattctacttttgacaggtgattcctctgtatctgaatcaaccgattaatctttaatgctcatgcattagattcactgggactattgtcggaatgggggattctgatccagctggctggcctgaatcaaaatggcgctcccttaaggtttatttctttcgccactttccatttaaataacatttattttctgagaatttcttacagatttttgtgttacttaggtgagatgggatgaagcttcttccatacctcgccctgaaagagtttctccctggcaaatagaacctgctgtaagccctcctcctgtcaacccactaccagttccaagaaccaagaggcttcgtccgaatgctaccgctttgccggctgactcttctgctatagcaaaagaaggtcagaccttgtcatcaatatgaaatctacagtatagcttcgttgtctttactaatgcacgtcttttcttcaatctagctgctacgaaagttgtggtcgagtctgaaccaaatggtacgcaaaggaccttccagacacaagagaatgcaaccccaaaaagtggtttcggcaatagcagcgagttagaaagtgctcagaaatcaatcatgcgtccatctggatttgatcgtgagaaaaataacactcccatacagtggaagctaggttcagatggtcggatgcagatgagcaagcctgagagttacagtgagatgctatctggatttcagccacctaaagatgtacaaatcccacagggtttctgttctttacctgagcagattactgcaggccattctaacttctggcacacagtaaatgctcagtatcaagatcaacagagcaatcacaatatgttccccagctcatggtccttcatgcctccaaatactcgccttggattaaacaaacagaactattcaatgattcaggaagctggtgtgttgtctcaaaggcctggaaatacaaagtttgggaatggagtttatgctgcactgccaggccgaggtactgagcaatactcagggggttggtttggccatatgatgccaaattcccacatggatgatacacagccacgcctgatcaagcctaaacctctggttgttgcccatggtgatgttcagaaagctaaaggtgcttcatgcaaactatttggaattcaccttgacagcccagcgaaatctgaacctttgaaatctccatcaagtgttgtatatgatgggacgccacaaacaccaggtgctactgaatggcgccgaccagatgtaactgaagtagagaaatgttctgatccttctaaggccatgaagccacttgatactccgcaaccagactctgttcctgagaagccttcttctcagcaagcttcacgaaacatgtcgtgcaaatcacaaggtgtatcaactagaagctgcaagaaggtaccactttcttgttattattgcacttatcacctctttgcaatctccaagttcttccttgtgaatgattttaaataattctccaacaagttttcctcccctcctagatatgcccaataagattaattttggagcacctttggatatacttcctccgtttcatattataagactttctagcattgcccacattcatatatatatatatgttaataaatctagacatatatgtgtgcctatattctttaacatctatatgaatgtaggcaatgctagaaagtcttataacctgaaacggaggtagtattatatttcaaaggtccaaatgtacaaacttgctcagtatttttttttgccaaagttaatatagctcaactcattctctaatctctcctatagatgcataatcaaacccttgtttcttacatataatctttccttcggaagcatgtttggcactacttataccatcctcaagtgctcagcttaattattttttctagattttccctgttttccaacatgatggttgataaactatacatttccaggtccacaagcaaggcattgcacttggcaggtctgtggaccttacaaagtttaatggctatgaagagttgattgctgagctggatgacatgtttgatttcaatggtgaactgaagggtcctaagaaggagtggatggttgtctacactgacaacgaaggtgacatgatgctagttggggatgatccctggatgtgagttaactcataaatgctttcctcattcgctgatctgatttaatgacatcacaaatgctgactgcatcggacaatcattcttgaacagtgaattctgcgacatggttcacaagatcttcatctacacaagagaagaggttcagcggatgaatccgggaaccctgaactcaagatcagaagatagtcatgctaattcaatggaaaggggctcagtcggcagagaaatgcgaggctgcttgtcaacctcgtctcttaattctgagaactgctaatgctttcccatctggtaacgtgagtagtggcatttcacctttcttcactataactagtaaagtataaacggcctccggtgctcatctttgttccatcatcttgctttctggcaggtcttttgaagtaacatgggagacaagaacgcgatgcatcgttataagaaaatgcatttcgtagtggagttaatgctttttttccccctttgatgtattggataagctcaaagtaccctatttgtagatggtgcttgtccttggtggtcaagttgcactcttatttgctgcagttttggttttctattttggtgaggtaagttgtcagccgccagtcctaccatataaatgttggtatgcgtagaaaagtaagctcagccctcccaccctgcacttcctctctctcagcactaagctgccacctccttgtaaatagcccctgtttaattgagtctaatatattatctaccttaactgacattcctttgtttcatcttgctaaattatagcagtagcctggtaagattattgtagcccaaattaacatgtgatctgagattttatttttgctttc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001074520.1 RefSeq:Os11g0523800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 11]]<br />
[[Category:Chromosome 11]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os02g0170300&diff=172379Os02g01703002014-05-25T13:31:09Z<p>HamletShaoE: </p>
<hr />
<div>The rice '''''OsMADS29''''' is a member of MADS-box transcription factors in rice, it belongs to class B genes of the [http://en.wikipedia.org/wiki/ABC_model ABC model of flower development] in plants<ref name="ref1" /><ref name="ref5" />.<br />
<br />
==Annotated Information==<br />
===Function===<br />
[[File:SilenceMads29.jpg|right|thumb|250px|'''Figure 1.''' ''Seeds from normal-type lines VS. transgenic lines (from reference<ref name="ref1" />).'']]<br />
''OsMADS29'' plays an important role during seed development of rice and silencing of ''OsMADS29'' Results in the seeds shrunken as well as a reduced grain-filling rate in rice<ref name="ref1" /><ref name="ref2" />. It is a key regulator of the degradation of the nucellus and nucellar projection, which undergoing PCD during early rice seed development<ref name="ref1" />.<br />
Down regulation of ''OsMADS29'' does not affect ovule development but causes seeds to abort or shrivel as they are most likely deficient in endosperm development and starch accumulation<ref name="ref2" />. <br><br />
After rice fertilization, the increased [http://en.wikipedia.org/wiki/Indole-3-acetic_acid IAA] content induces the expression of ''MADS29'', which then stimulates the degradation of the nucellus and the nucellar projection by directly stimulating a Cys protease and NBS-LRR proteins. Acting through ''MADS29'' or other pathways, auxin regulates the [http://en.wikipedia.org/wiki/Programmed_cell_death PCD]processes required for normal endosperm development and grain filling<ref name="ref1" />.<br />
<br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003700 GO:0003700], [http://amigo.geneontology.org/amigo/term/GO:0005634 GO:0005634], [http://amigo.geneontology.org/amigo/term/GO:0043565 GO:0043565]<br />
<br />
===Mutation===<br />
Figure 1 shows that during the first 6 days after flowering(DAF), there is no obvious difference between wide type line seed (ZH11) and A-MADS29 transgenic lines seeds (A-2, A-14, and A-33) in which the ''OsMADS29'' was suppressed. After 8 DAF, the A-MADS29 seeds become shrunken, and this phenotype persists until 30 DAF because of a defect in dry matter accumulation, whereas the seeds are fully filled with dry matter by 30 DAF in ZH11<ref name="ref1" />.<br />
<Br><Br><br />
===Expression===<br />
[[File:OsMads29_ExpressionPattern.jpg|right|thumb|500px|'''Figure 2.''' ''Expression analyses of OsMADS29(from reference <ref name="ref2"/>).'']]<br />
''OsMADS29'' is Specifically Expressed in Ovules and Developing Seeds<ref name="ref2" />.<br><br><br />
'''(1)''' RT-PCR analyses show that the expression of ''OsMADS29'' initiates at panicles 0.1~5 cm, then increases gradually with the development of panicles at 6-22 cm. After pollination, the expression level reaches the maximum value at 5 DAP-7 DAP, then decreases from 9 DAP. No expression of ''OsMADS29'' is detected in the vegetative organs (Figure 2A).<br>'''(2)''' Results of qRT-PCR show similar expression profiles of ''OsMADS29'' to those of the RT-PCR (Figure 2B).<br>'''(3)''' RT-PCR was also performed to examine the expression of ''OsMADS29'' in different floral organs. Like other known B(sister) genes, ''OsMADS29'' is specifically expressed in the pistils (Figure 2C).<br />
<br><br />
<br />
===Evolution===<br />
The phylogenetic analyses made by A. Becker ''et al.'' reavels that B(sister) genes are the sister clade of the DEF/GLO-like (or AP3/PI-like) genes comprising class B floral organ identity genes <ref name="ref3" />.<br />
The phylogeny analyses made by Xuelian Yang ''et al.'' shows that B(sister) genes of core eudicots and monocots constitute two different clades, suggesting that the most recent common ancestor of both taxa contained one B(sister) gene only. The clade of rice B(sister) genes is divided into three subclades, termed the '''''OsMADS29''''', [[Os06g0667200|'''''OsMADS30''''']] and [[Os04g0614100|'''''OsMADS31''''']] subclade<ref name="ref2" />.<br />
<br />
===Knowledge Extension===<br />
During flower development in higher plants, the identity of the different floral organs isspecified by different classes of homeotic selector genes, termed class A, B, C, D and E genes, with A specifying sepals, A+B+E petals, B+C+E stamens (male microsporophylls), C+E carpels (female megasporophylls), and D ovules<ref name="ref3" /><ref name="ref4" />. The genes providing the different floral homeotic functions have been cloned from several plant species<ref name="ref3" />. Nearly all of them belong to the family of MADS-box genes, which encode transcription factors. Almost all known MADS-domain proteins from vascular plants share a conserved structural organization, the so-called MIKC-type domain structure, including MADS (M), intervening (I), keratin-like (K) and C-terminal (C) domains<ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. Genes closely related to class B MADS-box genes have been identified by phylogenetic studies, and are referred to as B(sister genes)<ref name="ref3" />.<br />
<br />
==Labs working on this gene==<br />
*Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, Peoples Republic of China,<br><br />
*Department of Genetics, Friedrich Schiller University Jena, Jena, Germany<br><br />
*Plant Evo-Devo Group, The Institute of Botany, Justus-Liebig-University Gießen, Gießen, Germany<br><br />
*National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"><br />
Yin L L, Xue H W. The MADS29 transcription factor regulates the degradation of the nucellus and the nucellar projection during rice seed development[J]. The Plant Cell Online, 2012, 24(3): 1049-1065.</ref><br />
<ref name="ref2">Yang X, Wu F, Lin X, et al. Live and Let Die-The B(sister) MADS-Box Gene OsMADS29 Controls the Degeneration of Cells in Maternal Tissues during Seed Development of Rice (Oryza sativa)[J]. PloS one, 2012, 7(12): e51435.</ref><br />
<ref name="ref3"><br />
Becker A, Kaufmann K, Freialdenhoven A, et al. A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes[J]. Molecular Genetics and Genomics, 2002, 266(6): 942-950.</ref><br />
<ref name="ref4"><br />
Yamada K, Saraike T, Shitsukawa N, et al. Class D and B sister MADS-box genes are associated with ectopic ovule formation in the pistil-like stamens of alloplasmic wheat (Triticum aestivum L.)[J]. Plant molecular biology, 2009, 71(1): 1-14.</ref><br />
<ref name="ref5"><br />
Arora R, Agarwal P, Ray S, Singh A, Singh V, et al. (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8: 242.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os02g0170300|<br />
Description = Similar to MADS box protein ZMM17|<br />
Version = NM_001052563.1 GI:115444496 GeneID:4328443|<br />
Length = 4006 bp|<br />
Definition = Oryza sativa Japonica Group Os02g0170300, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 2|Chromosome 2]]|<br />
AP = Chromosome 2:3833127..3837132|<br />
CDS = 3833796..3834074,3834202..3834243,3834352..3834393,3834894..3835055,3835193..3835262<br>,3836519..3836706|<br />
GCID = <gbrowseImage1><br />
name=NC_008395:3833127..3837132<br />
source=RiceChromosome02<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008395:3833127..3837132<br />
source=RiceChromosome02<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggggcgcggcaagatcgagatcaagaggatcgagaacgcgacgaacaggcaggtgacattctcgaagaggcggggagggctactgaagaaggcgaacgagctcgccgtgctctgcgacgcccgcgtcggcgtcgtcatcttctccagcaccggcaagatgttcgagtactgcagccctacctgcagtttgagggaactcatcgagcattaccagaccgtcaccaacactcatttcgaggagatcaaccacgatcagcaaatatttgtggagatgactcggatgaggaacgagatggagaagctggacggtggcatcaggaggttcaccggcgacgacctctccaacctcacgctcgccgacatcaacgatctcgagcagcagctcgaattctccgtcaccaaagtccgtgcgagaaagcatcagctcctgaaccagcagctggacaaccttcgtcgcaaggagcacatcctggaagaccagaacagcttcctgtgccgcatgatcaacgagaaccatcatcaggcggcggtgggcggcggcgacgtgaaggcgatggtggagatggcgccggtgctgtcgatgctgacggcggcgccggcgtactacggcgaggagtcgtcgagcaccgcgctgcagctcaccccgccgctgcacgccgtcgacgccgccgccgccgccgggttccggctgcagccgacgcagcccaacctgcaggaccccggctgcagcagcagcagcttccatgccgccgccgccggccacggcctgcagctgtggtaa</cdnaseq>|<br />
AA = <aaseq>MGRGKIEIKRIENATNRQVTFSKRRGGLLKKANELAVLCDARVG VVIFSSTGKMFEYCSPTCSLRELIEHYQTVTNTHFEEINHDQQIFVEMTRMRNEMEKL DGGIRRFTGDDLSNLTLADINDLEQQLEFSVTKVRARKHQLLNQQLDNLRRKEHILED QNSFLCRMINENHHQAAVGGGDVKAMVEMAPVLSMLTAAPAYYGEESSSTALQLTPPL HAVDAAAAAGFRLQPTQPNLQDPGCSSSSFHAAAAGHGLQLW</aaseq>|<br />
DNA = <dnaseqindica>3059..3337#2890..2931#2740..2781#2078..2239#1871..1940#427..614#agcctttgaagcaagcttagcacttcacaaggtatgtacatagcacattactactcctgccctatctatctaccctgttcatgagtaattcaagaaaaaaaaaaggacaccttttctagctagttcttcatcctttcgcagcaaagagtttttacatctctagctactagttgttctcttctctacatgaaattttttctacttctgattgcaccctttacatagctgtggggggaaatccaatttgagcacccatgccttatgttgattttaacaaaattcgtccatgtatcgatatgttcataacttggccatttctgttcttcttcttcttcttcttcttcttcagtttcctcttgtgcagaagaaggagaaacaaaagaacacagaaattaaattaaactcgatcaggaaggtatagcaggcatggggcgcggcaagatcgagatcaagaggatcgagaacgcgacgaacaggcaggtgacattctcgaagaggcggggagggctactgaagaaggcgaacgagctcgccgtgctctgcgacgcccgcgtcggcgtcgtcatcttctccagcaccggcaagatgttcgagtactgcagccctacctgcaggtacggttcttgttttgttctcttatattatcagatgctgttcaatctttcctttctccagcttagtgtctcttgttctctttttagtgcttgatttgatgggttaattaatttcttgttttttgtcaaccaagagattaagttttcggctaagtttctctcggcctttattttgtttttcagagaaaattaactaactcatgcagtttctaccctttgttttctttgggcaagagtgtttaattatgatcatttgatctgttcatataatggatggatgccttgcatttattcttcatctgaactatttttcttgtcctgaactcctgatcgatcgagtttttcctaccttcattttaactattttcagtgtatatgtatgcatctgcagtttcctttgatatattttcgaagagccaagaatctattacaaaattaaatcatgatcaaaggcatacataagcaatgatctatatgccctagtgtctcttgtgacttgattacgcacttgtcttttacatctctgagcaacatatatgtatgtagatttgcaacttgatcctgaatttatagtcaactagttaattaatccttatttccctctttctaatgatttctaggatcgagctgggttttttaggtggatttccccaaaaaactatttcatatgtggctaatttaatcaaactaaaagatgtatatcaacagggaatataatttgaacaagtgtacgacagtacgaccatatcttatcttatgttatgcatgtttttatacttaaaaaaagatgcgaatataagagaatgacctaatattaaataattagaagaggtgaggtttcgaaccttggttgtctagtccaccactttgtggagctagccggaagatccccagacgtttctcacatgattttatactgttctgcagcatattatagttaattaatatgtgaatattcatgtgaagttctttcttccgatcccctgttcattcctgttattagttaagaaattttcgtttgtttcattttgatctaaaataatatactctctgtaagtatatacatcaccaagagaaaattctagctacaaaattaatttataccatctgatttgtacatcagagattgtcatttcttttttgaatgcgcaaaagaattacacatgcaccattccaattagatacatgaacttatcaaagtattaattaactcacaactaatcaaggtacttgtttcaatgtttgacaatatatagtttgagggaactcatcgagcattaccagaccgtcaccaacactcatttcgaggagatcaaccacgatcaggtatacattaattttacaatcagcaacacaatgtctgatcaatatcagaatatatatcgatctatctgccagcagttgaaatgaaattttctttcaaatgcactgatcaaatataattaatgtgcacatatatatagcaaatatttgtggagatgactcggatgaggaacgagatggagaagctggacggtggcatcaggaggttcaccggcgacgacctctccaacctcacgctcgccgacatcaacgatctcgagcagcagctcgaattctccgtcaccaaagtccgtgcgagaaaggtaattacttcctccatatcatattataagtcgttttaattttttttacaaatttatttaagtttaatcaagtttataaaaaatatattagtatttcaaaaacaaacattatcaaaatgtattcagtgatagatttaataaaattaatttggtattacatgtgttgctatttttttctataaatttaatcaaacttaaaagaaaaaaaattaaaatgacttgtaatatgaaatagagctagtaattgattaagaagatagtatttgatgaatgaatcattcttcagagttaatttagaatgatcagtctctgattcaatggtaaatggtaagtttagggtttagggattaattgatcccatagttttttcctcttttctgtaaagctttgctttcgtaagttttttattttgttatattcaatgaaataggtgtatctaagtgccgattcgttaaaaaaataaaaaatagttgtttcacattaattcttgcttgttgcagcatcagctcctgaaccagcagctggacaaccttcgtcgcaaggtaattaatttgcactactaaactgatcatgaaacaccaaatactttgctgtatgatgatgaaaaaaaaaatgattgattcaattctatgcatgaaattgatgaacaggagcacatcctggaagaccagaacagcttcctgtgccgcatggtatacgtatagttagttaatcagtaatcaagaattcattaaaatgttttgattcttgaagcacatatatgtacattaattatggtgtttggttgattcttgtacatgaaactatatatgaattcagatcaacgagaaccatcatcaggcggcggtgggcggcggcgacgtgaaggcgatggtggagatggcgccggtgctgtcgatgctgacggcggcgccggcgtactacggcgaggagtcgtcgagcaccgcgctgcagctcaccccgccgctgcacgccgtcgacgccgccgccgccgccgggttccggctgcagccgacgcagcccaacctgcaggaccccggctgcagcagcagcagcttccatgccgccgccgccggccacggcctgcagctgtggtaagaacaaacgaagcaaagcatacatggcacatcctgatactctcatcaggtgtgtgatgtgaatatatatatcgcaatgattttatctactagtttatgtacttcatccgttttataatataagtcattctagtatttttcatattcatattgatattaatgaatacatatatatatcaatataaatgtaggaaatgctagaataacttacattgtgaaacggagggagtataattcatcgcaacacagctgcgaattaatcatgcattgatatcattctgcagagatctagatgattgcttgctaattaagcacatgatggcattgtcgattctgggagctaggagtaacttggagaccatgaagatgcatgatcagctgatgatagacgatcgagttgggttgctgtgttgttcaattgttcatcgttctggacatatatatatatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtctaattagcacatcagaataatcaagcttttctacctagttaactagtacagctgctaagtaccttttgatttgttggtgtgtgaactactgaactggagttggatattaaggtctccatgcatttgcatggttaattagcagagagatcattgaggtttttaggatgtaac</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001052563.1 RefSeq:Os02g0170300]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 2]]<br />
[[Category:Chromosome 2]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0232900&diff=172378Os07g02329002014-05-25T13:30:22Z<p>HamletShaoE: /* Function */ adding GO links</p>
<hr />
<div>The rice ''Os07g0232900 '' was reported as ''Heavy metal ATPases 3 (OsHMA3)'' four times in 2010 and 2011 by researchers from Japan<ref name="ref1" /><ref name="ref2" /><ref name="ref3" /><ref name="ref4" />.<br />
<br />
==Annotated Information==<br />
===Function===<br />
[[File:OsHAM3_1.jpg|right|thumb|320px|'''Figure 1.''' ''Mutant VS. WT(from reference) <ref name="ref4" />.<br>(C and D) shows a Complementation test. Cd concentration in the shoots (C) and roots (D) of three independent transgenic lines carrying ''OsHMA3'' and empty vector in Anjana Dhan background. (E and F) shows the Effect of decreased expression of '''OsHMA3''' on Cd accumulation. Cd concentration in the shoots (E) and roots (F) of three independent RNAi lines and vector control plants in Nipponbare background.'']]<br />
[[File:OsHAM3_2.jpg|right|thumb|320px|'''Figure 2.''' ''Complementary Test of OsHMA3 in S. cerevisiae(Yeast) <ref name="ref2" />]]<br />
[[File:OsHAM3_3.jpg|right|thumb|320px|'''Figure 3.''' ''Phylogenetic relationship of '''HMA''' proteins in rice (black), Arabidopsis thaliana<br />
(blue), and Arabidopsis halleri (green)(from reference) <ref name="ref4" />.'']]<br />
* ''OsHAM3'' encodes a P1B-type ATPase, acting as a Cd transporter, which can control the ability of root-to-shoot Cd translocation<ref name = "ref2" /><ref name = "ref3" /><ref name = "ref4" />. This gene is involved in the efflux of divalent metal ions across a vacuole membrane<ref name = "ref3" />.<br />
* Defective function of ''OsHAM3'' leads to high Cd accumulation in 3 different rice cultivars: Cho-Ko-Koku, Anjana Dhan as well as Jarjan<ref name = "ref1" /><ref name = "ref2" /><ref name = "ref3" /><ref name = "ref4" />, while the rice cultivar Nipponbare with intact function of ''OsHAM3'' gets low accumulation rate of Cd. <br />
* ''OsHMA3'' from the low Cd-accumulating cultivar limits the translocation of Cd from the roots to the above-ground tissues by selectively sequestrating Cd into the root vacuoles, thus decrease the accumulation rate of Cd in the whole plant<ref name = "ref2" /><ref name = "ref4" />.<br />
* In contrast, the allelic gene ''OsHMA3mc'' from the high Cd-accumulating cultivar lost the function to act as a firewall of Cd because of a single amino acid mutation<ref name = "ref4" />.The study of this gene will be of great value for phytoremediation of Cd-polluted paddy Welds<ref name = "ref1" />.<br />
<br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003824 GO:0003824], [http://amigo.geneontology.org/amigo/term/GO:0006812 GO:0006812], [http://amigo.geneontology.org/amigo/term/GO:0008152 GO:0008152], [http://amigo.geneontology.org/amigo/term/GO:0016020 GO:0016020], [http://amigo.geneontology.org/amigo/term/GO:0016021 GO:0016021], [http://amigo.geneontology.org/amigo/term/GO:0030001 GO:0030001], [http://amigo.geneontology.org/amigo/term/GO:0046872 GO:0046872], [http://amigo.geneontology.org/amigo/term/GO:0046873 GO:0046873]<br />
<br />
===Wild Type & Mutations===<br />
'''Cd Accumulation Rates in different Rice plants, counted by ''Daisei Uenoa et al.'' '''<br />
* Analysis with three independent transgenic lines showed that introduction of ''OsHMA3'' from Nipponbare into Anjana Dhan resulted in decreased Cd accumulation in the shoots (P < 0.01) (Fig 1C), but increased Cd accumulation in the roots (P<0.01) (Fig 1D)<ref name = "ref4" />.<br />
* Furthermore, when ''OsHMA3'' expression was knocked down in Nipponbare by RNAi, the concentration of Cd in the shoot was increased by 2.1- to 2.5-times in the RNAi lines compared with the empty-vector control plants (P < 0.05) (Fig. 1E) and the root Cd concentration was decreased by 74 to 60% in the RNAi line (P < 0.05) (Fig 1F)<ref name = "ref4" />.<br><br />
'''Complementary Test of ''OsHMA3'' in'' S. cerevisiae(Yeast)'' by ''Hidenori Miyadate et al.'' ''' <br />
* The wild-type yeast strain ('''''BY4743''''') can grow, with only slight inhibition, in media containing up to 60 μM of CdCl2. The mutant strain ('''''YDR135c'''''), which lacks Cd transport to the vacuole, shows severe growth inhibition above 30 μM CdCl2(Fig 2)<ref name = "ref2" />.<br />
* Expression of ''OsHMA3'' in the mutant yeast strain increased its Cd tolerance('''''YDR135c-A63''''') so that its level of tolerance was only slightly inferior to that of the wild strain. By contrast, mutant yeast expressing ''OsHMA3mc'' did not grow at 30 μM CdCl2(''''YDR135c-A63-CKK'''''), indicating that ''OsHMA3mc'' had no effect on Cd sensitivity in YDR135c<ref name = "ref2" />(Fig 2).<br />
<br />
===Expression Pattern===<br />
* RT-PCR analysis by ''Hidenori Miyadate et al.'' showed that the expression level of ''OsHMA3'' was higher in the roots than in the leaves of Akita 63 and Cho-Ko-Koku seedlings grown in hydroponic culture containing 5 μg/L of CdCl2 for 14 d<ref name= "ref2" />.<br><br><br />
* RT-PCR analysis by ''Daisei Uenoa et al.'' showed that ''OsHMA3'' is mainly expressed in the roots at a similar level in Nipponbare and Anjana Dhan contrasting in Cd accumulation. Their Spatial analysis shows that there is no difference in the expression of ''OsHMA3'' among different root segments: 0 to 1 cm, 1 to 2 cm, and 2 to 3 cm from the apex of both cultivars.<ref name = "ref4" />.<br />
<br />
===Localization===<br />
Cellular and Subcellular Localization analysis by ''Hidenori Miyadate et al.'' and ''Daisei Ueno et al.'' showed that ''OsHMA3'' is localized at the vacuolar membrane of all root cells in rice<ref name = "ref2" /><ref name = "ref4" />.<br />
<br />
===Evolution===<br />
Phylogenetic analysis by ''Daisei Uenoa et al.'' shows that the amino acid sequence similarity of ''OsHMA3'' to ''HMA3'' proteins from other plants is very low, with 39.4% identity to the closest homolog in Arabidopsis (''AtHMA3'' from ecotype Wassilewskija) and ''AhHMA3'' from Arabidopsis halleri, a Zn-hyperaccumulating plant(Fig 3)<ref name = "ref4"/> .<br />
<br />
===Knowledge Extension===<br />
* Cadmium (Cd) is a highly toxic heavy metal for all organisms. In humans, Cd exposure has been associated with cancers of the prostate, lungs, and testes, kidney tubule damages, rhinitis, emphysema, osteomalacia, and bone fractures (1, 2). Cd also inhibits plant growth and development by binding to free sulfhydryl residues and interfering with homeostasis of essential elements, such as zinc, calcium, and iron, or causing their displacement from proteins<ref name = "ref4"/><ref name = "ref5"/>.<br><br><br />
<br />
* There has been an increasing interest in the use of hyperaccumulator plants to remediate Cd-contaminated soils. The hyperaccumulator plants reduce the soil Cd content by translocation and accumulating high concentrations of the heavy metal in their shoots. In the last decade, several plant species were identified as Cd hyperaccumulators, including ''Noccaea (Thlaspi) caerulescens'', ''Arabidopsis halleri'', ''Thlaspi praecox'', and ''Sedum alfredii'')<ref name = "ref5"/>.<br />
<br />
==Labs working on this gene==<br />
* Laboratory of Plant Genetics and Breeding, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Kaidoubata-Nishi 241-438, Shimoshinjyo-Nakano, Akita 010-0195, Japan<br />
* Akita Agricultural Experiment Station, Genpachizawa 34-1, Aikawa, Yuwa, Akita 010-1231, Japan<br />
* Department of Paddy Farming, National Agricultural Research Center for Tohoku Region, Yotsuya, Daisen 014-0102, Japan<br />
* Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, 305-8572 Ibaraki, Japan<br />
* Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Tezuka K, Miyadate H, Katou K, et al. A single recessive gene controls cadmium translocation in the cadmium hyperaccumulating rice cultivar Cho-Ko-Koku[J]. Theoretical and applied genetics, 2010, 120(6): 1175-1182.<br />
</ref><br />
* <ref name="ref2"><br />
Miyadate H, Adachi S, Hiraizumi A, et al. OsHMA3, a P1B‐type of ATPase affects root‐to‐shoot cadmium translocation in rice by mediating efflux into vacuoles[J]. New Phytologist, 2011, 189(1): 190-199.<br />
</ref><br />
* <ref name="ref3"><br />
Ueno D, Koyama E, Yamaji N, et al. Physiological, genetic, and molecular characterization of a high-Cd-accumulating rice cultivar, Jarjan[J]. Journal of experimental botany, 2011, 62(7): 2265-2272.<br />
</ref><br />
* <ref name="ref4"><br />
Ueno D, Yamaji N, Kono I, et al. Gene limiting cadmium accumulation in rice[J]. Proceedings of the National Academy of Sciences, 2010, 107(38): 16500-16505.<br />
</ref><br />
* <ref name="ref5"><br />
Sun J, Wang R, Liu Z, et al. Non-invasive microelectrode cadmium flux measurements reveal the spatial characteristics and real-time kinetics of cadmium transport in hyperaccumulator and nonhyperaccumulator ecotypes of ''Sedum alfredii''[J]. Journal of plant physiology, 2012.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0232900|<br />
Description = ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter family protein|<br />
Version = NM_001065775.2 GI:297606939 GeneID:4342783|<br />
Length = 3809 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0232900, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:7437901..7441709|<br />
CDS = 7437901..7439339,7439452..7439657,7439841..7440171,7440268..7440405,7440619..7440874<br>,7440963..7441318,7441421..7441709|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:7437901..7441709<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:7437901..7441709<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggccggaaaggatgaggcggaagggctcgaggcgaggctgctgctgctgccgcctgaggcggcggcggaggagccgacgaggtgtggcggcggcgacggcggcggcggcgggaggaagcggaagaagacgtaccttgatgtccttggcgtgtgctgctccgcggaggtcgcgctggtggagcggctgctcgcgccgctcgacggcgtccgcgtggtgtccgtcgtcgtggcgtcccgcaccgtcgtcgtcgagcacgaccccgccgccgccccggagtccgccatcgtgaaggcgctgaacaaggccggcctcgaggcgtcggtgcgagcctacggcagcagcggcgtggtcagccggtggccgagcccgtacatcgtcgcctccggcgtcctcctcacggcgtccttcttcgagtggctcttccctcccctgcagtgcctggccgtggcggccgtcgtcgccggcgcgccgccgatggtgcgccgtgggttcgccgcggcgagccggctgtcgctcgacatcaacgtcctcatgctcatcgccgtcgccggcgcgctctgcctcggcgactacacggaggccggcgccatcgtcttcctcttcaccaccgcagaatggctcgagacgctggcctgcacaaaggcgagcgccgggatgtcgtcgttgatgggcatgctgccggtgaaggcggtcatcgcgacgacgggcgaggttgtcagcgtgcgcgacgtccgcgtgggcgacgtcgtcgcggtcagggccggcgagatcgtccccgtcgacggcgtggtggtcgacggccagagcgaggtcgacgagaggagcctcaccggcgagtccttcccggtgccgaagcagccgcactccgaggtctgggccggcacaatgaactttgacggttacattgctgtgagaactacggctctcgccgagaactcgacggtggcgaagatggagaggctggtggaggcggcgcagaacagcaggtcgaagacgcagcggctgatcgattcgtgcgcaaagtactacacgccggccgtggtggttgttgcagcaggagtggccctgatcccggctctgctcggagcagatggccttgagcaatggtggaagctggctctggtgatgcttgtgagcgcgtgcccctgcgcattagtgctgtcgacaccggtggcatccttctgcgcaatgctgcgcgctgcgaggatggggatcttcatcaagggtggagatgttcttgaatcacttggggagatcagggccgtcgcgttcgacaagaccgggacgatcaccagaggagagttcagcatcgactcgttccatctggttggggatcacaaggttgagatggatcatcttctttactggattgcaagcattgagagcaagtcaagccacccaatggcagctgcacttgtggagtatgctcaatccaaatccatccaaccaaacccggaaaatgtgggcgattttcggatatatcccggggaggggatctatggagagatccatggaaagcacatctacattgggaacagaaggacattggcaagagcgtcatcacctcagtcaactcaagaaatgggtgagatgatcaagggcgtgtcgatcggctacgtgatctgcgacggcgagctcgccggcgtcttctcgctctccgacgactgccggaccggcgcggcggaggcgatccgggagcttggatcgctgggcatcaagtcggttatgctgaccggggacagcagcgcggcggcgacgcacgcgcagggccagctcggcggcgtcatggaggagctccactccgagctcctcccggaggacaaggtccggctcgtcagcggcctcaaggcgaggttcggcccgacgatgatggtcggggacgggatgaacgacgcggcggcgctggcggcggcggacgtgggcgtgtccatgggcatctccgggtcggcggcggcgatggagaccagccacgcgacgctcatgtcgagcgacgtgctcagggtccccgaggccgtcaggctcggccggtgcgcccgccggaccatcgccgtcaacgtggccggctcggtggccgtgaaggccgccgtgctcgcgctggccgcggcgtggcgccccgtgctctgggccgccgtgctcgccgacgtcgggacgtgcctcctcgtcgtgctcaacagcatgacgctgctcagggaggagtggaagggcggcgccaaggaggacggcgcgtgccgcgccacggcgaggtcgctggtgatgaggtcccagctcgccgccgactcccaagcacccaacgccgcagacgctggcgccgccggccgtgagcaaacgaacggctgccgttgctgtccgaagccgggcatgtcgcccgagcactcggttgtcatcgacatccgagccgacggcgagcgtcaagaagagcggccggccgaggcggccgtcgttgccaaatgttgcggcggaggcggcggcgagggcatccgctgcggagcctccaagaagccaactgcaacggtcgttgttgccaaatgttgcgggggcggcggcggcggcgagggcaccaggtgcggcgcgtccaagaatccggcaacggcggccgtcgttgccaaatgttgcagcggaggcggcggcgagggcatcggctgcggagcctccaagaagccaactgcaacggccgttgttgccaaatgttgcggcggcggcggcgagggcaccaggtgcgccgcgtccaagaagccggcaacggcggccgtcgttgccaaatgttgcggtggcgatggcggcgagggcaccggatgtggtgcctccaagaggtcgccgccggctgagggaagctgcagcggcggtgaaggcggtaccaatggtgttggtcgttgctgcacgagcgtgaagaggccaacctgttgcgacatgggagcggcggaggtgtccgattcttcgccggagacggcgaaagactgcagaaatgggaggtgttgcgcgaagacgatgaactccggtgaagtgaaaggatga</cdnaseq>|<br />
AA = <aaseq>MAGKDEAEGLEARLLLLPPEAAAEEPTRCGGGDGGGGGRKRKKT YLDVLGVCCSAEVALVERLLAPLDGVRVVSVVVASRTVVVEHDPAAAPESAIVKALNK AGLEASVRAYGSSGVVSRWPSPYIVASGVLLTASFFEWLFPPLQCLAVAAVVAGAPPM VRRGFAAASRLSLDINVLMLIAVAGALCLGDYTEAGAIVFLFTTAEWLETLACTKASA GMSSLMGMLPVKAVIATTGEVVSVRDVRVGDVVAVRAGEIVPVDGVVVDGQSEVDERS LTGESFPVPKQPHSEVWAGTMNFDGYIAVRTTALAENSTVAKMERLVEAAQNSRSKTQ RLIDSCAKYYTPAVVVVAAGVALIPALLGADGLEQWWKLALVMLVSACPCALVLSTPV ASFCAMLRAARMGIFIKGGDVLESLGEIRAVAFDKTGTITRGEFSIDSFHLVGDHKVE MDHLLYWIASIESKSSHPMAAALVEYAQSKSIQPNPENVGDFRIYPGEGIYGEIHGKH IYIGNRRTLARASSPQSTQEMGEMIKGVSIGYVICDGELAGVFSLSDDCRTGAAEAIR ELGSLGIKSVMLTGDSSAAATHAQGQLGGVMEELHSELLPEDKVRLVSGLKARFGPTM MVGDGMNDAAALAAADVGVSMGISGSAAAMETSHATLMSSDVLRVPEAVRLGRCARRT IAVNVAGSVAVKAAVLALAAAWRPVLWAAVLADVGTCLLVVLNSMTLLREEWKGGAKE DGACRATARSLVMRSQLAADSQAPNAADAGAAGREQTNGCRCCPKPGMSPEHSVVIDI RADGERQEERPAEAAVVAKCCGGGGGEGIRCGASKKPTATVVVAKCCGGGGGGEGTRC GASKNPATAAVVAKCCSGGGGEGIGCGASKKPTATAVVAKCCGGGGEGTRCAASKKPA TAAVVAKCCGGDGGEGTGCGASKRSPPAEGSCSGGEGGTNGVGRCCTSVKRPTCCDMG AAEVSDSSPETAKDCRNGRCCAKTMNSGEVKG</aaseq>|<br />
DNA = <dnaseqindica>2371..3809#2053..2258#1539..1869#1305..1442#836..1091#392..747#1..289#atggccggaaaggatgaggcggaagggctcgaggcgaggctgctgctgctgccgcctgaggcggcggcggaggagccgacgaggtgtggcggcggcgacggcggcggcggcgggaggaagcggaagaagacgtaccttgatgtccttggcgtgtgctgctccgcggaggtcgcgctggtggagcggctgctcgcgccgctcgacggcgtccgcgtggtgtccgtcgtcgtggcgtcccgcaccgtcgtcgtcgagcacgaccccgccgccgccccggagtccgccatcggtaagccaccgcgcgcgcgcgcgccattaatcctccacgcgattctcgcgcgagattctcactgaatcgagtcgtcgtcgtcgtctttgtcttggagtgcagtgaaggcgctgaacaaggccggcctcgaggcgtcggtgcgagcctacggcagcagcggcgtggtcagccggtggccgagcccgtacatcgtcgcctccggcgtcctcctcacggcgtccttcttcgagtggctcttccctcccctgcagtgcctggccgtggcggccgtcgtcgccggcgcgccgccgatggtgcgccgtgggttcgccgcggcgagccggctgtcgctcgacatcaacgtcctcatgctcatcgccgtcgccggcgcgctctgcctcggcgactacacggaggccggcgccatcgtcttcctcttcaccaccgcagaatggctcgagacgctggcctgcacaaaggtaggagtacatgtcaatgtcctcttcaccaaatccatggcgatcttggcacgaacccggacgaacactcacgttgcgaggtgtgcaggcgagcgccgggatgtcgtcgttgatgggcatgctgccggtgaaggcggtcatcgcgacgacgggcgaggttgtcagcgtgcgcgacgtccgcgtgggcgacgtcgtcgcggtcagggccggcgagatcgtccccgtcgacggcgtggtggtcgacggccagagcgaggtcgacgagaggagcctcaccggcgagtccttcccggtgccgaagcagccgcactccgaggtctgggccggcacaatgaactttgacggtaaacaaacaaacaatcaaaaaaatctctcatctcttagtttcagagttcccaaatgtacggaactctgaaacgtccgtgtcgttgaattgtccgtcttttctcatcagcttaagttctggtaaactgattgacgcatccaactcaatagtcacaatagcacacatttgttcatgtcatgatcaatgggattgagaggctgtcacgtttcaggttacattgctgtgagaactacggctctcgccgagaactcgacggtggcgaagatggagaggctggtggaggcggcgcagaacagcaggtcgaagacgcagcggctgatcgattcgtgcgcaaagtactacacgccgggtgcgcaatcggcatcgcctaaactctcaacatctccaattttacaacacaaaattcatcagtaacaaagacatttctgttcttggtgcgttgcagccgtggtggttgttgcagcaggagtggccctgatcccggctctgctcggagcagatggccttgagcaatggtggaagctggctctggtgatgcttgtgagcgcgtgcccctgcgcattagtgctgtcgacaccggtggcatccttctgcgcaatgctgcgcgctgcgaggatggggatcttcatcaagggtggagatgttcttgaatcacttggggagatcagggccgtcgcgttcgacaagaccgggacgatcaccagaggagagttcagcatcgactcgttccatctggttggggatcacaaggttgagatggatcatcttctttactggtaagactgagaaagaagatttcatttcagctcttggaatgcagctgctacactgaacaaatttgacagattttcaactgttgtcggtttacgacttgtcgaaaaatccttagtacttgtgatggtttgaattgacttgaacagtgaaatgcttggcacaaattatgtctttggttattgcaggattgcaagcattgagagcaagtcaagccacccaatggcagctgcacttgtggagtatgctcaatccaaatccatccaaccaaacccggaaaatgtgggcgattttcggatatatcccggggaggggatctatggagagatccatggaaagcacatctacattgggaacagaaggacattggcaagagcgtcatcacctcagtcaagtgagcaaaacacatcatttgtagtagtagtacagttcctgacaattaagcttcagaattagctgatcagctgaagctgagctgactgaactgaaatctgtgacgtttacagctcaagaaatgggtgagatgatcaagggcgtgtcgatcggctacgtgatctgcgacggcgagctcgccggcgtcttctcgctctccgacgactgccggaccggcgcggcggaggcgatccgggagcttggatcgctgggcatcaagtcggttatgctgaccggggacagcagcgcggcggcgacgcacgcgcagggccagctcggcggcgtcatggaggagctccactccgagctcctcccggaggacaaggtccggctcgtcagcggcctcaaggcgaggttcggcccgacgatgatggtcggggacgggatgaacgacgcggcggcgctggcggcggcggacgtgggcgtgtccatgggcatctccgggtcggcggcggcgatggagaccagccacgcgacgctcatgtcgagcgacgtgctcagggtccccgaggccgtcaggctcggccggtgcgcccgccggaccatcgccgtcaacgtggccggctcggtggccgtgaaggccgccgtgctcgcgctggccgcggcgtggcgccccgtgctctgggccgccgtgctcgccgacgtcgggacgtgcctcctcgtcgtgctcaacagcatgacgctgctcagggaggagtggaagggcggcgccaaggaggacggcgcgtgccgcgccacggcgaggtcgctggtgatgaggtcccagctcgccgccgactcccaagcacccaacgccgcagacgctggcgccgccggccgtgagcaaacgaacggctgccgttgctgtccgaagccgggcatgtcgcccgagcactcggttgtcatcgacatccgagccgacggcgagcgtcaagaagagcggccggccgaggcggccgtcgttgccaaatgttgcggcggaggcggcggcgagggcatccgctgcggagcctccaagaagccaactgcaacggtcgttgttgccaaatgttgcgggggcggcggcggcggcgagggcaccaggtgcggcgcgtccaagaatccggcaacggcggccgtcgttgccaaatgttgcagcggaggcggcggcgagggcatcggctgcggagcctccaagaagccaactgcaacggccgttgttgccaaatgttgcggcggcggcggcgagggcaccaggtgcgccgcgtccaagaagccggcaacggcggccgtcgttgccaaatgttgcggtggcgatggcggcgagggcaccggatgtggtgcctccaagaggtcgccgccggctgagggaagctgcagcggcggtgaaggcggtaccaatggtgttggtcgttgctgcacgagcgtgaagaggccaacctgttgcgacatgggagcggcggaggtgtccgattcttcgccggagacggcgaaagactgcagaaatgggaggtgttgcgcgaagacgatgaactccggtgaagtgaaaggatga</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065775.2 RefSeq:Os07g0232900]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os11g0559200&diff=172377Os11g05592002014-05-25T13:21:54Z<p>HamletShaoE: </p>
<hr />
<div>The rice ''Os11g0559200'' was recongized as '''''OsXa21''''' in 1990s. However, the related research of this gene can date back to the year 1977, when Indian Plant Pathologist Dr. S. Devadath found a strain of ''Oryza barthii'' from Manila is resistant to all the races of bacterial blight<ref name="ref1" />. <br />
<br />
==Annotated Information==<br />
[[File:Xa21-1.jpg|right|thumb|350px|'''Figure 1.''' ''Graphical representation of the chromosome of Xanthomonas oryzae pv. oryzae(from reference<ref name="ref7" />).'']]<br />
===Function===<br />
[http://en.wikipedia.org/wiki/Bacterial_blight_(barley) Bacterial blight] is the most destructive bacterial disease of rice distributed all over the world, especiallyin Asia and Africa. '''''OsXa21''''' is the first disease resistance gene cloned from rice, which encodes a receptor-like kinase and confers broad spectrum resistance against Xanthomonas oryzae pv. oryzae ( Xoo ). As a member of pattern recognition receptors (PRRs), '''''OsXa21''''' plays an imortant role in pathogen-associated molecular patterns (PAMPs). It is a resistance gene in plants which is critical to the activation of innate immune response.<br />
* Xa21 encodes a receptor-like kinase, which has 3 parts: a receptor-like kinase (RLK) with leucine-rich repeats (LRR) in the presumed extracellular domain, a transmembrane domain and a serine–threonine protein kinase domain<ref name="ref2" />, the last two part are the most important, because they have correlation with the resistance of Xa21. And this disease resistance gene is a member of a multigene family which has seven family members. Xa21D, an Xa21 gene family member, encodes a predicted protein consisting of a signal peptide and a LRR domain, which is highly similar to the LRR domain of XA21. RLKs play important roles in many biological processes, including development and growth, in both animals and plants<ref name="ref3" />. In the Xa21 gene family, LRRs of different members may have evolved to recognize different pathovars and may confer altered resistance phenotypes.<br />
*In 1992, Ronald located Xa21 on chromosome11<ref name="ref4" />. Based on the frequency with which they discovered polymorphic Xa21-1inked markers, they estimate the size of the introgressed region containing Xa21 to be approximately 800 kb<ref name="ref5" />.<br />
<br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0004672 GO:0004672], [http://amigo.geneontology.org/amigo/term/GO:0004674 GO:0004674], [http://amigo.geneontology.org/amigo/term/GO:0005524 GO:0005524], [http://amigo.geneontology.org/amigo/term/GO:0006468 GO:0006468]<br />
<br />
===Expression===<br />
* The expression analysis made by ''Chang-Jin Park1'' et al. in 2010 showed that ''Xoo'' infection could induce the expression of ''OsXa21'', then regulates XA21-mediated immune response (Figure 2). They further found that the constitutive expression of ''OsXa21'' could enhance resistance to Xoo and the overexpression of ''OsXa21'' up-regulate a new set of defense-related genes<ref name="ref8" />. <br><br />
[[File:Xa21-2.jpg|right|thumb|350px|'''Figure 2.''' ''The expression pattern of OsXa21 after infected by Xoo(from reference<ref name="ref8" />).'']]<br />
* Thus, they conclude that altering the regulation of ''OsXa21'' could be used for enhancing resistance to ''Xoo'' at multiple developmental stages<ref name="ref8" />.<br />
<br />
===Evolution===<br />
*Synteny and phylogenetic analysis showed that frequent gene translocation, duplication and/or loss, have occurred at Xa21 homologous loci, suggesting that they have undergone or are undergoing rapid generation of copy number variations. Many researchers have domenstated that during the evolution of the Xa21 gene family, it’s common to find gene duplication and diversification and they think these processes may associated with the creation of novel resistance phenotypes<ref name="ref3" />.<br />
*The study by Yang J et al. showed that Xa21 gene in different generation and genetic background could be stably inherited and presented sustained resistance to RBB and no re-sistance decline or loss were found in successive planting for 16 generations<ref name="ref6" />.<br />
===Gene Structure===<br />
[[File:Xa21-3.png|center|thumb|727px|'''Figure 3.''' ''Structure of OsXa21 (from NCBI BLASTP).'']]<br />
<br />
==Labs working on this gene==<br />
* Department of Plant Pathology and the Genome Center, University of California Davis, Davis, California 95616, USA. <br />
* Center for Engineering Plants for Resistance against Pathogens, University of California, Davis, California 9561 6<br />
* Department of Plant Molecular Systems Biotechnology, Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.<br />
* Department of Molecular Microbiology, School of Medicine, Washington University, St. Louis, MO 63110, USA.<br />
* State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China<br />
* Genetic Diversity Department, National Institute of Agrobiological Sciences (Tsukuba, Ibaraki 305–8602, Japan)<br />
* Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, South Korea<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
KHUSH G S, BACALANGCO E, Ogawa T. 18. A New Gene for Resistance to Bacterial Blight from O. longistaminata. Rice Genet Newslett 1990, 7: 121 ~ 122.<br />
</ref><br />
* <ref name="ref2"><br />
Ronald P C, Albano B, Tabien R, et al. Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21[J]. Molecular and General Genetics MGG, 1992, 236(1): 113-120.<br />
</ref><br />
* <ref name="ref3"><br />
Tan S, Wang D, Ding J, et al. Adaptive evolution of Xa21 homologs in Gramineae[J]. Genetica, 2011, 139(11-12): 1465-1475.<br />
</ref><br />
* <ref name="ref4"><br />
Song W Y, Wang G L, Chen L L, et al. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21[J]. Science, 1995, 270(5243): 1804-1806.<br />
</ref><br />
* <ref name="ref5"><br />
Andaya C B, Ronald P C. A catalytically impaired mutant of the rice Xa21 receptor kinase confers partial resistance to Xanthomonas oryzae pv oryzae[J]. Physiological and molecular plant pathology, 2003, 62(4): 203-208.<br />
</ref><br />
* <ref name="ref6"><br />
Yang J, Ni D, Wu J. Breeding and food safety evaluation of transgenic hybrid rice harboring Xa21 gene[J]. Molecular Plant Breeding, 2006, 14.<br />
</ref><br />
* <ref name="ref7"><br />
Ochiai H, Inoue Y, Takeya M, et al. Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity[J]. Japan Agricultural Research Quarterly, 2005, 39(4): 275.<br />
</ref><br />
* <ref name="ref8"><br />
Ronald P C, Albano B, Tabien R, et al. Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21[J]. Molecular and General Genetics MGG, 1992, 236(1): 113-120.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os11g0559200|<br />
Description = Protein kinase-like domain containing protein|<br />
Version = NM_001189679.1 GI:297728488 GeneID:9271075|<br />
Length = 3488 bp|<br />
Definition = Oryza sativa Japonica Group Os11g0559200, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 11|Chromosome 11]]|<br />
AP = Chromosome 11:22645462..22648949|<br />
CDS = 22645516..22648135,22648424..22648800|<br />
GCID = <gbrowseImage1><br />
name=NC_008404:22645462..22648949<br />
source=RiceChromosome11<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008404:22645462..22648949<br />
source=RiceChromosome11<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgatatcactcccattactgctcttcgtcctcttcttctctgcgctgctgctcttcccttcgagcagtgacgacgacggtggtggtgatgctgccggcgacgaactcgcgctgctctctttcaagtcatccctgctataccaggggggccagtcgctggcatcttggaacacgtccggccatggccagcactgcacatgggtgggtgtcgtgtgcggccgccggcacccacacagggtggtgaagctgcggctgcgctcctccaacctggccgggatcatctcgccgtcgctgggcaacctatccttcctcaggacgctgcaactcagcgacaaccacctgtccggcaagataccccaggagctcagccgtctcatcaggctccagcaactggtactgaatttcaacagcctatcgggtgagattccagctgctttgggcaatctaaccagtctctcggttcttgagctgactaacaatacactgtccggagcaatcccttcatctctgggcaaactcacaggtctcactgatcttgcactggctgaaaatacgctgtctggttccatcccatcatctttcggccaattgcgcagattatctttccttagcttagcctttaacaatttaagtggagcgatcccagatcctatttggaacatctcctctctcaccatattcgaagtcatatccaacaagctaagtggtacactgcctacaaatgcattcagtaatcttcctagtctgcaggaggtatacatgtattacaaccagtttcatggtcgtatcccggcatcgataggtaatgcttccaacatctcaatatttaccattggtttaaactcttttagcggtgttgttccaccggagattggaaggatgagaaatcttcagagactagagcttccagaaactcttttggaagctaaagaaacaaatgattggaaattcatgacggcattgacaaattgctccaatcttcaagaagtggaactgggaggttgtaaatttggtggagtcctccctgattctgtttccaatctttcctcttcgcttgtatctctctccattagagataacaaaatttcagggagcttacctagagatatcggtaatctcgttaatttacaatatctttctctcgctaacaactccttgacaggatcccttccctcttccttcagcaagcttaaaaatttacgtcgtctcactgtagataacaacaagttaattggttctctcccattcaccatcggtaatcttacacaactaactaatatggaggtccaatttaatgccttcggtggtacaataccaagcacacttggaaacctgaccaagctgtttcaaataaatcttggccacaataactttatagggcaaattcccattgaaatatttagcattcccgcactctctgaaattttggatgtgtcccatcataacttggagggatcaataccaaaagaaatagggaaacttaaaaatattgtcgaattccatgctgattcgaacaaattatcgggtgagatccctagcaccattggtgaatgccaacttctgcagcatcttttcctgcaaaacaatttcttaaatggtagcatcccaatagctctgactcagttgaaaggtctggacacacttgatctctcaggtaacaatttgtcaggtcagatacctatgtccttaggggacatgcctctgctccactcgctgaacctttcgttcaacagcttccacggtgaagtgccaaccaatggtgtttttgcaaatgcttctgaaatttacatccaaggcaatgcccatatttgcggtggcatacctgaactacatcttccgacgtgttccttaaaatcaagaaagaaaaagaaacatcaaattctgctgttagtggttgttatctgtctcgtttcgacacttgccgtcttttcgttactctacatgcttctaacctgtcataagagaagaaagaaagaagtccctgcaacgacatccatgcaaggccacccaatgatcacttacaagcagctggtaaaagcaacggatggtttttcgtccagccatttgttgggttctggatcttttggctctgtttacaaaggagaatttgatagtcaagatggtgaaatcacaagtcttgttgccgtgaaggtactaaagctggaaactccaaaggcactcaagagtttcacgtccgaatgcgaaacactgcgaaatactcgacaccggaatcttgtcaagatagttacgatttgctcgagcatcgataacagagggaatgatttcaaagcaattgtgtatgacttcatgcccaatggcagtctggaagattggctacaccctgaaacaaatgatcaagcagagcaaaggcacttgactctgcatcagagagtgaccatactacttgatgttgcatgtgcattggaccatcttcacttccatggccctgaacctattgtacactgtgatattaaatcaagcaatgtgttgttagatgctgatatggtagcccatgttggagactttggacttgcaagaatacttattgagggaagctcattgatgcaacagtcaacaagttcgatgggaatcagggggacaattggttacgcagcaccagagtatggtgtcgggaacactgcctcgacacatggagatatttacagttatggaattctagtgttggaaacagtaaccgggatgcggccggcagatagtacattcagaactggattgagcctccgtcagtacgttgaaccgggtctacatggtagactgatggatgttgttgacaggaagcttggtttggattccgagaaatggcttcaggctcgagatgtttcgccatgcagcagtattactgaatgccttgtttcactgcttagacttgggctgtcttgctctcaggaattgccatcgagtagaacgcaagccggagatgtcatcaatgaactgcgtgccatcaaagagtctctctcgatgtcatccgacatgtga</cdnaseq>|<br />
AA = <aaseq>MISLPLLLFVLFFSALLLFPSSSDDDGGGDAAGDELALLSFKSS LLYQGGQSLASWNTSGHGQHCTWVGVVCGRRHPHRVVKLRLRSSNLAGIISPSLGNLS FLRTLQLSDNHLSGKIPQELSRLIRLQQLVLNFNSLSGEIPAALGNLTSLSVLELTNN TLSGAIPSSLGKLTGLTDLALAENTLSGSIPSSFGQLRRLSFLSLAFNNLSGAIPDPI WNISSLTIFEVISNKLSGTLPTNAFSNLPSLQEVYMYYNQFHGRIPASIGNASNISIF TIGLNSFSGVVPPEIGRMRNLQRLELPETLLEAKETNDWKFMTALTNCSNLQEVELGG CKFGGVLPDSVSNLSSSLVSLSIRDNKISGSLPRDIGNLVNLQYLSLANNSLTGSLPS SFSKLKNLRRLTVDNNKLIGSLPFTIGNLTQLTNMEVQFNAFGGTIPSTLGNLTKLFQ INLGHNNFIGQIPIEIFSIPALSEILDVSHHNLEGSIPKEIGKLKNIVEFHADSNKLS GEIPSTIGECQLLQHLFLQNNFLNGSIPIALTQLKGLDTLDLSGNNLSGQIPMSLGDM PLLHSLNLSFNSFHGEVPTNGVFANASEIYIQGNAHICGGIPELHLPTCSLKSRKKKK HQILLLVVVICLVSTLAVFSLLYMLLTCHKRRKKEVPATTSMQGHPMITYKQLVKATD GFSSSHLLGSGSFGSVYKGEFDSQDGEITSLVAVKVLKLETPKALKSFTSECETLRNT RHRNLVKIVTICSSIDNRGNDFKAIVYDFMPNGSLEDWLHPETNDQAEQRHLTLHQRV TILLDVACALDHLHFHGPEPIVHCDIKSSNVLLDADMVAHVGDFGLARILIEGSSLMQ QSTSSMGIRGTIGYAAPEYGVGNTASTHGDIYSYGILVLETVTGMRPADSTFRTGLSL RQYVEPGLHGRLMDVVDRKLGLDSEKWLQARDVSPCSSITECLVSLLRLGLSCSQELP SSRTQAGDVINELRAIKESLSMSSDM</aaseq>|<br />
DNA = <dnaseqindica>55..2674#2963..3339#atctctcgctcttgctgtcttagcttgcaccgatattctctgcatctcggcacgatgatatcactcccattactgctcttcgtcctcttcttctctgcgctgctgctcttcccttcgagcagtgacgacgacggtggtggtgatgctgccggcgacgaactcgcgctgctctctttcaagtcatccctgctataccaggggggccagtcgctggcatcttggaacacgtccggccatggccagcactgcacatgggtgggtgtcgtgtgcggccgccggcacccacacagggtggtgaagctgcggctgcgctcctccaacctggccgggatcatctcgccgtcgctgggcaacctatccttcctcaggacgctgcaactcagcgacaaccacctgtccggcaagataccccaggagctcagccgtctcatcaggctccagcaactggtactgaatttcaacagcctatcgggtgagattccagctgctttgggcaatctaaccagtctctcggttcttgagctgactaacaatacactgtccggagcaatcccttcatctctgggcaaactcacaggtctcactgatcttgcactggctgaaaatacgctgtctggttccatcccatcatctttcggccaattgcgcagattatctttccttagcttagcctttaacaatttaagtggagcgatcccagatcctatttggaacatctcctctctcaccatattcgaagtcatatccaacaagctaagtggtacactgcctacaaatgcattcagtaatcttcctagtctgcaggaggtatacatgtattacaaccagtttcatggtcgtatcccggcatcgataggtaatgcttccaacatctcaatatttaccattggtttaaactcttttagcggtgttgttccaccggagattggaaggatgagaaatcttcagagactagagcttccagaaactcttttggaagctaaagaaacaaatgattggaaattcatgacggcattgacaaattgctccaatcttcaagaagtggaactgggaggttgtaaatttggtggagtcctccctgattctgtttccaatctttcctcttcgcttgtatctctctccattagagataacaaaatttcagggagcttacctagagatatcggtaatctcgttaatttacaatatctttctctcgctaacaactccttgacaggatcccttccctcttccttcagcaagcttaaaaatttacgtcgtctcactgtagataacaacaagttaattggttctctcccattcaccatcggtaatcttacacaactaactaatatggaggtccaatttaatgccttcggtggtacaataccaagcacacttggaaacctgaccaagctgtttcaaataaatcttggccacaataactttatagggcaaattcccattgaaatatttagcattcccgcactctctgaaattttggatgtgtcccatcataacttggagggatcaataccaaaagaaatagggaaacttaaaaatattgtcgaattccatgctgattcgaacaaattatcgggtgagatccctagcaccattggtgaatgccaacttctgcagcatcttttcctgcaaaacaatttcttaaatggtagcatcccaatagctctgactcagttgaaaggtctggacacacttgatctctcaggtaacaatttgtcaggtcagatacctatgtccttaggggacatgcctctgctccactcgctgaacctttcgttcaacagcttccacggtgaagtgccaaccaatggtgtttttgcaaatgcttctgaaatttacatccaaggcaatgcccatatttgcggtggcatacctgaactacatcttccgacgtgttccttaaaatcaagaaagaaaaagaaacatcaaattctgctgttagtggttgttatctgtctcgtttcgacacttgccgtcttttcgttactctacatgcttctaacctgtcataagagaagaaagaaagaagtccctgcaacgacatccatgcaaggccacccaatgatcacttacaagcagctggtaaaagcaacggatggtttttcgtccagccatttgttgggttctggatcttttggctctgtttacaaaggagaatttgatagtcaagatggtgaaatcacaagtcttgttgccgtgaaggtactaaagctggaaactccaaaggcactcaagagtttcacgtccgaatgcgaaacactgcgaaatactcgacaccggaatcttgtcaagatagttacgatttgctcgagcatcgataacagagggaatgatttcaaagcaattgtgtatgacttcatgcccaatggcagtctggaagattggctacaccctgaaacaaatgatcaagcagagcaaaggcacttgactctgcatcagagagtgaccatactacttgatgttgcatgtgcattggaccatcttcacttccatggccctgaacctattgtacactgtgatattaaatcaagcaatgtgttgttagatgctgatatggtagcccatgttggagactttggacttgcaagaatacttattgagggaagctcattgatgcaacagtcaacaagttcgatgggaatcagggggacaattggttacgcagcaccaggttaatcctaaactgtttatgtctacctcctttcattgttttttttagatttgctctggtccaacaaaaaatacctaaagatacagatacttgtacctcacaatattaaatagttttcgatcattgcattgttagatctaacgatcaggaaacgatttggtaccgtgcccgtgaggtatcggaatctcaagatattttttgttcgaccgtagcaaatctatttttttgtttgttttcttctctttaatgttttatgactatgaaataatttttatttctggaaaacagagtatggtgtcgggaacactgcctcgacacatggagatatttacagttatggaattctagtgttggaaacagtaaccgggatgcggccggcagatagtacattcagaactggattgagcctccgtcagtacgttgaaccgggtctacatggtagactgatggatgttgttgacaggaagcttggtttggattccgagaaatggcttcaggctcgagatgtttcgccatgcagcagtattactgaatgccttgtttcactgcttagacttgggctgtcttgctctcaggaattgccatcgagtagaacgcaagccggagatgtcatcaatgaactgcgtgccatcaaagagtctctctcgatgtcatccgacatgtgaagatgtgagacatgctgatgttatgtccgagtatttcgttgtaatctaatgtgaagggtgagtgtgtgactgcttggttgtaagctatttcctgatctgcccatcagatcatgtatctgttctattgttgtatttctcagaacaaccac</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001189679.1 RefSeq:Os11g0559200], [http://www.ricedata.cn/gene/list/15.htm China Rice Data Center] |<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 11]]<br />
[[Category:Chromosome 11]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0341600&diff=172376Os05g03416002014-05-25T13:08:08Z<p>HamletShaoE: </p>
<hr />
<div>the rice gene '''Os05g0341600''' was recongized as '''RAB 21''' in 1988, which is induced when plants are subject to water-stress.<br />
==Annotated Information==<br />
===Function===<br />
the rice gene '''Os05g0341600''' was recongized as '''RAB 21''' in 1988, which is induced when plants are subject to water-stress. encoding a basic, glycine-rich protein (mol.wt 16 529) which has a duplicated domain structure. Immunoblots probed with antibodies raised against Bgalactosidase/RAB 21 fusion protein detect RAB 21 protein only in cytosolic cell fractions. <ref name="ref1" /><br />
===Expression===<br />
RAB 21 mRNA and protein accumulate in rice embryos, leaves, roots and callus-derived suspension cells upon treatment with NaCl (200 mM) and/or the plant hormone abscisic acid (10 /tMABA). The effects of NaCI and ABA are not cumulative, suggesting that these two inducers share a common response pathway. Induction of RAB 21 mRNA accumulation by ABA is rapid (< 15 min in suspension cells) and does not require protein synthesis, indicating that preformed nuclear and/or cytosolic factors mediate the response to this hormone. We have characterized the RAB 21 gene by deternmining the complete nucleotide sequence of a nearly full-length cDNA and corresponding genomiccopy, and by mapping the start site of its major transcript. The proximal promoter region contains various GC-rich repeats.<br />
<br />
===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Mundy, J. and N.-H. Chua (1988). "Abscisic acid and water-stress induce the expression of a novel rice gene." The EMBO Journal 7(8): 2279.</ref><br />
</references><br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0341600|<br />
Description = Similar to Ras-related protein Rab-21|<br />
Version = NM_001061782.1 GI:115463294 GeneID:4338469|<br />
Length = 4497 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0341600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br />
AP = Chromosome 5:15997018..16001514|<br />
CDS = 15997421..15997539,15998086..15998174,15998470..15998635,15998717..15998777,15999640..15999776<br>,16001320..16001386|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:15997018..16001514<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:15997018..16001514<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgggctcgaagccgccgccgccgccgcagcccagcgtctccttcaagctcgtcctcctcggcgacgggagagtaggcaaaacatctcttgtgctgcggtatgtgaatgatgtcttctcagacaaacaggaagcaactgttcaagcttcatatttgacaaagcgccttgttgttgaaggtgtgcctattacgctctctatctgggatacagctggacaagagaagttccatgcactaggccctatatactatcgtgatgcagacgctgctcttttagtatatgacatcacagacaatgatacttttcttcgtgtcacaaagtgggtgaaagagcttaagcaaatggcaaataaagatattgttatggccattgcagcaaataaaagtgacctggttagatcaaaacacatagacactaatgaagcagcaagctatgcagaaagtattggggcaactctctttgttacttctgccaaagctggtactgggattgatgatatcttcagtgacatagccaagagattattagagagaagaaaaaacagctccgatggcttgtcactggctcatccaaagaaaggcattttaatcgtcgacgatgaacctgagaaagaacctccaccaaagtgctgctcatag</cdnaseq>|<br />
AA = <aaseq>MGSKPPPPPQPSVSFKLVLLGDGRVGKTSLVLRYVNDVFSDKQE ATVQASYLTKRLVVEGVPITLSIWDTAGQEKFHALGPIYYRDADAALLVYDITDNDTF LRVTKWVKELKQMANKDIVMAIAANKSDLVRSKHIDTNEAASYAESIGATLFVTSAKA GTGIDDIFSDIAKRLLERRKNSSDGLSLAHPKKGILIVDDEPEKEPPPKCCS</aaseq>|<br />
DNA = <dnaseqindica>3976..4094#3341..3429#2880..3045#2738..2798#1739..1875#129..195#tcccacacttctcctctctgaccacagcacacacgcaacaccgggacgggcgatccggaaggttctggaaccttctagaggctcgtaggagcctccggcggaacccctctcgcctcgcctcgcctccgatgggctcgaagccgccgccgccgccgcagcccagcgtctccttcaagctcgtcctcctcggcgacggtacggctatctccctctcccttccgatcccgcgaaccctcctcccccccttctcaacccccttttctgccgaattcccgatccttcagtttggggttggcgtgcgcaagaaaatagccacggaatctgggtgaattttggctgctcttgtggtgcgtgctgagccctagctagggttaggggaaagccgcagaatcatttgatctggtaccctgtgtaggtagctaaatctatagcttagacgagggagttgagcggttttgagctaagcttaccttttacttgattgccttcgaggcttagcggagtccaggagatgattagaccgagagggctactcatagaaacaatctaacaagtagaagcatattcgttcttatatagaagatttgtctagtgctagctgcagcggggactgctgcaaattcatgtggacacaaagtggcagctgaagggtggccatggagctggtggcagggaattcgtcttatgcaataggggtggataatatttcattttgatccgtgctctctgtccgcttttaagcttggattgtaatgtccagctgatctagttctatattaattggtggttttacttttcttgtcattaccttaaccaacccttgaaggcagggtcctagaaaaaaaaaattcagtatgactcagctttttggtcatctgtgtatgatgccatgggtcttacccatgttcctctagagaaagtgatgtgtgcctttttggaaaaatgatacagtatgtagtttgggaggagggggttttgatgggaaagtactacagtctttatttgggcatgcttcttagcaagtgcatgtaagtcatacatgggaatgtcaagagaatttttcttgaaaccaggcacgggtgggcattgatctaacatggtacacttgcttttcctagcattgttgaacattgactcattttgatttaggatcagcttacttatagcttagaagcaagcttggaaatcagtttgtgcattgccaaagcggaatcacgtttcatttgaagttggctaatttcaattttggaaaagaaaaaagttggagtagttttgaactgaggcaatgagcacaatgaaagaattttttaccacagtagacagtacttgataagtgatagcgccagcataatcaattgctgaaactctttaaccatgccttagtacttggctttacattttttgaatgaagatatatatgtgtttccatgcataaaagcattgttgatagtcttgtgggcatgtatcttataggttgggtcattagggtttgcttattgttataactttctgtcattgatttcagatttttaatggaagaggtgtttaggctgtcttgtaaccagtcctctgttggcccagcctatcaatgtgaaaactgataaacctaagtttaacttaggatgaattgatcataattatatgctccattttttcaatttcattgaaaagacatgtgattgaatacatttcatatttattaacacaaacaataacttttacttttctcttggcacagggagagtaggcaaaacatctcttgtgctgcggtatgtgaatgatgtcttctcagacaaacaggaagcaactgttcaagcttcatatttgacaaagcgccttgttgttgaaggtgtgcctattacgctctctatctgggtgcgttgtcatctctttgatttgcgataatttgttcaacattttttacctctttcattttctcttatgtcagttgcacacacttgtttgaagtaattgtttactaattttgctgttgggatgatattcaattatggtttcaaatcccacttatatgtgcccttgtatcagaaatcctagtaggagtcagaaaaggtgaaaccaacccaattttgttggattataatacgagattgggaatatttagagatatgtggacttagttcttcattaaaaaaggagtaaatttcatagaactacggatattttgacaaaactatcacagaactacagatttaaggtcaaatttatcccaaaactacagatttaaataaaactgttacatggtttgcttccattatagctaaagtccgagactctgtgtacttgaactcatgaagccaaacattagattgcttggacatgttcagctggcatacaacttgtctacaggtttcacggaaatgggaatgattaggtttattactctcctgttgattgatttgactctcattttgttgattgcctttttaatttaagtaagattttatcagtatggttgtgttcagttttttactgatgtgacggtatccttcatggaaatcttaaatctttaccagaatactgaaactagactttggtcctccttttggttagtttgtaggctttgcttgttctatcaacaaaagtatatttgctaccagtgactgccttctataactgagtaataacttatttccacgcgctggtcacttggttgtctcctttactttaagttcttcctgcaagatttttttagtatttaatttttcttggtttgcaggatacagctggacaagagaagttccatgcactaggccctatatactatcgtgatgcagacggtaatattcgtcttcttgttttgaattaaatatatcgaggtggatcactaaattcttttttatatcttttgatgactgcagctgctcttttagtatatgacatcacagacaatgatacttttcttcgtgtcacaaagtgggtgaaagagcttaagcaaatggcaaataaagatattgttatggccattgcagcaaataaaagtgacctggttagatcaaaacacatagacactaatgaagcagcaaggtattcttctttgttatcagttacaaatactacacagccaaaatatgtaatattgccctggtacttgagttagcaacttagcatcgttagtctttgagtagaacaaaagaaatatatgtgatatatactttatctgttgattaaactatttagatatatcagcatagtttcaacatataatctgcaatccttttatgattgtacagtttcttgaaaatgcgttcttttagttccatatttcctcttctctatctatttcatctaagtaatattgttactacatgtacatctccagctatgcagaaagtattggggcaactctctttgttacttctgccaaagctggtactgggattgatgatatcttcagtgacatagccaagagtaagtcttattgtgttagctattgctttcaattcatctccacatttttgccactttaacaaatactgctttgccaaaacttataagttgtaacattcagctattccattagaatgcggggtcatcaacgatagcatatagtttagttaacaatttcatgtttcactctattgagcagatttcgtttatcaaactcaattgttattcctcagattaatccattgtataacactcaatatttgcgaattccctcttcatctcaataacaaggtgggtatggacccacatgtcattggtatagaatgctgtattcgaagtggctatgttgtatgtagtttgtctagagctattcttgcaatgacataacttgcaataaatggatatgtatgcattcttaatcctactgattttctggacttgtcaccagggaattcaaacactgctaacatggaactatttatttccttttaagctgttgaaaatcgtatgtccctaactgattggtggttttcttaattgctatgccctcactaccgtttgttgtaggattattagagagaagaaaaaacagctccgatggcttgtcactggctcatccaaagaaaggcattttaatcgtcgacgatgaacctgagaaagaacctccaccaaagtgctgctcatagcgagattccaatgcaaatcacgtgggcataatgtcatagaaacctgcaattgatatgtgaaggatcaaatccttgcattaactttgctcatgctcttttggagctcaggagcaatgcaagtgtatactggttgattatttttagcttgtgtaaatactaaactcagttcatgaaattgttgtcaaatatagttgttcgatgatgacgattcgatatgccgaagaagttcatggccctttgtatatctgtaactcacaggttgcttatttactagctgttgttttgagggggttattttgatcatgtgcgtcgaaataattgtgtcgtgttgactgctgagtgtacatgtatcgtggttattccatctgaacctgcaatgtaaagcttccgtcccaattcccaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001061782.1 RefSeq:Os05g0341600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0341600&diff=172375Os05g03416002014-05-25T13:07:24Z<p>HamletShaoE: </p>
<hr />
<div>the rice gene '''Os05g0341600''' was recongized as '''RAB 21''' in 1988, which is induced when plants are subject to water-stress.<br />
==Annotated Information==<br />
===Function===<br />
the rice gene '''Os05g0341600''' was recongized as '''RAB 21''' in 1988, which is induced when plants are subject to water-stress. encoding a basic, glycine-rich protein (mol.wt 16 529) which has a duplicated domain structure. Immunoblots probed with antibodies raised against Bgalactosidase/RAB 21 fusion protein detect RAB 21 protein only in cytosolic cell fractions. <br />
===Expression===<br />
RAB 21 mRNA and protein accumulate in rice embryos, leaves, roots and callus-derived suspension cells upon treatment with NaCl (200 mM) and/or the plant hormone abscisic acid (10 /tMABA). The effects of NaCI and ABA are not cumulative, suggesting that these two inducers share a common response pathway. Induction of RAB 21 mRNA accumulation by ABA is rapid (< 15 min in suspension cells) and does not require protein synthesis, indicating that preformed nuclear and/or cytosolic factors mediate the response to this hormone. We have characterized the RAB 21 gene by deternmining the complete nucleotide sequence of a nearly full-length cDNA and corresponding genomiccopy, and by mapping the start site of its major transcript. The proximal promoter region contains various GC-rich repeats.<br />
<br />
===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Mundy, J. and N.-H. Chua (1988). "Abscisic acid and water-stress induce the expression of a novel rice gene." The EMBO Journal 7(8): 2279.</ref><br />
</references><br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0341600|<br />
Description = Similar to Ras-related protein Rab-21|<br />
Version = NM_001061782.1 GI:115463294 GeneID:4338469|<br />
Length = 4497 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0341600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br />
AP = Chromosome 5:15997018..16001514|<br />
CDS = 15997421..15997539,15998086..15998174,15998470..15998635,15998717..15998777,15999640..15999776<br>,16001320..16001386|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:15997018..16001514<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:15997018..16001514<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgggctcgaagccgccgccgccgccgcagcccagcgtctccttcaagctcgtcctcctcggcgacgggagagtaggcaaaacatctcttgtgctgcggtatgtgaatgatgtcttctcagacaaacaggaagcaactgttcaagcttcatatttgacaaagcgccttgttgttgaaggtgtgcctattacgctctctatctgggatacagctggacaagagaagttccatgcactaggccctatatactatcgtgatgcagacgctgctcttttagtatatgacatcacagacaatgatacttttcttcgtgtcacaaagtgggtgaaagagcttaagcaaatggcaaataaagatattgttatggccattgcagcaaataaaagtgacctggttagatcaaaacacatagacactaatgaagcagcaagctatgcagaaagtattggggcaactctctttgttacttctgccaaagctggtactgggattgatgatatcttcagtgacatagccaagagattattagagagaagaaaaaacagctccgatggcttgtcactggctcatccaaagaaaggcattttaatcgtcgacgatgaacctgagaaagaacctccaccaaagtgctgctcatag</cdnaseq>|<br />
AA = <aaseq>MGSKPPPPPQPSVSFKLVLLGDGRVGKTSLVLRYVNDVFSDKQE ATVQASYLTKRLVVEGVPITLSIWDTAGQEKFHALGPIYYRDADAALLVYDITDNDTF LRVTKWVKELKQMANKDIVMAIAANKSDLVRSKHIDTNEAASYAESIGATLFVTSAKA GTGIDDIFSDIAKRLLERRKNSSDGLSLAHPKKGILIVDDEPEKEPPPKCCS</aaseq>|<br />
DNA = <dnaseqindica>3976..4094#3341..3429#2880..3045#2738..2798#1739..1875#129..195#tcccacacttctcctctctgaccacagcacacacgcaacaccgggacgggcgatccggaaggttctggaaccttctagaggctcgtaggagcctccggcggaacccctctcgcctcgcctcgcctccgatgggctcgaagccgccgccgccgccgcagcccagcgtctccttcaagctcgtcctcctcggcgacggtacggctatctccctctcccttccgatcccgcgaaccctcctcccccccttctcaacccccttttctgccgaattcccgatccttcagtttggggttggcgtgcgcaagaaaatagccacggaatctgggtgaattttggctgctcttgtggtgcgtgctgagccctagctagggttaggggaaagccgcagaatcatttgatctggtaccctgtgtaggtagctaaatctatagcttagacgagggagttgagcggttttgagctaagcttaccttttacttgattgccttcgaggcttagcggagtccaggagatgattagaccgagagggctactcatagaaacaatctaacaagtagaagcatattcgttcttatatagaagatttgtctagtgctagctgcagcggggactgctgcaaattcatgtggacacaaagtggcagctgaagggtggccatggagctggtggcagggaattcgtcttatgcaataggggtggataatatttcattttgatccgtgctctctgtccgcttttaagcttggattgtaatgtccagctgatctagttctatattaattggtggttttacttttcttgtcattaccttaaccaacccttgaaggcagggtcctagaaaaaaaaaattcagtatgactcagctttttggtcatctgtgtatgatgccatgggtcttacccatgttcctctagagaaagtgatgtgtgcctttttggaaaaatgatacagtatgtagtttgggaggagggggttttgatgggaaagtactacagtctttatttgggcatgcttcttagcaagtgcatgtaagtcatacatgggaatgtcaagagaatttttcttgaaaccaggcacgggtgggcattgatctaacatggtacacttgcttttcctagcattgttgaacattgactcattttgatttaggatcagcttacttatagcttagaagcaagcttggaaatcagtttgtgcattgccaaagcggaatcacgtttcatttgaagttggctaatttcaattttggaaaagaaaaaagttggagtagttttgaactgaggcaatgagcacaatgaaagaattttttaccacagtagacagtacttgataagtgatagcgccagcataatcaattgctgaaactctttaaccatgccttagtacttggctttacattttttgaatgaagatatatatgtgtttccatgcataaaagcattgttgatagtcttgtgggcatgtatcttataggttgggtcattagggtttgcttattgttataactttctgtcattgatttcagatttttaatggaagaggtgtttaggctgtcttgtaaccagtcctctgttggcccagcctatcaatgtgaaaactgataaacctaagtttaacttaggatgaattgatcataattatatgctccattttttcaatttcattgaaaagacatgtgattgaatacatttcatatttattaacacaaacaataacttttacttttctcttggcacagggagagtaggcaaaacatctcttgtgctgcggtatgtgaatgatgtcttctcagacaaacaggaagcaactgttcaagcttcatatttgacaaagcgccttgttgttgaaggtgtgcctattacgctctctatctgggtgcgttgtcatctctttgatttgcgataatttgttcaacattttttacctctttcattttctcttatgtcagttgcacacacttgtttgaagtaattgtttactaattttgctgttgggatgatattcaattatggtttcaaatcccacttatatgtgcccttgtatcagaaatcctagtaggagtcagaaaaggtgaaaccaacccaattttgttggattataatacgagattgggaatatttagagatatgtggacttagttcttcattaaaaaaggagtaaatttcatagaactacggatattttgacaaaactatcacagaactacagatttaaggtcaaatttatcccaaaactacagatttaaataaaactgttacatggtttgcttccattatagctaaagtccgagactctgtgtacttgaactcatgaagccaaacattagattgcttggacatgttcagctggcatacaacttgtctacaggtttcacggaaatgggaatgattaggtttattactctcctgttgattgatttgactctcattttgttgattgcctttttaatttaagtaagattttatcagtatggttgtgttcagttttttactgatgtgacggtatccttcatggaaatcttaaatctttaccagaatactgaaactagactttggtcctccttttggttagtttgtaggctttgcttgttctatcaacaaaagtatatttgctaccagtgactgccttctataactgagtaataacttatttccacgcgctggtcacttggttgtctcctttactttaagttcttcctgcaagatttttttagtatttaatttttcttggtttgcaggatacagctggacaagagaagttccatgcactaggccctatatactatcgtgatgcagacggtaatattcgtcttcttgttttgaattaaatatatcgaggtggatcactaaattcttttttatatcttttgatgactgcagctgctcttttagtatatgacatcacagacaatgatacttttcttcgtgtcacaaagtgggtgaaagagcttaagcaaatggcaaataaagatattgttatggccattgcagcaaataaaagtgacctggttagatcaaaacacatagacactaatgaagcagcaaggtattcttctttgttatcagttacaaatactacacagccaaaatatgtaatattgccctggtacttgagttagcaacttagcatcgttagtctttgagtagaacaaaagaaatatatgtgatatatactttatctgttgattaaactatttagatatatcagcatagtttcaacatataatctgcaatccttttatgattgtacagtttcttgaaaatgcgttcttttagttccatatttcctcttctctatctatttcatctaagtaatattgttactacatgtacatctccagctatgcagaaagtattggggcaactctctttgttacttctgccaaagctggtactgggattgatgatatcttcagtgacatagccaagagtaagtcttattgtgttagctattgctttcaattcatctccacatttttgccactttaacaaatactgctttgccaaaacttataagttgtaacattcagctattccattagaatgcggggtcatcaacgatagcatatagtttagttaacaatttcatgtttcactctattgagcagatttcgtttatcaaactcaattgttattcctcagattaatccattgtataacactcaatatttgcgaattccctcttcatctcaataacaaggtgggtatggacccacatgtcattggtatagaatgctgtattcgaagtggctatgttgtatgtagtttgtctagagctattcttgcaatgacataacttgcaataaatggatatgtatgcattcttaatcctactgattttctggacttgtcaccagggaattcaaacactgctaacatggaactatttatttccttttaagctgttgaaaatcgtatgtccctaactgattggtggttttcttaattgctatgccctcactaccgtttgttgtaggattattagagagaagaaaaaacagctccgatggcttgtcactggctcatccaaagaaaggcattttaatcgtcgacgatgaacctgagaaagaacctccaccaaagtgctgctcatagcgagattccaatgcaaatcacgtgggcataatgtcatagaaacctgcaattgatatgtgaaggatcaaatccttgcattaactttgctcatgctcttttggagctcaggagcaatgcaagtgtatactggttgattatttttagcttgtgtaaatactaaactcagttcatgaaattgttgtcaaatatagttgttcgatgatgacgattcgatatgccgaagaagttcatggccctttgtatatctgtaactcacaggttgcttatttactagctgttgttttgagggggttattttgatcatgtgcgtcgaaataattgtgtcgtgttgactgctgagtgtacatgtatcgtggttattccatctgaacctgcaatgtaaagcttccgtcccaattcccaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001061782.1 RefSeq:Os05g0341600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0341600&diff=172374Os05g03416002014-05-25T13:06:52Z<p>HamletShaoE: </p>
<hr />
<div>the rice gene '''Os05g0341600''' was recongized as '''RAB 21''' in 1988, which is induced when plants are subject to water-stress.<br />
==Annotated Information==<br />
===Function===<br />
the rice gene '''Os05g0341600''' was recongized as '''RAB 21''' in 1988, which is induced when plants are subject to water-stress. encoding a basic, glycine-rich protein (mol.wt 16 529) which has a duplicated domain structure. Immunoblots probed with antibodies raised against Bgalactosidase/RAB 21 fusion protein detect RAB 21 protein only in cytosolic cell fractions. <br />
===Expression===<br />
RAB 21 mRNA and protein accumulate in rice embryos, leaves, roots and callus-derived suspension cells upon treatment with NaCl (200 mM) and/or the plant hormone abscisic acid (10 /tMABA). The effects of NaCI and ABA are not cumulative, suggesting that these two inducers share a common response pathway. Induction of RAB 21 mRNA accumulation by ABA is rapid (< 15 min in suspension cells) and does not require protein synthesis, indicating that preformed nuclear and/or cytosolic factors mediate the response to this hormone. We have characterized the RAB 21 gene by deternmining the complete nucleotide sequence of a nearly full-length cDNA and corresponding genomiccopy, and by mapping the start site of its major transcript. The proximal promoter region contains various GC-rich repeats.<br />
<br />
===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC457090/ Mundy, J. and N.-H. Chua (1988). "Abscisic acid and water-stress induce the expression of a novel rice gene." The EMBO Journal 7(8): 2279.]</ref><br />
</references><br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0341600|<br />
Description = Similar to Ras-related protein Rab-21|<br />
Version = NM_001061782.1 GI:115463294 GeneID:4338469|<br />
Length = 4497 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0341600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br />
AP = Chromosome 5:15997018..16001514|<br />
CDS = 15997421..15997539,15998086..15998174,15998470..15998635,15998717..15998777,15999640..15999776<br>,16001320..16001386|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:15997018..16001514<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:15997018..16001514<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgggctcgaagccgccgccgccgccgcagcccagcgtctccttcaagctcgtcctcctcggcgacgggagagtaggcaaaacatctcttgtgctgcggtatgtgaatgatgtcttctcagacaaacaggaagcaactgttcaagcttcatatttgacaaagcgccttgttgttgaaggtgtgcctattacgctctctatctgggatacagctggacaagagaagttccatgcactaggccctatatactatcgtgatgcagacgctgctcttttagtatatgacatcacagacaatgatacttttcttcgtgtcacaaagtgggtgaaagagcttaagcaaatggcaaataaagatattgttatggccattgcagcaaataaaagtgacctggttagatcaaaacacatagacactaatgaagcagcaagctatgcagaaagtattggggcaactctctttgttacttctgccaaagctggtactgggattgatgatatcttcagtgacatagccaagagattattagagagaagaaaaaacagctccgatggcttgtcactggctcatccaaagaaaggcattttaatcgtcgacgatgaacctgagaaagaacctccaccaaagtgctgctcatag</cdnaseq>|<br />
AA = <aaseq>MGSKPPPPPQPSVSFKLVLLGDGRVGKTSLVLRYVNDVFSDKQE ATVQASYLTKRLVVEGVPITLSIWDTAGQEKFHALGPIYYRDADAALLVYDITDNDTF LRVTKWVKELKQMANKDIVMAIAANKSDLVRSKHIDTNEAASYAESIGATLFVTSAKA GTGIDDIFSDIAKRLLERRKNSSDGLSLAHPKKGILIVDDEPEKEPPPKCCS</aaseq>|<br />
DNA = <dnaseqindica>3976..4094#3341..3429#2880..3045#2738..2798#1739..1875#129..195#tcccacacttctcctctctgaccacagcacacacgcaacaccgggacgggcgatccggaaggttctggaaccttctagaggctcgtaggagcctccggcggaacccctctcgcctcgcctcgcctccgatgggctcgaagccgccgccgccgccgcagcccagcgtctccttcaagctcgtcctcctcggcgacggtacggctatctccctctcccttccgatcccgcgaaccctcctcccccccttctcaacccccttttctgccgaattcccgatccttcagtttggggttggcgtgcgcaagaaaatagccacggaatctgggtgaattttggctgctcttgtggtgcgtgctgagccctagctagggttaggggaaagccgcagaatcatttgatctggtaccctgtgtaggtagctaaatctatagcttagacgagggagttgagcggttttgagctaagcttaccttttacttgattgccttcgaggcttagcggagtccaggagatgattagaccgagagggctactcatagaaacaatctaacaagtagaagcatattcgttcttatatagaagatttgtctagtgctagctgcagcggggactgctgcaaattcatgtggacacaaagtggcagctgaagggtggccatggagctggtggcagggaattcgtcttatgcaataggggtggataatatttcattttgatccgtgctctctgtccgcttttaagcttggattgtaatgtccagctgatctagttctatattaattggtggttttacttttcttgtcattaccttaaccaacccttgaaggcagggtcctagaaaaaaaaaattcagtatgactcagctttttggtcatctgtgtatgatgccatgggtcttacccatgttcctctagagaaagtgatgtgtgcctttttggaaaaatgatacagtatgtagtttgggaggagggggttttgatgggaaagtactacagtctttatttgggcatgcttcttagcaagtgcatgtaagtcatacatgggaatgtcaagagaatttttcttgaaaccaggcacgggtgggcattgatctaacatggtacacttgcttttcctagcattgttgaacattgactcattttgatttaggatcagcttacttatagcttagaagcaagcttggaaatcagtttgtgcattgccaaagcggaatcacgtttcatttgaagttggctaatttcaattttggaaaagaaaaaagttggagtagttttgaactgaggcaatgagcacaatgaaagaattttttaccacagtagacagtacttgataagtgatagcgccagcataatcaattgctgaaactctttaaccatgccttagtacttggctttacattttttgaatgaagatatatatgtgtttccatgcataaaagcattgttgatagtcttgtgggcatgtatcttataggttgggtcattagggtttgcttattgttataactttctgtcattgatttcagatttttaatggaagaggtgtttaggctgtcttgtaaccagtcctctgttggcccagcctatcaatgtgaaaactgataaacctaagtttaacttaggatgaattgatcataattatatgctccattttttcaatttcattgaaaagacatgtgattgaatacatttcatatttattaacacaaacaataacttttacttttctcttggcacagggagagtaggcaaaacatctcttgtgctgcggtatgtgaatgatgtcttctcagacaaacaggaagcaactgttcaagcttcatatttgacaaagcgccttgttgttgaaggtgtgcctattacgctctctatctgggtgcgttgtcatctctttgatttgcgataatttgttcaacattttttacctctttcattttctcttatgtcagttgcacacacttgtttgaagtaattgtttactaattttgctgttgggatgatattcaattatggtttcaaatcccacttatatgtgcccttgtatcagaaatcctagtaggagtcagaaaaggtgaaaccaacccaattttgttggattataatacgagattgggaatatttagagatatgtggacttagttcttcattaaaaaaggagtaaatttcatagaactacggatattttgacaaaactatcacagaactacagatttaaggtcaaatttatcccaaaactacagatttaaataaaactgttacatggtttgcttccattatagctaaagtccgagactctgtgtacttgaactcatgaagccaaacattagattgcttggacatgttcagctggcatacaacttgtctacaggtttcacggaaatgggaatgattaggtttattactctcctgttgattgatttgactctcattttgttgattgcctttttaatttaagtaagattttatcagtatggttgtgttcagttttttactgatgtgacggtatccttcatggaaatcttaaatctttaccagaatactgaaactagactttggtcctccttttggttagtttgtaggctttgcttgttctatcaacaaaagtatatttgctaccagtgactgccttctataactgagtaataacttatttccacgcgctggtcacttggttgtctcctttactttaagttcttcctgcaagatttttttagtatttaatttttcttggtttgcaggatacagctggacaagagaagttccatgcactaggccctatatactatcgtgatgcagacggtaatattcgtcttcttgttttgaattaaatatatcgaggtggatcactaaattcttttttatatcttttgatgactgcagctgctcttttagtatatgacatcacagacaatgatacttttcttcgtgtcacaaagtgggtgaaagagcttaagcaaatggcaaataaagatattgttatggccattgcagcaaataaaagtgacctggttagatcaaaacacatagacactaatgaagcagcaaggtattcttctttgttatcagttacaaatactacacagccaaaatatgtaatattgccctggtacttgagttagcaacttagcatcgttagtctttgagtagaacaaaagaaatatatgtgatatatactttatctgttgattaaactatttagatatatcagcatagtttcaacatataatctgcaatccttttatgattgtacagtttcttgaaaatgcgttcttttagttccatatttcctcttctctatctatttcatctaagtaatattgttactacatgtacatctccagctatgcagaaagtattggggcaactctctttgttacttctgccaaagctggtactgggattgatgatatcttcagtgacatagccaagagtaagtcttattgtgttagctattgctttcaattcatctccacatttttgccactttaacaaatactgctttgccaaaacttataagttgtaacattcagctattccattagaatgcggggtcatcaacgatagcatatagtttagttaacaatttcatgtttcactctattgagcagatttcgtttatcaaactcaattgttattcctcagattaatccattgtataacactcaatatttgcgaattccctcttcatctcaataacaaggtgggtatggacccacatgtcattggtatagaatgctgtattcgaagtggctatgttgtatgtagtttgtctagagctattcttgcaatgacataacttgcaataaatggatatgtatgcattcttaatcctactgattttctggacttgtcaccagggaattcaaacactgctaacatggaactatttatttccttttaagctgttgaaaatcgtatgtccctaactgattggtggttttcttaattgctatgccctcactaccgtttgttgtaggattattagagagaagaaaaaacagctccgatggcttgtcactggctcatccaaagaaaggcattttaatcgtcgacgatgaacctgagaaagaacctccaccaaagtgctgctcatagcgagattccaatgcaaatcacgtgggcataatgtcatagaaacctgcaattgatatgtgaaggatcaaatccttgcattaactttgctcatgctcttttggagctcaggagcaatgcaagtgtatactggttgattatttttagcttgtgtaaatactaaactcagttcatgaaattgttgtcaaatatagttgttcgatgatgacgattcgatatgccgaagaagttcatggccctttgtatatctgtaactcacaggttgcttatttactagctgttgttttgagggggttattttgatcatgtgcgtcgaaataattgtgtcgtgttgactgctgagtgtacatgtatcgtggttattccatctgaacctgcaatgtaaagcttccgtcccaattcccaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001061782.1 RefSeq:Os05g0341600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>HamletShaoEhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0883800&diff=169992Os01g08838002014-05-20T08:12:39Z<p>HamletShaoE: /* Function */ -- adding GO links</p>
<hr />
<div>The rice ''semidwarf-1 (sd1)'' gene is well known as the "green revolution gene" and controls the plant height of rice.<br />
<br />
== Annotated Information ==<br />
=== Function ===<br />
[[File:Example.jpg|right|thumb|150px|''Semidwarf VS. normal-type rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
<br />
This gene is originally derived from the Chinese cultivar Dee-Geo-Woo-Gen (DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2). SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected <ref name="ref1" />. It is not surprising that a rice semidwarfing gene encodes GA20-ox since successful production of semidwarf plants using antisense or overexpressed GA20-ox genes has been reported in Arabidopsis, Solanum dulcamara, potato, and lettuce <ref name="ref3" />.<br />
It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and reduced amount of G20<ref name="ref3" />. However, there is slight difference between different strains. The extent of GA1 is lower in Doongara (semi-dwarf rice strain) when compared with Kyeema (tall), while there is no significant difference between Calrose76 (semi-dwarf rice strain) and Calrose (tall). Calrose76 has lower contents of GA44 and of GA19 than Calrose, while there is no significant difference between Doongara (semi-dwarf rice strain) and Kyeema (tall) <ref name="ref2" />.<br />
<br />
'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0005506 GO:0005506], [http://amigo.geneontology.org/amigo/term/GO:0016216 GO:0016216], [http://amigo.geneontology.org/amigo/term/GO:0017000 GO:0017000]<br />
<br />
=== Mutation ===<br />
'Dee-Geo-Woo-Gen' (semi-dwarf rice strain): A 383-base-pair deletion from the genome (A 280-bp deletion within the coding region), which induces a frameshift that creates a stop codon in SD1, may be related with the semi-dwarf phenotype <ref name="ref1" /><ref name="ref2" />.<br />
<br />
Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 <ref name="ref2" />.<br />
<br />
It has been found that introgression of a chromosomal block containing the SD1 allele from tropical japonica is associated with a change in growth patterns in BHA1 (one weedy rice population) <ref name="ref7" />.<br />
<br />
=== Expression ===<br />
This gene is strongly expressed in the leaf blade, stem and unopened flower, whereas GA20ox-1 is predominantly expressed in the unopened flower <ref name="ref1" />. <br />
<br />
Among the DGWG-type sd-1 mutants, IR24 and Habataki have little transcript of this gene, while Milyang 23 expresses a normal or greater amount of truncated transcript. No significant difference is observed between Calrose and its single-nucleotide-substitution mutant Calrose 76 <ref name="ref3" />.<br />
<br />
Analysis of the tissue- and stage-specificity of transcription of sd1 in Nipponbare revealed that this<br />
gene was expressed within 48 hr after sowing, as well as in 10-day-old plants, 30-day-old leaves, and flowering panicles; no transcription is detected in 24-hr-old seedlings or in 14-day-old roots. Transcript accumulates predominantly in adult leaves <ref name="ref3" />.<br />
<br />
{| class='wikitable' style="text-align:center"<br />
|-<br />
! | Primer<br />
! | Forward primer<br />
! | Reverse primer<br />
|-<br />
| rowspan="3"|Gene amplication<br />
| | 5'-CAACTCACTCCCGCTCAACACAGC-3'<br />
| | 5'-TTTGAAATGCAATGTCGTCCACC-3' (used to amplify exon 1 <ref name="ref2" />)<br />
|-<br />
| | 5'-GCGCCAATGGGGTAATTAAAACG-3'<br />
| | 5'-GGCATTCCATTGTTTGTGATTGG-3' (used to amplify exon 2 <ref name="ref2" />)<br />
|-<br />
| | 5'-GTTTGTCCTTGTCGCGTTGCTCAG-3'<br />
| | 5'-TCTGTTCGTTCCGTTTCGTTCCG-3' (used to amplify exon 3 <ref name="ref2" />)<br />
|-<br />
| rowspan="2"|RT-PCR<br />
| | 5'-CAACTCACTCCCGCTCAACACAGC-3'<br />
| | 5'-GTTCGTTCCGTTTCGGTTCCG-3' <ref name="ref3" /><br />
|-<br />
| | 5'-AGCTGGACATGCCCGTGGTC-3'<br />
| | 5'-TTGAGCTGCTGTCCGCGAAG-3' <ref name="ref3" /><br />
|}<br />
<br />
=== Evolution ===<br />
This gene is conserved in ''Arabidopsis'' (47% identity) and pea (50% identity). GA20ox-2 shows 47.8% identity to<br />
GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis <ref name="ref1" /><ref name="ref2" />.<br />
<br />
=== Knowledge Extension ===<br />
<br />
[[File:Gibberellin SD1 RHT Signal.PNG|right|thumb|500px|''Gibberellin signalling pathway (from reference <ref name="ref4" />).'']]<br />
<br />
Except ''sd1'', another ‘green revolution’ gene named ''Rht1'', which encodes a GA signal suppressor DELLA protein. The deletion in the N-terminal region of the native RHT1 constitutively suppresses GA signaling, consequently resulting in a dominant semi-dwarf phenotype <ref name="ref5" />. Both sd1 and Rht1 are associated with GA pathway, indicating the importance of GA in the regulation of developmental processes and making it a prime target for improving crop yield <ref name="ref4" />. <br />
<br />
The wheat green-revolution gene Rht (for ‘reduced height’) <ref name="ref5" /> is a gain-of-function allele caused by a mutation in a transcription factor that is associated with the gibberellin signalling pathway. As wheat has a hexaploid genome, it does not contain recessive alleles such as ''sd1'' in rice that might otherwise be used to produce a semi-dwarf strain of wheat. Although the genetic and biochemical functions of the rice SD1 and wheat RHT proteins are completely different (that is, recessive versus dominant, loss-of-function versus gain-offunction events, enzyme versus transcription factor, respectively), the products of both genes are linked with gibberellin malfunction <ref name="ref1" />.<br />
<br />
In rice, ''Slr1'' gene encodes the DELLA protein. Three semi-dominant dwarf mutants (''Slr1-d1'', ''Slr1-d2'' and ''Slr1-d3'') associated with this gene have been identified, which were caused by gain-of-function mutations in the N-terminal region of SLR1. These three mutants are responsive to GA at a reduced rate, with later SLRl degradation, and showing reduced interaction activity with GID1 (GA receptor) comparing with wild type rice <ref name="ref6" />.<br />
<br />
== Labs working on this gene ==<br />
*Bioscience Center, and Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan<br />
*Honda R&D, Wako Research Center, Wako 351-0193, Japan<br />
*International Rice Research Institute, Manila, DAPO Box 7777, Philippines<br />
*BioResources Center, and Plant Molecular Biology Laboratory, Riken, Tsukuba 305-0074, Japan<br />
*Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, GPO Box 1600, Canberra ACT 2601, Australia<br />
*Plant Genome Center, 1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan<br />
<br />
== References ==<br />
<references><br />
<ref name="ref1">Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.</ref><br />
<ref name="ref2">Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.</ref><br />
<ref name="ref3">Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, et al. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9: 11-17.</ref><br />
<ref name="ref4">Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.</ref><br />
<ref name="ref5">Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.</ref><br />
<ref name="ref6">Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, et al. (2009) Isolation and characterization of dominant dwarf mutants, ''Slr1-d'', in rice. Mol Genet Genomics 281: 223-231.</ref><br />
<ref name="ref7">Reagon M, Thurber CS, Olsen KM, Jia Y, Caicedo AL (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Mol Ecol 20: 3743-3756.</ref><br />
</references><br />
<br />
== Structured Information ==<br />
{{JaponicaGene|<br />
GeneName = Os01g0883800|<br />
Description = Gibberellin 20 oxidase 2 (EC 1.14.11.-) (Gibberellin C-20 oxidase 2) (GA 20-oxidase 2) (Os20ox2) (Semidwarf-1 protein)|<br />
Version = NM_001051549.1 GI:115441468 GeneID:4325003|<br />
Length = 2743 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0883800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:40138313..40141055|<br />
CDS = 40138313..40138869,40138972..40139293,40140765..40141055|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:40138313..40141055<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:40138313..40141055<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtggccgagcaccccacgccaccacagccgcaccaaccaccgcccatggactccaccgccggctctggcattgccgccccggcggcggcggcggtgtgcgacctgaggatggagcccaagatcccggagccattcgtgtggccgaacggcgacgcgaggccggcgtcggcggcggagctggacatgcccgtggtcgacgtgggcgtgctccgcgacggcgacgccgaggggctgcgccgcgccgcggcgcaggtggccgccgcgtgcgccacgcacgggttcttccaggtgtccgagcacggcgtcgacgccgctctggcgcgcgccgcgctcgacggcgccagcgacttcttccgcctcccgctcgccgagaagcgccgcgcgcgccgcgtcccgggcaccgtgtccggctacaccagcgcccacgccgaccgcttcgcctccaagctcccatggaaggagaccctctccttcggcttccacgaccgcgccgccgcccccgtcgtcgccgactacttctccagcaccctcggccccgacttcgcgccaatggggagggtgtaccagaagtactgcgaggagatgaaggagctgtcgctgacgatcatggaactcctggagctgagcctgggcgtggagcgaggctactacagggagttcttcgcggacagcagctcaatcatgcggtgcaactactacccgccatgcccggagccggagcggacgctcggcacgggcccgcactgcgaccccaccgccctcaccatcctcctccaggacgacgtcggcggcctcgaggtcctcgtcgacggcgaatggcgccccgtcagccccgtccccggcgccatggtcatcaacatcggcgacaccttcatggcgctgtcgaacgggaggtataagagctgcctgcacagggcggtggtgaaccagcggcgggagcggcggtcgctggcgttcttcctgtgcccgcgggaggacagggtggtgcggccgccgccgagcgccgccacgccgcagcactacccggacttcacctgggccgacctcatgcgcttcacgcagcgccactaccgcgccgacacccgcacgctcgacgccttcacgcgctggctcgcgccgccggccgccgacgccgccgcgacggcgcaggtcgaggcggccagctga</cdnaseq>|<br />
AA = <aaseq>MVAEHPTPPQPHQPPPMDSTAGSGIAAPAAAAVCDLRMEPKIPE PFVWPNGDARPASAAELDMPVVDVGVLRDGDAEGLRRAAAQVAAACATHGFFQVSEHG VDAALARAALDGASDFFRLPLAEKRRARRVPGTVSGYTSAHADRFASKLPWKETLSFG FHDRAAAPVVADYFSSTLGPDFAPMGRVYQKYCEEMKELSLTIMELLELSLGVERGYY REFFADSSSIMRCNYYPPCPEPERTLGTGPHCDPTALTILLQDDVGGLEVLVDGEWRP VSPVPGAMVINIGDTFMALSNGRYKSCLHRAVVNQRRERRSLAFFLCPREDRVVRPPP SAATPQHYPDFTWADLMRFTQRHYRADTRTLDAFTRWLAPPAADAAATAQVEAAS</aaseq>|<br />
DNA = <dnaseqindica>1..557#660..981#2453..2743#atggtggccgagcaccccacgccaccacagccgcaccaaccaccgcccatggactccaccgccggctctggcattgccgccccggcggcggcggcggtgtgcgacctgaggatggagcccaagatcccggagccattcgtgtggccgaacggcgacgcgaggccggcgtcggcggcggagctggacatgcccgtggtcgacgtgggcgtgctccgcgacggcgacgccgaggggctgcgccgcgccgcggcgcaggtggccgccgcgtgcgccacgcacgggttcttccaggtgtccgagcacggcgtcgacgccgctctggcgcgcgccgcgctcgacggcgccagcgacttcttccgcctcccgctcgccgagaagcgccgcgcgcgccgcgtcccgggcaccgtgtccggctacaccagcgcccacgccgaccgcttcgcctccaagctcccatggaaggagaccctctccttcggcttccacgaccgcgccgccgcccccgtcgtcgccgactacttctccagcaccctcggccccgacttcgcgccaatggggtaattaaaacgatggtggacgacattgcatttcaaattcaaaacaaattcaaaacacaccgaccgagattatgctgaattcaaacgcgtttgtgcgcgcaggagggtgtaccagaagtactgcgaggagatgaaggagctgtcgctgacgatcatggaactcctggagctgagcctgggcgtggagcgaggctactacagggagttcttcgcggacagcagctcaatcatgcggtgcaactactacccgccatgcccggagccggagcggacgctcggcacgggcccgcactgcgaccccaccgccctcaccatcctcctccaggacgacgtcggcggcctcgaggtcctcgtcgacggcgaatggcgccccgtcagccccgtccccggcgccatggtcatcaacatcggcgacaccttcatggtaaaccatctcctattctcctctcctctgttctcctctgcttcgaagcaacagaacaagtaattcaagcttttttttctctctcgcgcgaaattgacgagaaaaataagatcgtggtaggggcggggctttcagctgaaagcgggaagaaaccgacctgacgtgatttctctgttccaatcacaaacaatggaatgccccactcctccatgtgttatgatttatctcacatcttatagttaataggagtaagtaacaagctacttttttcatattatagttcgtttgattttttttttttaaagtttttttagttttatccaaatttattgaaaaacttagcaacgtttataataccaaattagtctcatttagtttaatattgtatatattttgataatatatttatgttatattaaaaatattactatatttttctataaacattattaaaagccatttataatataaaatggaaggagtaattaatatggatctcccccgacatgagaatattttccgatggtgtgacgacgccatgtaagcttcggtgggcctggacggccagaggtgccaacagccacgtccaacaacccctgggtccccccctaacactccaaacagtagtgagtagtgtctcgtcgcgttttagtatttgatgacaaacaaagtgtgagttgagttagccaccaccaacttgcacacgagcacatacatttgtgtccattctcgccagtcacttccatctctagtcctaactcctatctagcgatgtaagcggataatttcatcatccgtatataaacctgtttgttatagttaatttcctatataatactataacagtatacattttaaaagaaaacaaaattaggataaacaggccctgctcctatccatccatggcacttggaaggaccagactcggtcatgccatgccaagccaagatatgggttatggaagagtagagaagaggagagatgagagataagcatgcgttctcctcctcgttggatgtgtattttggagggatttgtgtagtagtagcagcggcgccgcggggacggatgcggatggtggcgctttcggtggcgttttcccgggggggttttggtttggcgcttgggggggatggcatggcgcggcgtgcggctgcacgccacacacacgcgcgcgcacgcacgtacgtcgtcgtcgccgcgggcggacggtagcttagggtggtgtgttccgcgcgcgggcgcggattgttccatgccgatcgatttggcgccaccctcgccgcggctcttgtcgcgtcgtgcgcctctctcgcgcggtttgtccttgtcgcgttgctcagccggcgacgggggcacggacattggcgatgtagccctgcacgtgtcggcctctccgttgatgaatgatgatgtatgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcaggcgctgtcgaacgggaggtataagagctgcctgcacagggcggtggtgaaccagcggcgggagcggcggtcgctggcgttcttcctgtgcccgcgggaggacagggtggtgcggccgccgccgagcgccgccacgccgcagcactacccggacttcacctgggccgacctcatgcgcttcacgcagcgccactaccgcgccgacacccgcacgctcgacgccttcacgcgctggctcgcgccgccggccgccgacgccgccgcgacggcgcaggtcgaggcggccagctga</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001051549.1 RefSeq:Os01g0883800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>HamletShaoE