Os07g0563300 - Revision history

Xysj2012: /* Structured Information */

2015-06-12T08:45:59Z

‎Structured Information

Shijc at 16:21, 1 June 2014

2014-06-01T16:21:59Z

Shijc at 03:25, 31 May 2014

2014-05-31T03:25:40Z

Shijc at 03:22, 31 May 2014

2014-05-31T03:22:51Z

Shijc at 03:17, 31 May 2014

2014-05-31T03:17:04Z

Shijc at 03:13, 31 May 2014

2014-05-31T03:13:21Z

124.16.129.48 at 20:38, 22 July 2012

2012-07-22T20:38:24Z

127.0.0.1: Created page with "{{JaponicaGene| GeneName = Os07g0563300| Description = The start codon is not identified.| Version = NM_001066530.2 GI:297607459 GeneID:4343608| Length = 3190 bp| Definit..."

2012-06-24T08:41:51Z

Created page with "{{JaponicaGene| GeneName = Os07g0563300| Description = The start codon is not identified.| Version = NM_001066530.2 GI:297607459 GeneID:4343608| Length = 3190 bp| Definit..."

New page

{{JaponicaGene|
GeneName = Os07g0563300|
Description = The start codon is not identified.|
Version = NM_001066530.2 GI:297607459 GeneID:4343608|
Length = 3190 bp|
Definition = Oryza sativa Japonica Group Os07g0563300, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|
AP = Chromosome 7:23199693..23202882|
CDS = 23199693..23199764,23199991..23200040,23200390..23200503,23201052..23201119,23201879..23202438<br>|
GCID = <gbrowseImage1>
name=NC_008400:23199693..23202882
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:23199693..23202882
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>gaattacttcgtcctcctcctaaggccccttcaattgttgttgttgatggccatgagtttgaggaatatgaggagccaccaatacttgggaggaggacatattttgtgacagaccaatcaggtgagaatcatcaatgggctcaatgtgaggattgctctaagtggcgtaaactgccggtggacgcccttttgccctctaagtggacctgctctgacaataaatgggattctgaaaggtcttcctgtgattctgcccaagagataaatatggaggagcttggcgaaatgattcctatcaaacctggtgctgcaaaaaagaccaaagggaaggtagatactgacaatattgatgtttcagatgggctggacacactcgcaaatcttgcaattcttggtgaaggtgaatctctcccttcccagccaaccacaaggcatccccgccatcgccctggctgctcatgcatagtctgcatacaaccacccagcggaaagggaccaaagcacaaacagacgtgcacttgcaacgtctgtatgacagtgcgacgccgtttcaggacgcttatgatgcggcgcgagaagcgccagcagtcagagaaggactctggggtgcctcgcaaaagagagccaggtcaatccagcgagccagttccacaatctggctctggtgctcatccaaccagtactagctctcctcaccagagagcagataccaacggcgaaggtcctgaagacatgtccattgacaacaagaggacctcctctcctgtcaagaaccagattgacctgaacagtcagcctgagcgggaagacgagcagtcaccgaaatccgatgcgacgagactcctcagggacaacccaacctag</cdnaseq>|
AA = <aaseq>ELLRPPPKAPSIVVVDGHEFEEYEEPPILGRRTYFVTDQSGENH QWAQCEDCSKWRKLPVDALLPSKWTCSDNKWDSERSSCDSAQEINMEELGEMIPIKPG AAKKTKGKVDTDNIDVSDGLDTLANLAILGEGESLPSQPTTRHPRHRPGCSCIVCIQP PSGKGPKHKQTCTCNVCMTVRRRFRTLMMRREKRQQSEKDSGVPRKREPGQSSEPVPQ SGSGAHPTSTSSPHQRADTNGEGPEDMSIDNKRTSSPVKNQIDLNSQPEREDEQSPKS DATRLLRDNPT</aaseq>|
DNA = <dnaseqindica>1..72#299..348#698..811#1360..1427#2187..2746#gaattacttcgtcctcctcctaaggccccttcaattgttgttgttgatggccatgagtttgaggaatatgaggtatgctgtgcattttattatttcttttagcattcagatcttggctagtgggcacaggcctgcaaacttgagccctattcagctgttcaatgttatgggacaattactatctgagacatagtttggagcatgcttaagcttatttgcattcgtgacttgctttactgtgttcttggtatagaagattaaacacatatcttctatattgacgtcctataattttcaggagccaccaatacttgggaggaggacatattttgtgacagaccaatcagggtaatgctcttagctttgctatctgcatttgttatatatgtggaaaaggacccagacagaccattccagttctttctttttagtaacatttatctcaacactttttctcataatgcttaacttatctagctaccttaattttttatgtgttttttttcaatgttttggaaacttttaattgttgaaaccattaatggtctatctgaatagaattatcctattggtgcatgatgagacgacaatataaattctcttgacttccatttgtaggactcccaacagtttactttttggaaagtacagtagcatcttttttacttgcttacaaatgatcatcattttttaccagtgagaatcatcaatgggctcaatgtgaggattgctctaagtggcgtaaactgccggtggacgcccttttgccctctaagtggacctgctctgacaataaatgggattctgaaaggtgacctgctattttagaaccattcagccttttgtatgctgtatttatgattagctacaatagaaaaacgtatttacaaatgttctaggtagggatgcaagtgggctgacccgtgaacccacatataggtcaaataagtgggtaacccgtaggttcccgtgtcatggcccagcttgccacacctagggctgcaagtgggttgaccagtgaacccactgggttacccactaatttggcctataatagggttcgcgggttggtccacttgcatcctaagttcaaggatagctcttagggttatgcttatggttcttttttgttaccgaatttcaattctattaaccctatttccacccatcagttctttataaatattgcaatcacgaagtttgagctgtctgtttcttaaatctacggtggaatttagcatgtttgaacacaagaatagcttttttttttctttctgttcacgtgtggttggtaggatggtgggatagtctcaatttactttacacacgtagctaataaccaccactacttatcactaggtcttcctgtgattctgcccaagagataaatatggaggagcttggcgaaatgattcctatcaaacctggtatgtatatgttctagtgatttatctatgctgatgtagaagctccatttctgctagtagttctttttaaatagcatgccaaatatgaattccaaaaggataataaattggagaggttcactacgaacaattggctgtatagaactatgtgctactgtgctacatgccagagcctacaaaagtacatcctgaggcatgtaaggctggttgatatctatcactactgatggctggatgtcacaatgaagcatcatagtattagtacatgttatagttggcaatgggccgaactacaaaaacgacttgccatgatccagcctgaggcatgtaaggctggttgatatctatcactactgatggctggattcacaatgaagcattggcaatgggccgaactacaaaaacgacttgccatgatccagcctgaggcatgtaaggctggttgatatctatcactactgatggctggattcacaatgaagcatcatagtattagtacatgatatagttggcaatgggccgaactacaaaaacgacttgccatgatccactgtgttgagaatgccatcttgaaccaacacatccccaatgttactttggggctacatatttctatctgtggtaccagtatgaaagtagtcaatgtttgcataatgccactatattttctttgctgtgtggtaggctataactgcactaaatgatctactataattactgttctagcatttacttaaaattcatgttgttgcatttcaggtgctgcaaaaaagaccaaagggaaggtagatactgacaatattgatgtttcagatgggctggacacactcgcaaatcttgcaattcttggtgaaggtgaatctctcccttcccagccaaccacaaggcatccccgccatcgccctggctgctcatgcatagtctgcatacaaccacccagcggaaagggaccaaagcacaaacagacgtgcacttgcaacgtctgtatgacagtgcgacgccgtttcaggacgcttatgatgcggcgcgagaagcgccagcagtcagagaaggactctggggtgcctcgcaaaagagagccaggtcaatccagcgagccagttccacaatctggctctggtgctcatccaaccagtactagctctcctcaccagagagcagataccaacggcgaaggtcctgaagacatgtccattgacaacaagaggacctcctctcctgtcaagaaccagattgacctgaacagtcagcctgagcgggaagacgagcagtcaccgaaatccgatgcgacgagactcctcagggacaacccaacctagggctgcctgcccaaaagggaagtcatactggcgatggtagataaccgatgaaaaagataatgtctataccaatggagaaatgcggcgggcggatttgtagtgtagctctgtagatgttacctttctataccaaagatctagtttatcctgtggcgggagagatccagttttaatgttatcataccatagaaccaggcgtcggtgttgtagtagaacccgttgctgtttgcctagggcccgttgctttaccctgtatgtagtgatgtagcgtgagagcggcgcccttcggcagcatgtacctctgggcaaatttatttcatgtaccggatcatccatccctgtgcaaggagaggatttactatgttgcttaccggggtggtttccctttggcattatagcatgcattcatatctatagtgtgatctgacgtgataatgtttacca</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001066530.2 RefSeq:Os07g0563300]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

@@ Line 60: / Line 60: @@
 <ref name="ref7"> Curaba, J., Moritz, T., Blervaque, R., Parcy, F., Raz, V., Herzog, M. and Vachon, G. (2004) AtGA3ox2, a key gene responsible for bioactive gib- berellin biosynthesis, is regulated during embryogenesis by LEAFY COTYLEDON2 and FUSCA3 in Arabidopsis. Plant Physiol. 136, 3660 - 3669. </ref>
 <ref name="ref8"> Gazzarrini, S., Tsuchiya, Y., Lumba, S., Okamoto, M. and McCourt, P. (2004) The transcription factor FUSCA3 controls developmental timing in Ara- bidopsis through the hormones gibberellin and abscisic acid. Dev. Cell, 7, 373 -385. </ref>
 ==Structured Information==

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===Function===
-[[File:Shijc-Fig3.jpg|right|thumb|300px|''Proposed model for GD1-regulated GA homeostasis. (from reference <ref name="ref2" />).'']]
+[[File:Shijc-Fig3.jpg|right|thumb|150px|''Proposed model for GD1-regulated GA homeostasis. (from reference <ref name="ref2" />).'']]
 GD1 encodes a B3 domain-containing protein that shares high similarity with VAL proteins in Arabidopsis which are critical determinants in seed and vegetative development <ref name="ref1" />. The EAR motif in the C - terminus of GD1 functions as an active repression domain, suggesting that GD1 is involved in seed germination and seedling development by negatively regulating target gene expression. The molecular mechanisms controlling the embryo pathway are probably conserved between monocot and dicot species, at least to some extent. Like other B3 factors, GD1 binds to the RY element through the B3 domain. <ref name="ref2" />
@@ Line 9: / Line 11: @@
 ===mutation===
-[[File:Shijc-Fig4.jpg|right|thumb|300px|''Genomic DNA fragment used for complementation. (from reference <ref name="ref2" />).'']]
+[[File:Shijc-Fig4.jpg|right|thumb|200px|''Genomic DNA fragment used for complementation. (from reference <ref name="ref2" />).'']]
 the T-DNA insertion is responsible for the mutant ''gd1''. A 13 kb genomic fragment containing the entire 7246 bp GD1 coding region, a 4614 bp upstream region and a 1092 bp downstream sequence was cloned into binary vector pCAMBIA1300 and transformed into calli derived from the heterozygous seeds. The individual transformants were conﬁrmed by PCR using primers P1, P2 and P3.
@@ Line 29: / Line 31: @@
 ===Expression===
 The highest expression level of GD1 was detected in leaf blades and ﬂowers, whereas the expression level was relatively low in young shoots, leaf sheaths, roots and stems. We next examined the expression patterns of GD1 under ABA and GA treatments. The transcript of GD1 in leaves showed a slight increase upon ABA treatment, but the expression of GD1 was increased twofold 6 h after GA treatment. GD1 expression was strongly up-regulated by sucrose after 1 and 6 h. <ref name="ref2" />

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===Function===
-[[File:Shijc-Fig3.jpg|right|thumb|300px|''Diagram of alcoholic fermentation pathway in plants. (from reference <ref name="ref13" />).'']]
+[[File:Shijc-Fig3.jpg|right|thumb|300px|''Proposed model for GD1-regulated GA homeostasis. (from reference <ref name="ref2" />).'']]
 GD1 encodes a B3 domain-containing protein that shares high similarity with VAL proteins in Arabidopsis which are critical determinants in seed and vegetative development <ref name="ref1" />. The EAR motif in the C - terminus of GD1 functions as an active repression domain, suggesting that GD1 is involved in seed germination and seedling development by negatively regulating target gene expression. The molecular mechanisms controlling the embryo pathway are probably conserved between monocot and dicot species, at least to some extent. Like other B3 factors, GD1 binds to the RY element through the B3 domain. <ref name="ref2" />
@@ Line 9: / Line 9: @@
 ===mutation===
-[[File:Shijc-Fig4.jpg|right|thumb|300px|''Diagram of alcoholic fermentation pathway in plants. (from reference <ref name="ref13" />).'']]
+[[File:Shijc-Fig4.jpg|right|thumb|300px|''Genomic DNA fragment used for complementation. (from reference <ref name="ref2" />).'']]
-the T-DNA insertion is responsible for the mutant ‘’gd1’’. A 13 kb genomic fragment containing the entire 7246 bp GD1 coding region, a 4614 bp upstream region and a 1092 bp downstream sequence was cloned into binary vector pCAMBIA1300 and transformed into calli derived from the heterozygous seeds. The individual transformants were conﬁrmed by PCR using primers P1, P2 and P3.
+the T-DNA insertion is responsible for the mutant ''gd1''. A 13 kb genomic fragment containing the entire 7246 bp GD1 coding region, a 4614 bp upstream region and a 1092 bp downstream sequence was cloned into binary vector pCAMBIA1300 and transformed into calli derived from the heterozygous seeds. The individual transformants were conﬁrmed by PCR using primers P1, P2 and P3.
 {| class='wikitable' style="text-align:center"
@@ Line 29: / Line 29: @@
 ===Expression===
-[[File:Shijc-Fig5.jpg|right|thumb|300px|''Diagram of alcoholic fermentation pathway in plants. (from reference <ref name="ref13" />).'']]
+[[File:Shijc-Fig5.jpg|right|thumb|300px|''Phenotype of the rice gd1 mutant. (from reference <ref name="ref2" />).'']]
 The highest expression level of GD1 was detected in leaf blades and ﬂowers, whereas the expression level was relatively low in young shoots, leaf sheaths, roots and stems. We next examined the expression patterns of GD1 under ABA and GA treatments. The transcript of GD1 in leaves showed a slight increase upon ABA treatment, but the expression of GD1 was increased twofold 6 h after GA treatment. GD1 expression was strongly up-regulated by sucrose after 1 and 6 h. <ref name="ref2" />

@@ Line 5: / Line 5: @@
 [[File:Shijc-Fig3.jpg|right|thumb|300px|''Diagram of alcoholic fermentation pathway in plants. (from reference <ref name="ref13" />).'']]
-GD1 encodes a B3 domain-containing protein that shares high similarity with VAL proteins in Arabidopsis which are critical determinants in seed and vegetative development <ref name="ref1" />. The EAR motif in the C – terminus of GD1 functions as an active repression domain, suggesting that GD1 is involved in seed germination and seedling development by negatively regulating target gene expression. The molecular mechanisms controlling the embryo pathway are probably conserved between monocot and dicot species, at least to some extent. Like other B3 factors, GD1 binds to the RY element through the B3 domain. <ref name="ref2" />
+GD1 encodes a B3 domain-containing protein that shares high similarity with VAL proteins in Arabidopsis which are critical determinants in seed and vegetative development <ref name="ref1" />. The EAR motif in the C - terminus of GD1 functions as an active repression domain, suggesting that GD1 is involved in seed germination and seedling development by negatively regulating target gene expression. The molecular mechanisms controlling the embryo pathway are probably conserved between monocot and dicot species, at least to some extent. Like other B3 factors, GD1 binds to the RY element through the B3 domain. <ref name="ref2" />
 GD1 participates in maintaining GA homeostasis by positively regulating GA biosynthesis and negatively regulating GA deactivation. Inconsistent expression changes for OsCPS1 and OsKO1, which are also involved in GA biosynthesis, were probably due to the differentially developmental manner. <ref name="ref3" /> <ref name="ref4" /> <ref name="ref5" /> The oscillation of GA concentration is critical for regulating seed germination and seedling development. The levels of bioactive GAs are maintained via feedback and feed-forward regulation of GA metabolism, and several factors that inﬂuence GA metabolism have been identiﬁed. <ref name="ref6" /> GA biosynthesis was also shown to be regulated by the LEC2 and FUS3 pathways. <ref name="ref7" /> <ref name="ref8" /> A scenario for the possible role of GD1 in the regulation of B3 transcription factors and GA metabolism: GA induces GD1 expression, and GD1 negatively regulates B3 transcription factors such as OsLFL1 and GD1 itself, then directly or indirectly modulates the GA level, regulating seed germination and seedling development. <ref name="ref2" />
@@ Line 58: / Line 58: @@
 <ref name="ref5"> Hedden, P. and Phillips, A.L. (2000) Gibberellin metabolism: new insights revealed by the genes. Trends Plant Sci. 5, 523 - 530. </ref>
 <ref name="ref6"> Yamaguchi, S. (2008) Gibberellin metabolism and its regulation. Annu. Rev. Plant Biol. 59, 225 - 251. </ref>
-<ref name="ref7"> Gazzarrini, S., Tsuchiya, Y., Lumba, S., Okamoto, M. and McCourt, P. (2004) The transcription factor FUSCA3 controls developmental timing in Ara- bidopsis through the hormones gibberellin and abscisic acid. Dev. Cell, 7, 373 -385. </ref>
+<ref name="ref7"> Curaba, J., Moritz, T., Blervaque, R., Parcy, F., Raz, V., Herzog, M. and Vachon, G. (2004) AtGA3ox2, a key gene responsible for bioactive gib- berellin biosynthesis, is regulated during embryogenesis by LEAFY COTYLEDON2 and FUSCA3 in Arabidopsis. Plant Physiol. 136, 3660 - 3669. </ref>
 ==Structured Information==

@@ Line 1: / Line 1: @@
-Please input one-sentence summary here.
+The rice ''GD1'' gene encodes a B3 domain transcriptional repressor. It regulates seed germination and seedling development by integrating GA and carbohydrate metabolism.
 ==Annotated Information==
 ===Function===
-Please input function information here.
+[[File:Shijc-Fig3.jpg|right|thumb|300px|''Diagram of alcoholic fermentation pathway in plants. (from reference <ref name="ref13" />).'']]
 ===Expression===
-Please input expression information here.
+[[File:Shijc-Fig5.jpg|right|thumb|300px|''Diagram of alcoholic fermentation pathway in plants. (from reference <ref name="ref13" />).'']]
-===Evolution===
+The highest expression level of GD1 was detected in leaf blades and ﬂowers, whereas the expression level was relatively low in young shoots, leaf sheaths, roots and stems. We next examined the expression patterns of GD1 under ABA and GA treatments. The transcript of GD1 in leaves showed a slight increase upon ABA treatment, but the expression of GD1 was increased twofold 6 h after GA treatment. GD1 expression was strongly up-regulated by sucrose after 1 and 6 h. <ref name="ref2" />
-You can also add sub-section(s) at will.
+===Alternative Splicing===
 ==Labs working on this gene==
-Please input related labs here.
+State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
 ==References==
-Please input cited references here.
+<references>
 ==Structured Information==

@@ Line 63: / Line 63: @@
 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

← Older revision		Revision as of 20:38, 22 July 2012
Line 1:		Line 1:
		+	Please input one-sentence summary here.
		+
		+	==Annotated Information==
		+	===Function===
		+	Please input function information here.
		+
		+	===Expression===
		+	Please input expression information here.
		+
		+	===Evolution===
		+	Please input evolution information here.
		+
		+	You can also add sub-section(s) at will.
		+
		+	==Labs working on this gene==
		+	Please input related labs here.
		+
		+	==References==
		+	Please input cited references here.
		+
		+	==Structured Information==
	{{JaponicaGene\|		{{JaponicaGene\|
	GeneName = Os07g0563300\|		GeneName = Os07g0563300\|