Difference between revisions of "Os01g0785400"
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===Genomic organization and chromosomal distribution=== | ===Genomic organization and chromosomal distribution=== | ||
[[File:Exon–intron organization of rice GH3 genes.jpg|right|thumb|300px|'''Figure 1.''' ''Exon–intron organization of rice GH3 genes (from reference<ref name="ref2" />).'']] | [[File:Exon–intron organization of rice GH3 genes.jpg|right|thumb|300px|'''Figure 1.''' ''Exon–intron organization of rice GH3 genes (from reference<ref name="ref2" />).'']] | ||
| − | 1.Exon–intron organization of rice GH3 genes.Coding sequences of OsGH3 genes are disrupted by one to four introns except for OsGH3-6 and -9, which do not harbor any intron. Although the exon–intron organization of OsGH3 genes in terms of their numbers does not seem to be very similar, their intron phasing is highly conserved, which is indicative of exon shuffling.(Fig.1) | + | 1.Exon–intron organization of rice GH3 genes.Coding sequences of OsGH3 genes are disrupted by one to four introns except for OsGH3-6 and -9, which do not harbor any intron. Although the exon–intron organization of OsGH3 genes in terms of their numbers does not seem to be very similar, their intron phasing is highly conserved, which is indicative of exon shuffling.(Fig.1)<ref name="ref2" /> |
| − | 2.Genomic distribution of GH3 genes on rice chromosomes. White ovals on the chromosomes (vertical bars) indicate the position of centromeres. The arrows next to gene names show the direction of transcription. The numbers in parentheses designate the position of the first exon of corresponding GH3 gene in megabases (Mb) on rice chromosome pseudomolecules available at TIGR (release 3). The chromosome numbers are indicated at the top of each bar.(Fig.2) | + | 2.Genomic distribution of GH3 genes on rice chromosomes. White ovals on the chromosomes (vertical bars) indicate the position of centromeres. The arrows next to gene names show the direction of transcription. The numbers in parentheses designate the position of the first exon of corresponding GH3 gene in megabases (Mb) on rice chromosome pseudomolecules available at TIGR (release 3). The chromosome numbers are indicated at the top of each bar.(Fig.2)<ref name="ref2" /> |
[[File:Genomic distribution of GH3 genes on rice chromosomes.jpg|thumb|300px|'''Figure 2.''' ''Genomic distribution of GH3 genes on rice chromosomes (from reference<ref name="ref2" />).'']] | [[File:Genomic distribution of GH3 genes on rice chromosomes.jpg|thumb|300px|'''Figure 2.''' ''Genomic distribution of GH3 genes on rice chromosomes (from reference<ref name="ref2" />).'']] | ||
Revision as of 17:32, 6 June 2014
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Contents
Annotated Information
Function
GH3 is one kind of early auxin-responsive genes that widely exists in numerous plants. GH3 belongs to the luciferase superfamily and contains highly conserved regions and variable regions. The GH3 proteins are classified into three groups on the basis of the protein structure and function, and group II GH3 genes encode IAA–amido synthetases, which help to maintain auxin homeostasis by conjugating excess IAA to amino acids. Previous studies showed that the GH3 proteins in Arabidopsis modulate multiple developmental processes including photo-morphogenesis, light and auxin signaling, and auxin homeostasis. In rice, GH3 proteins have been structurally analyzed and studies showed that OsGH3-2 participates in the microRNA-mediated auxin signal transduction pathway, OsGH3-8 maintains auxin homeostasis and functions in basal disease resistance, and OsGH3-13 regulates plant architecture and drought tolerance.[1]
Gene Family
The information on rice genomic sequence provides a powerful tool to identify putative homologous proteins by database searches with genes of known function from other organisms. The overall analysis of the complete genome of rice revealed that auxin-inducible GH3 gene family is comprised of 12 members(Table1). However, in A. thaliana, 19 GH3 genes, along with an additional partial gene (coding only for amino terminal third of the protein), have been reported.
Genomic organization and chromosomal distribution
1.Exon–intron organization of rice GH3 genes.Coding sequences of OsGH3 genes are disrupted by one to four introns except for OsGH3-6 and -9, which do not harbor any intron. Although the exon–intron organization of OsGH3 genes in terms of their numbers does not seem to be very similar, their intron phasing is highly conserved, which is indicative of exon shuffling.(Fig.1)[2]
2.Genomic distribution of GH3 genes on rice chromosomes. White ovals on the chromosomes (vertical bars) indicate the position of centromeres. The arrows next to gene names show the direction of transcription. The numbers in parentheses designate the position of the first exon of corresponding GH3 gene in megabases (Mb) on rice chromosome pseudomolecules available at TIGR (release 3). The chromosome numbers are indicated at the top of each bar.(Fig.2)[2]
Expression
OsGH3.1 overexpression in rice causes a dwarf phenotype and depletion in free auxin.Phenotype of untransformed control plants and transgenic lines 7, 31, and 36 (from left to right). Transformants were classified into two different groups: mild (lines 7 and 31) and severe (line 36) dwarfs. Mild dwarfs did not show any morphological or flowering abnormality whereas severe dwarfs showed flowering delay and developed sterile flowers and multiple secondary tillers.[3] "
Evolution
LC1 Is Expressed in Various Tissues. qRT–PCR analysis revealed that LC1 is expressed in roots, shoots, flowers, seedlings, leaves, and sheaths, with a higher expression in collars. Promoter–GUS fusion study indicated that LC1 is highly transcribed in the seedlings, stems, leaves, and young flowers. It is very interesting to notice that, in mature leaves, LC1 is highly expressed in the sheaths and the collars, while only expressed in the main veins of the blades. [1]
References
- ↑ 1.0 1.1 Zhao S Q, Xiang J J, Xue H W. Studies on the Rice Leaf INCLINATION1 (LC1), an IAA–amido Synthetase, Reveal the Effects of Auxin in Leaf Inclination Control[J]. Molecular plant, 2013, 6(1): 174-187.
- ↑ 2.0 2.1 2.2 2.3 Mukesh Jain . Navneet Kaur . Akhilesh K. Tyagi .Jitendra P. Khurana. The auxin-responsive GH3 gene family in rice (Oryza sativa)[J].Funct Integr Genomics (2006) 6: 36–46.
- ↑ Concha Domingo,Fernando Andrés,Didier Tharreau,Domingo J. Iglesias,and Manuel Talón. Constitutive expression of OsGH3.1 reduces auxin content and enhances defense response and resistance to a fungal pathogen in rice[J].MPMI Vol. 22, No. 2, 2009, pp. 201–210.
Structured Information
| Gene Name |
Os01g0785400 |
|---|---|
| Description |
GH3 auxin-responsive promoter family protein |
| Version |
NM_001051002.1 GI:115440374 GeneID:4327043 |
| Length |
2486 bp |
| Definition |
Oryza sativa Japonica Group Os01g0785400, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 1:35064294..35066779 |
| Sequence Coding Region |
35064438..35064763,35064906..35065804,35065915..35066522 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008394:35064294..35066779 source=RiceChromosome01 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008394:35064294..35066779 source=RiceChromosome01 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgccggaagcaccgaccgccaagacagcaccggcctacggctacgcccccggggcgcacgccgaggcgctcgagttcatcgagcacgtcacggcgaacgccgggcaggtgcagcggcgcgtgctcggcgagatcctggcgcagaacgcgccggccgagtacctgcgccggtacggaatccccgggtcccccgacgttgtcgacgccttccgccgcctcgtcccgctcgtcacatacgagggcctccagccagacatcctccgcatcgccaacggcgacacctcgccgatcttctccgggaagcctatctccgaattcctcacgagctcgggcacgtcgggaggggagaggaagctcatgccgaccatcgccgacgagatgaacaggcggtcgctgctgtacagcctgctgatgccggtgatgagccagtcggtgtccgggctcgacaaaggcaaggcgatgtacctgctcttcgtgaaggcggagtcgcgcacgccgggcgggctcgcggcgcggccggtgctcacaagctactaccggagccggcagttcctcgaccgtccgcgcgacccctacacatcttacacgagccccgacgaggccatcctgtgcgtggactcctaccagagcatgtacgcgcagctgctctgcggcctcgtccaccgcgccgacgtgctgcgcgtgggcgccgtgttcgcctccggcttcctccgcgccatccatttcctcgagaagcactgggcgcgcctctgccacgacatccgcaccggcgagctcgacccggagatcaccgaccgcgtggtgcgcgacgccgtcgggcgggtgctccgcgccgacccggcgctcgccgacgcgatcgaggacgagtgcgctagggcgtcgtgggagggcatcatccggcgcctgtggccacgcaccaagtacatcgacgtgatcgtgaccggcaccatgtcgcagtacatcccgacgctcgagttctacggcggcggcctgccgctgacgtgcaccatgtacgcctcttcggagtgctacttcggcctcaacctgaatcccatgtgcaagcccagcgacgtcgcctacacgctcatccccaccatgtgctactacgagttcctccccgtcaattgcaacaatgccactgccgaggcgagccaccgcgacctcgtcgacctggtcgacgtaaagctcgggcacgagtacgagctcgtggtcaccacgtattccgggttgtatcgttatcgcgtgggcgacgtgctgagggtggcggggttcaagaacaaggccccgatgttcagcttcgtgcggcggcagaacgtggcgctgagcgtcgactcggacaagacggacgagacggagctgcacgcggcggtgagcggcgcggtgcagcacctggcgccgttcggcgcgtcgctggtggagtacacgagctacgcggacgcggccaccatcccgggccactacgtgctgttctgggagctgcgcgccggcagcacggcggtgccggcgtccgtgttcgaggagtgctgcctgtccgtggaggaggcactgaacagcgtctaccggcagggccgcgcgtgcgacaggtccatcggcccgctcgagatacgcgtcgtggcggagggcaccttcgacaagctcatggactacgcgatcagccggggcgcgtccatcaaccagtacaaggcgccgcggtgcgtgcgccctggcccggtcgtcgagctgctcgacgcgagggtgcagggcaagtacttcagtcccaagtgccccaagtggagccccgggaacaagcaatggaacaaaagcaaggatctggtcggcaagggagacgcctaa</cdnaseq> |
| Protein Sequence |
<aaseq>MPEAPTAKTAPAYGYAPGAHAEALEFIEHVTANAGQVQRRVLGE ILAQNAPAEYLRRYGIPGSPDVVDAFRRLVPLVTYEGLQPDILRIANGDTSPIFSGKP ISEFLTSSGTSGGERKLMPTIADEMNRRSLLYSLLMPVMSQSVSGLDKGKAMYLLFVK AESRTPGGLAARPVLTSYYRSRQFLDRPRDPYTSYTSPDEAILCVDSYQSMYAQLLCG LVHRADVLRVGAVFASGFLRAIHFLEKHWARLCHDIRTGELDPEITDRVVRDAVGRVL RADPALADAIEDECARASWEGIIRRLWPRTKYIDVIVTGTMSQYIPTLEFYGGGLPLT CTMYASSECYFGLNLNPMCKPSDVAYTLIPTMCYYEFLPVNCNNATAEASHRDLVDLV DVKLGHEYELVVTTYSGLYRYRVGDVLRVAGFKNKAPMFSFVRRQNVALSVDSDKTDE TELHAAVSGAVQHLAPFGASLVEYTSYADAATIPGHYVLFWELRAGSTAVPASVFEEC CLSVEEALNSVYRQGRACDRSIGPLEIRVVAEGTFDKLMDYAISRGASINQYKAPRCV RPGPVVELLDARVQGKYFSPKCPKWSPGNKQWNKSKDLVGKGDA</aaseq> |
| Gene Sequence |
<dnaseqindica>145..470#613..1511#1622..2229#cacaaaccaagctccataccgctgcctacatctctggttagtagccaccaaggtccaaggagtaacacgctccgtgagagaccgaaatccagggagcacaaattgcacatttgcaccaagcacactcgctgcagctgcagtgacatgccggaagcaccgaccgccaagacagcaccggcctacggctacgcccccggggcgcacgccgaggcgctcgagttcatcgagcacgtcacggcgaacgccgggcaggtgcagcggcgcgtgctcggcgagatcctggcgcagaacgcgccggccgagtacctgcgccggtacggaatccccgggtcccccgacgttgtcgacgccttccgccgcctcgtcccgctcgtcacatacgagggcctccagccagacatcctccgcatcgccaacggcgacacctcgccgatcttctccgggaagcctatctccgaattcctcacgaggtatagcacaatatataacgtgacatgttcatgcttccccgtgtgtgtacgcacgcacgctgctgcgtgcaaaacctagaaagacgtacgagttcatatctgtacagatcttcatgcaatggaatttcatcatgtccaccagctcgggcacgtcgggaggggagaggaagctcatgccgaccatcgccgacgagatgaacaggcggtcgctgctgtacagcctgctgatgccggtgatgagccagtcggtgtccgggctcgacaaaggcaaggcgatgtacctgctcttcgtgaaggcggagtcgcgcacgccgggcgggctcgcggcgcggccggtgctcacaagctactaccggagccggcagttcctcgaccgtccgcgcgacccctacacatcttacacgagccccgacgaggccatcctgtgcgtggactcctaccagagcatgtacgcgcagctgctctgcggcctcgtccaccgcgccgacgtgctgcgcgtgggcgccgtgttcgcctccggcttcctccgcgccatccatttcctcgagaagcactgggcgcgcctctgccacgacatccgcaccggcgagctcgacccggagatcaccgaccgcgtggtgcgcgacgccgtcgggcgggtgctccgcgccgacccggcgctcgccgacgcgatcgaggacgagtgcgctagggcgtcgtgggagggcatcatccggcgcctgtggccacgcaccaagtacatcgacgtgatcgtgaccggcaccatgtcgcagtacatcccgacgctcgagttctacggcggcggcctgccgctgacgtgcaccatgtacgcctcttcggagtgctacttcggcctcaacctgaatcccatgtgcaagcccagcgacgtcgcctacacgctcatccccaccatgtgctactacgagttcctccccgtcaattgcaacaatgccactgccgaggcgagccaccgcgacctcgtcgacctggtcgacgtaaagctcgggcacgagtacgagctcgtggtcaccacgtattccggtaaatctgccttacctcttcgacacataacgtggccgcgcgcgatggatgatatatattcttatatgcagtagtaatatatataattaacagttttgcgattgtgacagggttgtatcgttatcgcgtgggcgacgtgctgagggtggcggggttcaagaacaaggccccgatgttcagcttcgtgcggcggcagaacgtggcgctgagcgtcgactcggacaagacggacgagacggagctgcacgcggcggtgagcggcgcggtgcagcacctggcgccgttcggcgcgtcgctggtggagtacacgagctacgcggacgcggccaccatcccgggccactacgtgctgttctgggagctgcgcgccggcagcacggcggtgccggcgtccgtgttcgaggagtgctgcctgtccgtggaggaggcactgaacagcgtctaccggcagggccgcgcgtgcgacaggtccatcggcccgctcgagatacgcgtcgtggcggagggcaccttcgacaagctcatggactacgcgatcagccggggcgcgtccatcaaccagtacaaggcgccgcggtgcgtgcgccctggcccggtcgtcgagctgctcgacgcgagggtgcagggcaagtacttcagtcccaagtgccccaagtggagccccgggaacaagcaatggaacaaaagcaaggatctggtcggcaagggagacgcctaatattgaagctagagggtgatgatctgatcgagtatttgtgtgagctggtaattaattaacggtacatgcatatggtcattggtcgatatgtttctttagggatatgataattcatgtttgaattatctctgatgctgcgagaggatcgaatagttatgagatgacgacttagcctatatgatcatttgctttactctttctctgctgtaacgcagtatatgttatttcctccgtctcaaaatataagcatttttagt</dnaseqindica> |
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