Difference between revisions of "Os03g0188400"
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It is necessary to reexamine the predicted genes with use of experimental data and systematically analyze the alternatively spliced transcripts in the rice genome. | It is necessary to reexamine the predicted genes with use of experimental data and systematically analyze the alternatively spliced transcripts in the rice genome. | ||
ESTs are regarded as direct evidence of gene expression. With suitable algorithms and well-curated ESTs, the inherent errors in EST information can be effectively reduced in gene/isoform annotations. | ESTs are regarded as direct evidence of gene expression. With suitable algorithms and well-curated ESTs, the inherent errors in EST information can be effectively reduced in gene/isoform annotations. | ||
| + | EST sequences: | ||
| + | 1.Accession: D40346.1 | ||
| + | Description:RICS2264A Rice shoot Oryza sativa (japonica cultivar-group) cDNA, mRNA sequence | ||
| + | Library ID:193 | ||
| + | End:569497 | ||
| + | Tissue:stem | ||
| + | 2.Accession:BF145188.1 | ||
| + | Description:EI35K24 Normalized rice cDNA library Oryza sativa cDNA clone EI35K24 similar to Pathogen induced defense- responsive sequence, mRNA sequence | ||
| + | Clone:EI35K24 | ||
| + | Library ID:6983 | ||
| + | GI:40385992 | ||
| + | Tissue:mixed | ||
| + | 3.Accession:CF993041.1 | ||
| + | Description:22185rsicee_7682.y1 Oryza sativa cv. LYP9 tillering whole plant cDNA library Oryza sativa (indica cultivar-group) cDNA 5', mRNA sequence | ||
| + | Library ID:14617 | ||
| + | GI:58594733 | ||
| + | End:5' | ||
| + | Tissue:whole plant | ||
| + | 4.Accession:CK011973.1 | ||
| + | Description:24659rsicef_0866.y1 Oryza sativa cv. PA64s panicle sterile cDNA library Oryza sativa (indica cultivar-group) cDNA 5', mRNA sequence | ||
| + | Library ID:14618 | ||
| + | GI:58601445 | ||
| + | End:5' | ||
| + | Tissue:panicle | ||
| + | 5.Accession:BX901684 | ||
| + | Description:BX901684 Oryza sativa library (Han B) Oryza sativa cDNA clone p726b05p5, mRNA sequence | ||
| + | Library ID:15105 | ||
| + | Clone:p726b05p5 | ||
| + | GI:40491772 | ||
| + | Tissue:unspecified_tissue | ||
| + | |||
| + | |||
| + | |||
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Revision as of 04:59, 6 June 2014
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Contents
Annotated Information
Previous studies have contributed to the development of over 6000 DNA markers3-5 (http://rgp.dna.affrc.go.jp/; http://www.gramene.org) that provide genome coverage of approximately one marker every 0.25 cM, or every 75-100 kb. Most are expressed sequence tags (ESTs) that are widely used as the basis for physical map construction, sequence assembly and comparative genome analysis, but polymorphism detection within the cultivated rice gene pool is inefficient.
1. Os03g0188400 - Cytokinin-inducible type-A response regulator OsRR6 overexpression effect on rice leaves 2. Os03g0188400 - Abscisic acid and gibberellin effect on calluses (dye-swap) 3. Os03g0188400 - Abscisic acid and gibberellin effect on calluses 4. Os03g0188400 - Silent Information Regulator 2-related gene OsSRT1 knockdown effect on rice leaves 5. Os03g0188400 - Lipopolysaccharide and chitin oligosaccharide effect on rice cells 6. Os03g0188400 - Benzothiadiazole effect on Oryza sativa leaves
Expression
It is necessary to reexamine the predicted genes with use of experimental data and systematically analyze the alternatively spliced transcripts in the rice genome. ESTs are regarded as direct evidence of gene expression. With suitable algorithms and well-curated ESTs, the inherent errors in EST information can be effectively reduced in gene/isoform annotations.
EST sequences: 1.Accession: D40346.1 Description:RICS2264A Rice shoot Oryza sativa (japonica cultivar-group) cDNA, mRNA sequence Library ID:193 End:569497
Tissue:stem
2.Accession:BF145188.1 Description:EI35K24 Normalized rice cDNA library Oryza sativa cDNA clone EI35K24 similar to Pathogen induced defense- responsive sequence, mRNA sequence
Clone:EI35K24
Library ID:6983 GI:40385992
Tissue:mixed
3.Accession:CF993041.1 Description:22185rsicee_7682.y1 Oryza sativa cv. LYP9 tillering whole plant cDNA library Oryza sativa (indica cultivar-group) cDNA 5', mRNA sequence Library ID:14617 GI:58594733
End:5'
Tissue:whole plant
4.Accession:CK011973.1 Description:24659rsicef_0866.y1 Oryza sativa cv. PA64s panicle sterile cDNA library Oryza sativa (indica cultivar-group) cDNA 5', mRNA sequence Library ID:14618 GI:58601445
End:5'
Tissue:panicle
5.Accession:BX901684 Description:BX901684 Oryza sativa library (Han B) Oryza sativa cDNA clone p726b05p5, mRNA sequence Library ID:15105
Clone:p726b05p5
GI:40491772
Tissue:unspecified_tissue
Evolution
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Labs working on this gene
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References
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Structured Information
| Gene Name |
Os03g0188400 |
|---|---|
| Description |
Basic helix-loop-helix dimerisation region bHLH domain containing protein |
| Version |
NM_001055752.1 GI:115451232 GeneID:4331887 |
| Length |
1580 bp |
| Definition |
Oryza sativa Japonica Group Os03g0188400, 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 3:4607271..4608850 |
| Sequence Coding Region |
4607376..4607801,4607897..4608355,4608529..4608633 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008396:4607271..4608850 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008396:4607271..4608850 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggcgttagaggccgtggtgtttccgcagggccatttcggctacgggtgcggaagggactcgccggcgtacgggatgccgtggtgcgacgtcctggctgctgccggcggcggcggcggcttcggtgagttttacggagtggacgagtgggatgaccagctgcaggtcgcctccgtggatgagtgggaggtggcatccaaggataactcggatgcttccacggagggcaaggcggcggcggcggagcgggcggagccggtggccgccgggaggaggaaacggaggcggacgaaggtcgtcaagaacaaggaggagatcgagtgccagcggatgacccacattgccgtcgagcgcaaccgccgccgccagatgaacgagtacctcgccgtgctccgctccctcatgccggcgtcctactcgcagaggggtgatcaagcatcgatcgtcggaggagcaatcaactacgtgaaggagctggagcagctactgcagtcgctggaagtccaaaagagcctcaagaaccgcagcggcgccatggacgccgccggcgattcccctttcgccggcttcttcagcttcccacagtactccacgtcgcctcgcactggctgcagcgccgccgccagcgccgggagctccggcagtgcgagcagcgtcgtcatggacgacacggcgggctccgcggagagcggccggcagtcggcggccatcgccgacatcgaggtgaccatggtggaagggcacgcgagcctcaaggtgctcgcgcggcggcgaccgaagcagctgctgaagctggtcgtcgggctgcagcagctgcgcatcccgccgctgcatctcaacgtgaccaccgtcgacgccatggtcctctactccttcagcctcaaggtggaggatgattccaagctgggctctgtggaagacattgccaccgctgtgcatcagatcctgggcagcattcagcagcaggaggccgtcctctccatcagctga</cdnaseq> |
| Protein Sequence |
<aaseq>MALEAVVFPQGHFGYGCGRDSPAYGMPWCDVLAAAGGGGGFGEF YGVDEWDDQLQVASVDEWEVASKDNSDASTEGKAAAAERAEPVAAGRRKRRRTKVVKN KEEIECQRMTHIAVERNRRRQMNEYLAVLRSLMPASYSQRGDQASIVGGAINYVKELE QLLQSLEVQKSLKNRSGAMDAAGDSPFAGFFSFPQYSTSPRTGCSAAASAGSSGSASS VVMDDTAGSAESGRQSAAIADIEVTMVEGHASLKVLARRRPKQLLKLVVGLQQLRIPP LHLNVTTVDAMVLYSFSLKVEDDSKLGSVEDIATAVHQILGSIQQQEAVLSIS</aaseq> |
| Gene Sequence |
<dnaseqindica>106..531#627..1085#1259..1363#aactcactctttaattcgcctccccctgaatcgtgtgcgtatcgtatcgtggcgtcgtcagttcgcgaaaaaaaacgcccgttcgttttgccgggtgcgtgcaggatggcgttagaggccgtggtgtttccgcagggccatttcggctacgggtgcggaagggactcgccggcgtacgggatgccgtggtgcgacgtcctggctgctgccggcggcggcggcggcttcggtgagttttacggagtggacgagtgggatgaccagctgcaggtcgcctccgtggatgagtgggaggtggcatccaaggataactcggatgcttccacggagggcaaggcggcggcggcggagcgggcggagccggtggccgccgggaggaggaaacggaggcggacgaaggtcgtcaagaacaaggaggagatcgagtgccagcggatgacccacattgccgtcgagcgcaaccgccgccgccagatgaacgagtacctcgccgtgctccgctccctcatgccggcgtcctactcgcagagggtacaacactaactacgcatgcttcaattaatcgcttttacgcatactgttatgattcgttaatcatcattaaatcgaatccattttctgctcagggtgatcaagcatcgatcgtcggaggagcaatcaactacgtgaaggagctggagcagctactgcagtcgctggaagtccaaaagagcctcaagaaccgcagcggcgccatggacgccgccggcgattcccctttcgccggcttcttcagcttcccacagtactccacgtcgcctcgcactggctgcagcgccgccgccagcgccgggagctccggcagtgcgagcagcgtcgtcatggacgacacggcgggctccgcggagagcggccggcagtcggcggccatcgccgacatcgaggtgaccatggtggaagggcacgcgagcctcaaggtgctcgcgcggcggcgaccgaagcagctgctgaagctggtcgtcgggctgcagcagctgcgcatcccgccgctgcatctcaacgtgaccaccgtcgacgccatggtcctctactccttcagcctcaaggtaaaaaccaatcgacaatttgcacctattttactaccacgactgcatgcttagttagtttaggctagcagcacagacaaattaagcgattggaacgtcgcgggtgagcgaagattcgctcccatttttctacaacgccgatgataatgtcatcgctttcgtttggatgttaggtggaggatgattccaagctgggctctgtggaagacattgccaccgctgtgcatcagatcctgggcagcattcagcagcaggaggccgtcctctccatcagctgacgccgcgatcgatggagacgacaaccgagacggccgccatgtgaagcctctgcctcgtccgtcctggaaatggaaccatggcgcctcgatcgatagcttgttagcttgtaatgtgtgaatgtgattgtaccctagccaacagagtgctgcatgcatgcagtatctccggcgaccttaatgagaaatctataccaacattttgagctcttgtaaacgt</dnaseqindica> |
| External Link(s) |
