Difference between revisions of "Os09g0439800"
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===Mutation=== | ===Mutation=== | ||
Comparing the sequence of this ORF in the IR64 (a leading paddy cultivar widely grown in Asia, showed shallow rooting in an upland field) and KP (an upland cultivar from the Philippines, showed deep rooting) accessions identified a single 1-bp deletion within exon 4 in IR64 (Fig. 1b), resulting in the introduction of a premature stop codon. Transforming an 8.7-kb genomic fragment of KP containing the candidate gene into IR64 increased the ratio of deep rooting (an index of downward root growth; Online Methods) compared to IR64 transformed with the vector control<ref name="ref1" />. | Comparing the sequence of this ORF in the IR64 (a leading paddy cultivar widely grown in Asia, showed shallow rooting in an upland field) and KP (an upland cultivar from the Philippines, showed deep rooting) accessions identified a single 1-bp deletion within exon 4 in IR64 (Fig. 1b), resulting in the introduction of a premature stop codon. Transforming an 8.7-kb genomic fragment of KP containing the candidate gene into IR64 increased the ratio of deep rooting (an index of downward root growth; Online Methods) compared to IR64 transformed with the vector control<ref name="ref1" />. | ||
| − | [[File: | + | [[File:FigureYL2.jpg|center|thumb|680px|'''Figure 2.''' ''Mutation and Structure of DRO1 based on annotation of Os09g0439800 (LOC_Os09g26840.1) (from reference<ref name="ref1" />).'']] |
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===Expression=== | ===Expression=== | ||
The predicted protein product of DRO1 has no similarity to known proteins. Genes found in monocots had higher homology to DRO1 than genes found in dicots, DRO1 is not predicted to encode a signal peptide or a transmembrane domain but is predicted to encode two putative N-myristoylation sites associated with lipid modification,suggesting that DRO1 is associated with a membrane protein or with the plasma membrane<ref name="ref1" />. | The predicted protein product of DRO1 has no similarity to known proteins. Genes found in monocots had higher homology to DRO1 than genes found in dicots, DRO1 is not predicted to encode a signal peptide or a transmembrane domain but is predicted to encode two putative N-myristoylation sites associated with lipid modification,suggesting that DRO1 is associated with a membrane protein or with the plasma membrane<ref name="ref1" />. | ||
Revision as of 03:50, 11 May 2014
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Contents
Annotated Information
Function
This gene, named DEEPER ROOTING 1 (DRO1), is a rice quantitative trait locus controlling root growth angle(Figure 1). It is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction[1].
GO assignment(s): GO:0009734
Mutation
Comparing the sequence of this ORF in the IR64 (a leading paddy cultivar widely grown in Asia, showed shallow rooting in an upland field) and KP (an upland cultivar from the Philippines, showed deep rooting) accessions identified a single 1-bp deletion within exon 4 in IR64 (Fig. 1b), resulting in the introduction of a premature stop codon. Transforming an 8.7-kb genomic fragment of KP containing the candidate gene into IR64 increased the ratio of deep rooting (an index of downward root growth; Online Methods) compared to IR64 transformed with the vector control[1].
Expression
The predicted protein product of DRO1 has no similarity to known proteins. Genes found in monocots had higher homology to DRO1 than genes found in dicots, DRO1 is not predicted to encode a signal peptide or a transmembrane domain but is predicted to encode two putative N-myristoylation sites associated with lipid modification,suggesting that DRO1 is associated with a membrane protein or with the plasma membrane[1].
Evolution
Please input evolution information here.
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Labs working on this gene
- National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
- International Center for Tropical Agriculture (CIAT), Cali, Colombia.
- Faculty of Science, University of Valle, Cali, Colombia.
References
Structured Information
| Gene Name |
Os09g0439800 |
|---|---|
| Description |
Conserved hypothetical protein |
| Version |
NM_001069813.1 GI:115479368 GeneID:4347169 |
| Length |
3058 bp |
| Definition |
Oryza sativa Japonica Group Os09g0439800, 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 9:16961491..16964548 |
| Sequence Coding Region |
16961864..16961883,16961980..16962151,16962243..16962721,16964085..16964163,16964280..16964285 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008402:16961491..16964548 source=RiceChromosome09 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008402:16961491..16964548 source=RiceChromosome09 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgaagattttcagctgggtagccaacaagatcagtgggaagcaagaagcaaatcggtttcccgcaaattcttctgcgccttaccgtgctaacgtgtcagattgtcgaaaggatgaattcagtgattggccccaatcattgcttgctattgggacatttggaaataagcagattgaggaggtagctcaggtggagaattcatccgacaatgtgcagtcagtgcaagataccgtcaaatttacagaggaagaagtagacaagatacggaaagaattcgaaacgctactagcaatcaaagatcaagcagaagctcaacgctcgcatgatgatgaccaagtaggtttacaaaagcgtgccgatggggaagacaatgagaagcatattagacagttgatcaacaaaaggatcattgtaagtaaatcaaagaattcgttaggaaagaaaggaaatacactcaagccgagatcagtcgcttcgttgctcaagttattcatgtgtaagggtggctttacctccgtagttccagaaccaaggaacacatttcctcaatcaagaatggagaagttgctcaaggcaatattgcagaagaaaatacacccgcaaaattcttccacgctagttgctaagaggcatttggactggaagccagatgagacagaaatcaatgagtgcctggaggatgcactgcgtgatctagacgatgatggtgcaaaatgggtcaaaactgattcagagtatattgtgcttgaaatgtaa</cdnaseq> |
| Protein Sequence |
<aaseq>MKIFSWVANKISGKQEANRFPANSSAPYRANVSDCRKDEFSDWP QSLLAIGTFGNKQIEEVAQVENSSDNVQSVQDTVKFTEEEVDKIRKEFETLLAIKDQA EAQRSHDDDQVGLQKRADGEDNEKHIRQLINKRIIVSKSKNSLGKKGNTLKPRSVASL LKLFMCKGGFTSVVPEPRNTFPQSRMEKLLKAILQKKIHPQNSSTLVAKRHLDWKPDE TEINECLEDALRDLDDDGAKWVKTDSEYIVLEM</aaseq> |
| Gene Sequence |
<dnaseqindica>2666..2685#2398..2569#1828..2306#386..464#264..269#agatgaagtatagcaagctatcctacagccagccacgctgcaccgaaccctccaatccttggaacttgaaccccttcaaatcacacccagtaggctactagtagtacttctctgcaccaattccatcgccaatagcagccactacaagtcttacatctctcctttcctcctctctctgccattgctaggagcttgcatttcttggtagcttcatcagctagctgctttctccctccccaatctctcattcttcaggccaggatatgaaggtaaaggctcaaaccatcggtgtgattaatcatttcagagaggttaatagatttgaagtgttggtagtgttgatccatttcttgatggcatcatgaggcttgggttttctctgcagattttcagctgggtagccaacaagatcagtgggaagcaagaagcaaatcggtttcccgcaaattcttctgcgccttaccgtgagtgtacctgaactttcagtttccttgtaaattctttcagaactaaggtgattgttgttcaccaggcttcatgctgttcttatgaaatgtttccctgttccttgaggggagagggagagtacggacagtaatttggaagccgtttcctaatttgatattttctttctgtcattctgctgcagttataatgtctttacctcttagcagtttctgcttaggcatcatttgccttattcatttctggatacgatgatactttattgctttgtcctaatttaatcttttcctgctgtcattctgctccatttatggtgtctttacctcttagcagtttccgcttaggcatcatttgccatgttcatttctgaatatgctgatatactttgttgtcttggtagccatatacaagagtgaacgatttaaaggtttctcctaattgctagtaacagaacgcttttcgctctgcgattttctggattaccatcccctgattcctgagtaacctatcacaacgccaatgtgatggagcaaacattgatgtattatgacaatgttgtttctgatcctttgagaaaattttcttatatgcacttgggtgttgtttggaacgcaggaatttcactggaaacagttcaattatcgcacttccggaaaaaaaattcctgcattttaaacggcgctttaagttcagtaggagttttcaattttattttcctcttccctagcacgaaaagtgagagatttttgtgcatatgttatacccccaaaggactatttcatggcctgatgcccgccacgccaatatctctgtaaagcactgcttccaactagtcagtatgggtcaaagtcttgactaagtgcaaccctgcaagcaagtgtttccaactagtcagtatggcttcaattatttagttgatttataaccccaaccctccacttgtgaccaagaagaatttgatttgagcagacaatatcctgacctcggatggtttcgtaaatcgtactaaggaatcagatctgagccactagtccagctggactacagtacattatttatctctcaagattacataaaaagactactattgtacagagaatgcattgtttaagtggtaacaactgctgtgataagttattcctggtatacagaaaaatggcaggtgaaaacatcagggagtggagtaagcatgggcagacattgtacttaaagagtgataggccaatgagaatcactgggtgtttaaggattaaaaatttgtggtccatgctctagacatccaatttatgctaatatgaacttaggaccatatatttatgtttgtttactgatcttgcggcttaatcgagttctaatgcgcaggtgctaacgtgtcagattgtcgaaaggatgaattcagtgattggccccaatcattgcttgctattgggacatttggaaataagcagattgaggaggtagctcaggtggagaattcatccgacaatgtgcagtcagtgcaagataccgtcaaatttacagaggaagaagtagacaagatacggaaagaattcgaaacgctactagcaatcaaagatcaagcagaagctcaacgctcgcatgatgatgaccaagtaggtttacaaaagcgtgccgatggggaagacaatgagaagcatattagacagttgatcaacaaaaggatcattgtaagtaaatcaaagaattcgttaggaaagaaaggaaatacactcaagccgagatcagtcgcttcgttgctcaagttattcatgtgtaagggtggctttacctccgtagttccagaaccaaggaacacatttcctcaatcaagaatggagaaggtacacagtgaaattctttttttcttatgtaacatgataagttttacatactttctcgtcctcttattatcttatatgatgttcattgcagttgctcaaggcaatattgcagaagaaaatacacccgcaaaattcttccacgctagttgctaagaggcatttggactggaagccagatgagacagaaatcaatgagtgcctggaggatgcactgcgtgatctagacgatgatggtgcaaaatgggtcaaaactgattcagagtgtaagtagcatacttgcctatcatgaattgaaccttttcttttgccacttttgtcaatggagcaactgactgaatatgaacttttcttgtttccagatattgtgcttgaaatgtaaagttgggtgaatatgttagttcgttcatgccaggtatatacctttctttgatccccaaattttcaactcaactcaaatgtgaattatccttgatctagcatgtctctctgttttgatctgattagtgtgattccaatctgcaggttccaaaggtcctggcaagcttggggtttatggtgttactacgtaatgatataaatatgggatatagttagcaatgaagctctatgatcatgtaatgctcctccattatttctgacatgaaccatctgtaatttgaatcatgataaggaggttctgggacaaaggcctattccatgtgtctactctcttctgccctgaaactgtaaagaacgcattcaattttttcaac</dnaseqindica> |
| External Link(s) |
