Os03g0188400
The rice Os03g0188400 is described as basic helix-loop-helix dimerisation region bHLH domain containing protein and it belongs to Oryza sativa Japonica Group.
Contents
Function
Several studies have made contribution to the development of over 6000 DNA markers3-5 (http://rgp.dna.affrc.go.jp/; http://www.gramene.org)which 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 sequence assembly , physical map construction and comparative genome analysis, but polymorphism detection within the cultivated rice gene pool isn't efficient. The basic helix-loop-helix (bHLH) motif can be found in many proteins required during diverse developmental processes such as sex determination, segmentation, neurogenesis, and myogenesis.
These proteins appear to regulate the choice between alternate pathways and effect changes in cell fate. Biochemical and structural studies suggest that the HLH domain mediates protein homo dimerization or hetero dimerization, while the basic region is required for the HLH dimers to make specific contacts with DNA. Different classes of bHLH proteins act as either positive or negative regulators of transcription. Three evolutionarily conserved domains—the bHLH,as well as Orange, and WRPW domains—are required for complete Hairy function. Analysis of the Hairy/E(SPL)m8 basic, HLH,or bHLH swaps showed that all of these altered Hairy proteins still caused female lethality, albeit less efficiently
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 essential to reexamine the predicted genes with 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
The O. sativa rice accessions show differentiation into five groups: aromatic, indica,aus, temperate japonica, and tropical japonica. This deep genetic structure is a legacy of structure in ancestral rice populations. Within Oryza sativa, there is an ancient and well-established divergence between the two major subspecies, indica and japonica. There is a hypothesis that indica and japonica are derived from independent domestication events from an ancestral rice that had allelic already differentiated into (at least) two gene pools (Caiand Morishima 2002; Ma and Bennetzen 2004; Yamariumunder the SMMwas assessed to determine whether naka et al. 2004). The differences between the indica and japonica subspecies are very apparent at all levels of analysis. Differences between nonsticky (indica) and sticky (japonica) rice are documented in Chinese literature as early as 100 AD (Matsuo et al. 1997). Japonica is typically found in temperate East Asia, upland areas of Southeast Asia, and high elevations in South Asia. Recent studies trace the molecular evolution of event that led to the evolution of modern maize (Matmaize offer several points of comparison that help illumi- suoka et al. 2002). Phylogenetic analysis and FST values demonstrate a close evolutionary relationship between the aromatic, temperate japonica, and tropical japonica subpopulations, which comprise the Japonica varietal group, while the indica and aus subpopulations have a distinct ancestry and are recognized as members of the Indica varietal group. The deep genetic structure in rice may also result from autogamous breeding system. While both breeding system and domestication history have had large effects on the structuring of diversity in rice, the independent population histories of the groups have also formed the gene pools. Recently, a second mutation in the BADH2 gene, badh2.2, was found to be associated with fragrance within a limited set of germplasm from China. Evidence that there may be additional mutations in the pathway leading to 2AP synthesis comes from a rigorous study involving a diverse panel of fragrant germplasm that identified several accessions, mostly from Southeast Asia, that had elevated levels of 2AP but did not carry the badh2.1 allele. Studies demonstrated that the Group V accessions, both fragrant and nonfragrant, cluster with the ancestral Japonica accessions both across the BADH2 gene and across the entire 5.3-Mb region of chromosome 8 surveyed.
Labs working on this gene
Plant Breeding Department, Cornell University, Ithaca, New York
Department of Agriculture-Agricultural Research Service Dale Bumpers
National Rice Research Center, Stuttgart, Arizona Cornell University, Department of Plant Breeding and Genetics, Ithaca, NY 14853; Grain Quality Nutrition and Postharvest Centre, International Rice Research Institute, Los Ban˜ os, Philippines Plant Breeding Dept, Cornell University, Ithaca Cold Spring Harbor Lab, International Rice Research Institute, P.O. Box 933, Manila National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University
Institute of the Society for Tecno-innovation of Agriculture, Forestry and Fisheries (STAFF)
Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan, Applied Genomics Laboratory, Department of Molecular Genetics, National Institute of Agrobiological Sciences
USDA Center for Agricultural Bioinformatics, Theory Center, Cornell University, Ithaca,
References
Garris A J, Tai T H, Coburn J, et al. Genetic structure and diversity in Oryza sativa L[J]. Genetics, 2005, 169(3): 1631-1638.
Michael J. K, Mariafe N. C, Melissa A. F, et al. The origin and evolution of fragrance in rice (Oryza sativa L.), PNAS ,2009, 106 (34): 14444–14449.
Susan R. M, Leonid T, Yunbi X, et al. Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.) [J]. DNA Research,2002, 199–207.
http://www.metalife.com/UniGene/Os%2031303_1838177
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) |
