Os06g0157700

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Annotated Information

Function

Please input function information here. The rice photoperiod sensitivity gene Hd3 was originally detected as a heading date-related quantitative trait locus localized on chromosome 6 of rice. But the effect is small, it is a minor QTL located on chromosome 6 between RFLP markers R1952-C1032, and isolated with the four markers contain R2749, R1962, R2967 and C764 (Yamamoto et al., 1997). Furthermore, it was found the site of Hd3 was composed of two sub-sites Hd3a and Hd3b, both sites had additive effects. In the short daylight, Hd3a locus alleles from Kasalath promoted the heading; however, in the long sunshine or large fields, Hd3b locus alleles from Kasalath delayed heading. Hd3a and molecular markers B174 were separated as well as Hd3b and molecular markers R1952 did, the genetic distance is about 1.6cM (Monna, et al., 2002)

Expression

Please input expression information here. The full length of Hd3a cDNA is 847bp contains four exons encoding 178 amino acid protein products. Sequence analysis showed: Kasalath and Nipponbare allele coding region has a single base substitution, and a 2-synonymous nucleotide substitutions. This codon in Nipponbare is proline, while aspartic acid in Kasalath. And both alleles are functional, however, Hd3a in Kasalath promotes more powerful. The expression patterns of Hd1 and Hd3a were analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and low levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions. (Luan et al., 2009)

Evolution

Please input evolution information here. A previous study revealed that the Kasalath allele of Hd3a promotes heading under short-day conditions. The rice Heading date 1 (Hd1) gene, a homolog of CONSTANS (CO), has been shown to promote heading under short-day conditions. Besides, the amount of Hd3a mRNA is up-regulated by Hd1 under short-day conditions, suggesting that Hd3a promotes heading under the control of Hd1. These results indicate that Hd3a encodes a protein closely related to Arabidopsis FT and that the function and regulatory relationship with Hd1 and CO, respectively. Furthermore, Hd3a and FT are conserved between rice and Arabidopsis. (Kojima et al., 2002)

Homology

Japanese scholars indicate, RICE FLOWERING LOCUS T1 (RFT1), and Heading date 3a (Hd3a) homology is the main activating factor of a long day under the conditions. (Ogiso-Tanaka et al. 2013)

Labs working on this gene

Please input related labs here. Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305, Japan Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305, Japan Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan Bio-oriented Technology Research Advancement Institution, Omiya, Saitama 331-8537, Japan,Bio-oriented Technology Research Advancement Institution, Omiya, Saitama 331-8537, Japan Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, People’s Republic of China, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, People’s Republic of China State Key Laboratory of Plant Physiology and Biochemistry, National Center for the Evaluation of Agricultural Wild Plants (Rice), Laboratory of Crop Heterosis and Utilization of the Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, People’s Republic of China Chemistry and Life Science College, Tianjin Normal University, Tianjin, People’s Republic of China Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, 305-0854 Japan Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation, Kawaguchi, Saitama, 332-0012 Japan Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan

References

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Structured Information

Gene Name	Os06g0157700
Description	Similar to SP3D
Version	NM_001063395.1 GI:115466521 GeneID:4340185
Length	2449 bp
Definition	Oryza sativa Japonica Group Os06g0157700, 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	Chromosome 6
Location	Chromosome 6:2939005..2941453
Sequence Coding Region	2939157..2939363,2939526..2939587,2939721..2939761,2941069..2941298
Expression	GEO Profiles:Os06g0157700
Genome Context	<gbrowseImage1> name=NC_008399:2939005..2941453 source=RiceChromosome06 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008399:2939005..2941453 source=RiceChromosome06 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atggccggaagtggcagggacagggaccctcttgtggttggtagggttgtgggtgatgtgctggacgcgttcgtccggagcaccaacctcaaggtcacctatggctccaagaccgtgtccaatggctgcgagctcaagccgtccatggtcacccaccagcctagggtcgaggtcggcggcaatgacatgaggacattctacacccttgtgatggtagacccagatgcaccaagcccaagtgaccctaaccttagggagtatctacattggttggtcactgatattcctggtactactgcagcgtcatttgggcaagaggtgatgtgctacgagagcccaaggccaaccatggggatccaccggctggtgttcgtgctgttccagcagctggggcgtcagacagtgtacgcgcccgggtggcgtcagaacttcaacaccaaggacttcgccgagctctacaacctcggctcgccggtcgccgccgtctacttcaactgccagcgcgaggcaggctccggcggcaggagggtctacccctag</cdnaseq>
Protein Sequence	<aaseq>MAGSGRDRDPLVVGRVVGDVLDAFVRSTNLKVTYGSKTVSNGCE LKPSMVTHQPRVEVGGNDMRTFYTLVMVDPDAPSPSDPNLREYLHWLVTDIPGTTAAS FGQEVMCYESPRPTMGIHRLVFVLFQQLGRQTVYAPGWRQNFNTKDFAELYNLGSPVA AVYFNCQREAGSGGRRVYP</aaseq>
Gene Sequence	<dnaseqindica>153..359#522..583#717..757#2065..2294#tgcaccacacacagttcagctagcagatcacctagctagatagctgcctctatcacagtatatttgctccctgcaacttgctgctgctgcaatagctagcagctgcagctagtaagcaaaactataaaccttcagggttttttgcaagatcgatggccggaagtggcagggacagggaccctcttgtggttggtagggttgtgggtgatgtgctggacgcgttcgtccggagcaccaacctcaaggtcacctatggctccaagaccgtgtccaatggctgcgagctcaagccgtccatggtcacccaccagcctagggtcgaggtcggcggcaatgacatgaggacattctacacccttgtatgtgagctctaccatgtgtcgtagttggtgcagagaccagaagttatactttctttcattattatattatagaaaaatttgtttggtacttaacccaagatgactttaaaatgcattaatttgatgtttgtcatggttttttgtggtgtgtacctgaaggtgatggtagacccagatgcaccaagcccaagtgaccctaaccttagggagtatctacattggtaagcacactaatgttaagctagcgcacttgttttcatgcaatgatcaaaataatcactgctagctgatttacatacataaccacatcttgactgcatgatgggttgatcatcttaatttgtttgtccacaggttggtcactgatattcctggtactactgcagcgtcatttggtcagtattaaacgatcaaatggtttagattgatttgatttcccacttaaatacattgcagtataaaactaacagaggtaaattgtctttccatactattgtttgggggggggggggcagggggcagtgagttgttgagcattttccctcactcgcgagcccccagtttgccgcattaattccccatcatccttcaccaccacaaaaaaaaaagtgatttggagaaggatacgctcctccaaataatttttaacaagttcaccaccacaacgaggcaccgacaaccgccatgagtccacgcaccctgcagctagtcgtgccaccagcaccacagttagccacaccgcgagcaatccacgccatcacttgccgctgtgagtccacgatcacacgcctcgatcagccagctgccatgatatgtcggcttgggcttggattctgcaacataccatgtccccatcgatggcaccacactctaattcgccaacacaacactgaagggatcggatcgggagggctagctcactcaagatagtgacgggatgattcgatgggaattccatggggaacaaagcacaaaatcattaaaatgtccttttcaattccatggcaaattcctaaagcaatactctctctccattctataatgtaggttgcacactcatttcaagattcaactttcaaaacatttgactaacgatttgtataatataaattgaattttatttgatagaaataatattattggattgatatttcaatatactttcatatggttataattttgttactacaaactttatagtatattagaaattataaataaaaaattagttttgtagaccgtacatgccaagtttgaccataccatattatgaaaaagagggagtagtaaccttgtttatatttgcaatatatactccctccgtttctaaatatctgacgctgttgactttttaaacatgtttgaccgttcgtcttattaaaaaataagtaattattaattcttttcctatcatttgatttattgttaaatatatttttatgcagacatatagttttacatatttcataaaagtttttgaataagaagaatgatcgtcaaatatttagaaacgaggggagtatattgctagtaaattttactgtaaagtcatgtttcttcatgtgtcttttttagaacatttcttcttcatgtgttccaatcaattttttcgatctccaccaccactaccacagttgtatgtgtagtagctagctgttgcacatgctcatgttaatctgaatctgtccatggttttttgcagggcaagaggtgatgtgctacgagagcccaaggccaaccatggggatccaccggctggtgttcgtgctgttccagcagctggggcgtcagacagtgtacgcgcccgggtggcgtcagaacttcaacaccaaggacttcgccgagctctacaacctcggctcgccggtcgccgccgtctacttcaactgccagcgcgaggcaggctccggcggcaggagggtctacccctagctaacgatgatcccgatcgatctgctgcatgctcactatcatcatccagcatgctatacattgcaggttcagacaattgaaatgattctcgacacacaacatatatatgatggtgtaattaattatgcaattaaatagctgagcaaggctaaggt</dnaseqindica>
External Link(s)	NCBI Gene:Os06g0157700, RefSeq:Os06g0157700