Information report for qSH1;RIL1
Gene Details
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Functional Descriptions
- Here, we studied nucleotide variation at the shattering loci, sh4 and qSH1, for cultivated rice, Oryza sativa ssp.
- We revealed that the qSH1 gene, a major quantitative trait locus of seed shattering in rice, encodes a BEL1-type homeobox gene and demonstrated that a single-nucleotide polymorphism (SNP) in the 5’ regulatory region of the qSH1 gene caused loss of seed shattering owing to the absence of abscission layer formation.
- Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice.
- Special interest was the detection of the most significant association SNP, sf0136352825, which was less than 95 kb from the seed shattering gene qSH1.
- In addition, both RI and RIL1 seem to be involved in meristem maintenance, because the ri RIL1 double mutant failed to establish or maintain the shoot apical meristem during embryogenesis.
Functional Keywords
- shattering , seed , awn , seed-shattering , shoot , meristem , shoot-apical-meristem
Literature and News
- An SNP caused loss of seed shattering during rice domestication . DOI: 10.1126/science.1126410 ; PMID: 16614172
- Selection on grain shattering genes and rates of rice domestication . DOI: 10.1111/j.1469-8137.2009.02984.x ; PMID: 19674325
- Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice . DOI: 10.1007/s12041-016-0679-1 ; PMID: 27659335
- BELL1-like homeobox genes regulate inflorescence architecture and meristem maintenance in rice . DOI: 10.1111/tpj.14230 ; PMID: 30657229
Gene Resources
- UniProt: A0A0P0VAE7
- EMBL: AP004127, AP008207, CM000138
- EnsemblPlants: Os01t0848400-01
- Gramene: Os01t0848400-01
- KEGG: dosa:Os01g0848400, osa:4324855
- InterPro: IPR001356, IPR006563, IPR008422
- PANTHER: PTHR11850
- SUPFAM: SSF46689
- PROSITE: PS50071
- Gene3D: 1.10.10.60
- OrthoDB: A0A0P0VAE7
- SWISS-MODEL: A0A0P0VAE7
- Conserved Domain Database: cd00086
Sequences
cDNA Sequence
- >LOC_Os01g62920.1
CGGCCTTTCTGCTTTCGCTTTCACAGTTTCACGGCTTACCATTTCCTTCCCATCTCTCCCTCCCGCCACCCCCCTCTTTCTCCCCCTCCGTGTCTCGCCTTTGCAGAAAGAAAGGCGCCACGAACCCAGCAACAACACCCAGCACAAAGGCGAAACGGGGAAAAAGAGGAGGAAAACAACAAGAGGACGCGAGGGGTCGGGGTGGGAGAGGGAGGCTACACTACAGCAGCAGCAGAAGCAGAGCGGGAGAGTGATGAGGGAGTGAGACCAGGCCAGCCAAGCCAGGCCCGGGCGCTCGGAAAGTGCGGAGCCGTTTCCCCTCTATCTCCACTCTCTCCAGGGCCAGGTGCTCACTGCGCTGCGCCTCTTCGCACGCACCACCCGTACTACGTGCCCACCCGCGCGCGCGCCGAGGAGAAGAGACCCACGACCGTACGTGCGTGCGCGCCATGTCGTCCGCCGCTGGGGGCGGCGGGTACGGCGGCGGCCAGGGTGGAGGCGCGGAGCACCACCACCACCACCACGGGCACGCCGGTCACCTCCTGCTCCACCACCATCCGCAGCACGTGGCCGGCGCGGCCGTTGCGGCAGCGGCCGCGGCGGCGGGCGGGCAGATGTACCACGTGCCCCAGCACAGCCGGCGCGAGAAGCTCCGGTTCCCGCCGGACGCCGGGGACTCGCCACCGCCTCATGGTCATGGTCATGGTCATGCCCCGCAGCAGCAGCAGCAGCACGGGTCGTGGCCTCCGCCCCCGGCGTTCTACTCGTACGCGTCCTCGTCGTCGTCGTACTCCCCGCACAGCCCTACTCTAGCGCAGGCGCAGCTGGTGGCGCACGGGCTGGCGCCGCCGCTCCCGCAGATCCCGACGCAGAACTTCTCGCTGTCGCTCTCCTCCGCGTCGTCGAATCCTCCACCACCGCAGGCGCAGCCGAGGAGGCAGCTCGGCGGCCTCGCGCAGGCCACGGGGCCGTTCGGTCCCTTCACCGGCTACGCCGCCGTGCTCGGCCGGTCCCGTTTCCTCGGCCCGGCAGAGAAGCTGTTCGAGGAGATCTGCGACGTCGGCGGCGCTGCTTCGCACGTCGACCGCACCATCTCCGACGAGGGCCTGCTCGACGCGGATCCGATGGACGGCGTCGATCATGACGTCGTTGATCACGACCTCGGCGGCGCTGACCGCGCAGCGGCCGACGCTGGCCCCATCTCGGGGGCCGAGCAGCAGTGGAAGAAGACGAAGCTCATCTCCATGATGGAAGAGGTTTGCAAGAGGTACCGGCAGTACTACCAGCAGGTTCAGGCTGTGATGGCCTCGTTCGAGACCGTCGCCGGGTTCAGCAACGCCGCGCCGTTCGCGGCATTGGCGCTGAGGGCGATGGCGAAGCACTTCAAGTGCTTGAAGAGCATGATTCTGAACCAGCTGCGCAACACGAGCAACAAGGTCGCTGTGAAGGACGGGCTAAACAAGGAGATCGCCGTGTTCGGGCTCGCCGGGGGTAGCAGCGGCGGCGCCGGCCTCCAGCGAGCGAACAGCGCGAGCGCGTTCGGCCAGCCGCACAATATTTGGCGCCCACAGAGGGGGCTCCCCGAGCGCGCTGTGTCCGTTTTACGCGCGTGGCTGTTCGAACACTTCCTGCACCCGTATCCTACCGATGGTGATAAGCAAATGCTAGCAAAACAAACAGGCTTGACACGCAACCAGGTATCGAACTGGTTTATCAACGCAAGGGTTAGGTTGTGGAAGCCAATGGTGGAAGAAATTCACAACCTAGAGATGAGGCAAATGCACAAGCACTCGGTGGTTGACAAGGGCCAGCATAGCGTGCATCATCAGGCCCAGCATTCTTCGCAGTGCAGCGGGAATCCCTCCGTTCCTTCGGACTCCCATCCTGGACAGAGCAGCAGCATAACTCGGAACCACAACACCGCTGCCTCCCAGGGCTTCCCGGATGAGCTCTCCCAGATGTCCCAGTCCATCCAGGGACAGGTGAGCTTCGCATACAACGGGCTGACCTCGCAGCACAACATTGCATCACCACATCATCAGCACCAGCAGGTCGGCGGTGTTGGTATCGGAGGCGGCAATGGCGGTGTCTCCCTCACCCTTGGTCTTCACCAGAACAACAGGGTCTGCATCGCCGAGCCTCTCCCGGCTGCTCTCCCGGCCAACCTAGCTCACCGTTTCGGACTGGAGGAAGTCAGTGACGCCTATGTGATGAGCTCATTTGGAGGTCAGGACCGGCATTTCGGGAAGGAGATTGGTGGTCACTTGCTGCATGATTTTGTCGGGTGATTGTGGCTGCTGCCTCAGGTTGCTGGTGATGCACTTGTAATGTACTGCTAGTATGATGTTAGGATGGTATATAAGTCAATCACTTGGCGACATGGCTTGATGATCAGTCTGAATCAATTTGTTCGGAGGGTGAAAAAACATTGATCTTCCCTTCATGTAGATCCAGGTATGCTGTCAAATATTTGACACCTTGCGGGCTATAGAGAGATTGACAATACCTTCCCAAGGCAGTAAAGTTGTGTACCATTTGTTATATGCTTAGATTAATCCTTGTACTGTGATGACGAAATGGGCTTAGCTGGCAGAGAAAAAGAAGCTGATGTTATGGCCAAAAAGTGAGGTGATCCTACCAAATGTACTAAAGTAGCTGAAGCTTCAATTTGTCGCTGTAGAATAAGACCTGCTAGGATTTATCTTTCAGCCTGTTTTGTTAGCCTTTCTGCCTTCTTTGGGTGAGCAGTATTAAACTAAGTTAGTAGACTTTTTTCTAAGTATGTCTTGTATCCTTAGACGGGGGTAGCCTCCTAAAGCTTGGACAAACCATGATTTGACCATTTGTTAACCTCTAACTGGCCTCTGTTACACTAATAA
CDS Sequence
- >LOC_Os01g62920.1
ATGTCGTCCGCCGCTGGGGGCGGCGGGTACGGCGGCGGCCAGGGTGGAGGCGCGGAGCACCACCACCACCACCACGGGCACGCCGGTCACCTCCTGCTCCACCACCATCCGCAGCACGTGGCCGGCGCGGCCGTTGCGGCAGCGGCCGCGGCGGCGGGCGGGCAGATGTACCACGTGCCCCAGCACAGCCGGCGCGAGAAGCTCCGGTTCCCGCCGGACGCCGGGGACTCGCCACCGCCTCATGGTCATGGTCATGGTCATGCCCCGCAGCAGCAGCAGCAGCACGGGTCGTGGCCTCCGCCCCCGGCGTTCTACTCGTACGCGTCCTCGTCGTCGTCGTACTCCCCGCACAGCCCTACTCTAGCGCAGGCGCAGCTGGTGGCGCACGGGCTGGCGCCGCCGCTCCCGCAGATCCCGACGCAGAACTTCTCGCTGTCGCTCTCCTCCGCGTCGTCGAATCCTCCACCACCGCAGGCGCAGCCGAGGAGGCAGCTCGGCGGCCTCGCGCAGGCCACGGGGCCGTTCGGTCCCTTCACCGGCTACGCCGCCGTGCTCGGCCGGTCCCGTTTCCTCGGCCCGGCAGAGAAGCTGTTCGAGGAGATCTGCGACGTCGGCGGCGCTGCTTCGCACGTCGACCGCACCATCTCCGACGAGGGCCTGCTCGACGCGGATCCGATGGACGGCGTCGATCATGACGTCGTTGATCACGACCTCGGCGGCGCTGACCGCGCAGCGGCCGACGCTGGCCCCATCTCGGGGGCCGAGCAGCAGTGGAAGAAGACGAAGCTCATCTCCATGATGGAAGAGGTTTGCAAGAGGTACCGGCAGTACTACCAGCAGGTTCAGGCTGTGATGGCCTCGTTCGAGACCGTCGCCGGGTTCAGCAACGCCGCGCCGTTCGCGGCATTGGCGCTGAGGGCGATGGCGAAGCACTTCAAGTGCTTGAAGAGCATGATTCTGAACCAGCTGCGCAACACGAGCAACAAGGTCGCTGTGAAGGACGGGCTAAACAAGGAGATCGCCGTGTTCGGGCTCGCCGGGGGTAGCAGCGGCGGCGCCGGCCTCCAGCGAGCGAACAGCGCGAGCGCGTTCGGCCAGCCGCACAATATTTGGCGCCCACAGAGGGGGCTCCCCGAGCGCGCTGTGTCCGTTTTACGCGCGTGGCTGTTCGAACACTTCCTGCACCCGTATCCTACCGATGGTGATAAGCAAATGCTAGCAAAACAAACAGGCTTGACACGCAACCAGGTATCGAACTGGTTTATCAACGCAAGGGTTAGGTTGTGGAAGCCAATGGTGGAAGAAATTCACAACCTAGAGATGAGGCAAATGCACAAGCACTCGGTGGTTGACAAGGGCCAGCATAGCGTGCATCATCAGGCCCAGCATTCTTCGCAGTGCAGCGGGAATCCCTCCGTTCCTTCGGACTCCCATCCTGGACAGAGCAGCAGCATAACTCGGAACCACAACACCGCTGCCTCCCAGGGCTTCCCGGATGAGCTCTCCCAGATGTCCCAGTCCATCCAGGGACAGGTGAGCTTCGCATACAACGGGCTGACCTCGCAGCACAACATTGCATCACCACATCATCAGCACCAGCAGGTCGGCGGTGTTGGTATCGGAGGCGGCAATGGCGGTGTCTCCCTCACCCTTGGTCTTCACCAGAACAACAGGGTCTGCATCGCCGAGCCTCTCCCGGCTGCTCTCCCGGCCAACCTAGCTCACCGTTTCGGACTGGAGGAAGTCAGTGACGCCTATGTGATGAGCTCATTTGGAGGTCAGGACCGGCATTTCGGGAAGGAGATTGGTGGTCACTTGCTGCATGATTTTGTCGGGTGA
Protein Sequence
- >LOC_Os01g62920.1
MSSAAGGGGYGGGQGGGAEHHHHHHGHAGHLLLHHHPQHVAGAAVAAAAAAAGGQMYHVPQHSRREKLRFPPDAGDSPPPHGHGHGHAPQQQQQHGSWPPPPAFYSYASSSSSYSPHSPTLAQAQLVAHGLAPPLPQIPTQNFSLSLSSASSNPPPPQAQPRRQLGGLAQATGPFGPFTGYAAVLGRSRFLGPAEKLFEEICDVGGAASHVDRTISDEGLLDADPMDGVDHDVVDHDLGGADRAAADAGPISGAEQQWKKTKLISMMEEVCKRYRQYYQQVQAVMASFETVAGFSNAAPFAALALRAMAKHFKCLKSMILNQLRNTSNKVAVKDGLNKEIAVFGLAGGSSGGAGLQRANSASAFGQPHNIWRPQRGLPERAVSVLRAWLFEHFLHPYPTDGDKQMLAKQTGLTRNQVSNWFINARVRLWKPMVEEIHNLEMRQMHKHSVVDKGQHSVHHQAQHSSQCSGNPSVPSDSHPGQSSSITRNHNTAASQGFPDELSQMSQSIQGQVSFAYNGLTSQHNIASPHHQHQQVGGVGIGGGNGGVSLTLGLHQNNRVCIAEPLPAALPANLAHRFGLEEVSDAYVMSSFGGQDRHFGKEIGGHLLHDFVG*