Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice.

Basic Info

Gene ID		OGI # \| Score			Accession \| Assembly \| Annotation			Location		Links
OsAzu_04g0009170		OGI:04053240 \| 16/16			Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)			Chr04:15072947-15077190		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		ATGTCCTCCCGCCCCCGCCTCTCCTCCATCTTCGCCGCTTCCACCGCGGCGTCGACCACCACCACCGTCGCGGCATCGCCATCGCGCCCGCTCCCTCCTGCGTACGCCGCGTTCCAGGAGCGCCTGAGGTCGGGAACGCTCGGGCCCGACGACGCACGCCAACTGTTCGACGAATTGCTACTGCGCCGCGACGACCCTGCCCCTGCCCCCGCCCCCGCGCGCGCCATCAGCGACATCCTCGCTGCGCTCGCCCGCGCGCCGCCTTCCGCCGCCTGCAGTGATGGCCCCGCCCTGGCCGTCGAGCTGTTCAAACGGATGGACCGATGGGCATGCCCCCATGCGGCCGCTGATGCTCTCACCATCTACACCTACAACATCCTCATCGACTGCTACCGCCGAATGCACCGTCCAGAGCTAGCGCTTGCTGTCTTCGGCCGCTTGCTCAGGACGGGCCTGGGTCCGGATGTGTGTTCGTACAACACGCTCATCGACGGTTTCTCTAAGGAGGGCGAGGTGGACAAAGCTTACGAGTTGTTCTATAAGATGATAGAACAGTCCGTTTCGCCTGATGTGGTCACTTATAACTCACTCATCGATGGGCTCTGCAAGACAAAGGAAATGGTGAAGTCTGAGCGTGTTCTGGAGCAGATGGTTGATGCCGGTATTCGACCTAATAACAAGACATACAATAGCCTGATATATGGATATTCCACTGCGGGAATGTGGAAGGAGTCGGTTAGAGTGTTCAAAGAAATGTCAAGCTCCGGTCTCATACCATGTGTTGTTAATTGCAACTCCTTCATTCATGCTCTCTGCAGGCACAATAGAATCAAAGAAGCAAAAGATATTTTTGATTCAATGGTTCTGAAGGGCCCCAAACCTAACATTATCTCCTACTCTACCCTGCTTCATGGGTATGCTGCTGAAGGTTGCTTTGCCAACATGAATAGCCTCGTTAATTTGATGGTATCTAAAGGTATTGTACCTAACCACCGTTTTTTCAACATACTGATTAATGCATATGCTCGTTGTGGGATGATGGATAAGGCTATGCTTATATTTGAAGACATGCAGAACAAAGGAATGATCCCTGACACTGTCACATTTGCAACCGTGATATCTTCTCTTTGCAGAATTGGCAGGTTGGATGATGCTCTGCACAAATTCAACCACATGGTTGATATTGGTGTACCACCGAGTGAGGCTGTTTACCGCTGTCTGATCCAGGGTTGTTGTAATCATGGTGAGTTGGTAAAAGCCAAGGAATTGATTTCTGAAATGATGAACAAGGATATTCCTCCTCCTGGTGTCAAGTATTTCAGTTCAATAATAAACAACCTGTGCAAAGAGGGAAGGGTAGCAGAAGGGAAAGATATCATGGACATGATGGTACAAACGGGGCAAAGGCCTAATGTTGTTACTTTTAATTCATTGATGGAGGGATATTGCTTAGTTGGTAATATGGAGGAGGCATTTGCATTACTTGATGCTATGGCATCAATTGGCATTGAACTGAATTGTTACATATATGGTACGCTTGTTGATGGCTATTGTAAAAATGGAAGGATTGATGATGCATTGACTGTATTCAGAGACATGTTGCACAAGGGAGTCAAGCCTACAAGTGTTTTATATAACATCATTCTCCATGGGTTATTTCAGGCCAGGAGGACAACTGCTGCAAAGAAAATGTTCCATGAGATGATTGAAAGTGGAACGACCGTGAGCATTCAGACATACGGTGTTGTGCTTGGTGGACTTTGTAGAAACAATTGCACCGATGAAGCAAATATGCTGTTGGAGAAATTATTTGCTATGAATGTAAAATTTGATATCATTACTTTCAATATTGTGATTAGTGCAATGCTCAAAGTTGGCAGAAGGCAAGAGGCTAAGGAATTGTTTGCTGCTATCTCAACTTATGGGTTGGTGCCTACCGTACATACCTACAACTTGATGATATCAAATCTTATAAAAGAAGAGTCATACGAAGAGGCTGACAATCTCTTTATATCAGTGGAGAAGAGTGGCCGTGCTCCTGACTCTCGTCTTCTTAATCATATCGTCAGGATGTTACTCAAGAAAGCTGAGGTTGCCAAAGCTAGTAATTATCTGTCTATAATTGACGAGAATAACCTCACTCTTGAAGCTTCAACTATTTCTTTACTGGCTTCTCTCTTCTCAAGGGAAGGTAAATGTCGGGAGCATATAAAATTGCTCCCTGCAAAGTATCAGTTTCTTTAGTTAGCTTGGCACTTGTAATACATTGTTGTATCTGAAATTACATTAAACATATGGCACTCTTGAGTTTATTGTGCTCCTACAGAAAGAACAAAACATGCCTCAGAAAAGTCAGGTATTGATTCTTTTGTTATTATTGTTTTTCTAAGAGACGTTGTTGTTGTCTATGATGCTATATTTGTGTTTTGAAATTGTGACCATGTGTATTCTATGTTTTTTTTTAAGAAATAAGAAAGCTAGACAATGGAGTGCAAAACAAATGGTTGTATTTCTAAACATGATAACGTGTAATGGACAAGGTAGTCAGGTATGTATAGTAGAACCTATCTGTAGATAATAATTTTGAGTTCCTTTTGGTAAAAATCTTGACCCCGGTAATTTTGCATACTCTTTAACAGCAGTATTTTGACCAACTATGGTATTTAGCATATATTCTTCCTGCTGCAAGGGAAGAAATGGTCGATCCCTTGTAGGAGTTCAGAGTTGAACCGTGTATTACAGTTCTCTTTCAAAGCCCACAGGATGAAAATACACTTAGCAGCTCACGTTATTCATTCTTTAGCAATAATGCAATTGGCCCCACATAAAGTTCTGTGCATTCTTAATGAGCCTGATGAACTGCTGAGCGAGCCATGTTGCTGAAATGGCACGATTTGATTCTTATGACATCTGTGATATATGCTGGGAACTCCATACCAGTTTTTGAGATCTGTAATTTTTTTAGCAGGCCACAAAGCATCATACTGGAGCTTTGCTCACTTCTGCTATCCTCATACTGGAGCATTTTTAGAATGTGTTTGTTGACATGACATGCCTTTTGTTTCTATCGGAATGACAGTAATGATGGCGTAGGATTAAATAGGTCAATCGTTTAACTTGGCATGCACCACAGATGCTCCAGCTTGTGCGTTTCATTACTGAACTGGAAAATGCTCCTGGTGGGGTCCAGCAATTGTAGAAGCACCAAAACAATGCAGAAAATAGTAAAACCATATAATCATTTATGCCTTTTAGATACTCAGGGGGAACCTTCTGAAACATGCCTCTCCAGTCCTAAGGAGTTGTCAGGCTCATCCAATAAGAATTTGCAACAGGTCAGATTTTCTCTAGGATTACTAATCCAATTCATGTCCCCATTGGTGGTTACTCTGTTCTTCTGGAACTACTACATGTTGTAATCTAGCGATGGCCGTTTCGGTGCTTGGCTTCCCTCTCTGTAGCATGTGTTTGGGCGGATGGCACATGGTTTGGGGCGTGTGCTCTGGTGCACATCCTTCCTCGACAGCCAGCTATCGATGAAAAACTTTTCTTATAACTTTTTCTTCCTATCTTAATTACATTGAATGACCTCCTTCAGTCATTCCGGCAAAATACATGTTGTAATCTCACCGGTTGTTTCTAGATACTGGACTAATCTTTTCCTTTGTAAAATTTTGTTTCCATTTCACTCTTCGATATGAATTCCAGCACATACAGTACCCGTAACTATTGATGTTGTTTTAATTGATTCATACACCATATCTGTATTCCTTTTTGTTCTTCAGATTTATGAGAGTTCATGCCAAACTTTGCTTTATTCTTTCTTTCCAATAGGACAGATGATGTTATGGACTGATTTGGAGAAATAGCAATATATTTGTTTGGGCGGCAGGTAGAGAGAAAAAGATAGAAGAAGGAAGAACCCTGCAGAAGGGAGAAGATACTCGGTAAAGCTTATCTCTTGATTTCCTAGTATGCCATTTGCAATTTGTCTGTTGCTTCTCATGCACCTGATTTTCTGCCCTTCCAATGACAGGTGATGCATGGTTCATAGAGGTGAGATGAGCACCCAACTAGGCAACTATTGCAGTATGATTTCCTCTGCACCTTTATTGATGATAGCATACACTGAAGCTTCAACTACTTTCTTTCTTCTGGACTCGATTTTGTCAGTATGAGCAGTAGAACTTGGTGCATACAGATCAGATGGCTATTCTTCTGTTGACGAGAACTCACTGCACTGA More
CDS seq		ATGTCCTCCCGCCCCCGCCTCTCCTCCATCTTCGCCGCTTCCACCGCGGCGTCGACCACCACCACCGTCGCGGCATCGCCATCGCGCCCGCTCCCTCCTGCGTACGCCGCGTTCCAGGAGCGCCTGAGGTCGGGAACGCTCGGGCCCGACGACGCACGCCAACTGTTCGACGAATTGCTACTGCGCCGCGACGACCCTGCCCCTGCCCCCGCCCCCGCGCGCGCCATCAGCGACATCCTCGCTGCGCTCGCCCGCGCGCCGCCTTCCGCCGCCTGCAGTGATGGCCCCGCCCTGGCCGTCGAGCTGTTCAAACGGATGGACCGATGGGCATGCCCCCATGCGGCCGCTGATGCTCTCACCATCTACACCTACAACATCCTCATCGACTGCTACCGCCGAATGCACCGTCCAGAGCTAGCGCTTGCTGTCTTCGGCCGCTTGCTCAGGACGGGCCTGGGTCCGGATGTGTGTTCGTACAACACGCTCATCGACGGTTTCTCTAAGGAGGGCGAGGTGGACAAAGCTTACGAGTTGTTCTATAAGATGATAGAACAGTCCGTTTCGCCTGATGTGGTCACTTATAACTCACTCATCGATGGGCTCTGCAAGACAAAGGAAATGGTGAAGTCTGAGCGTGTTCTGGAGCAGATGGTTGATGCCGGTATTCGACCTAATAACAAGACATACAATAGCCTGATATATGGATATTCCACTGCGGGAATGTGGAAGGAGTCGGTTAGAGTGTTCAAAGAAATGTCAAGCTCCGGTCTCATACCATGTGTTGTTAATTGCAACTCCTTCATTCATGCTCTCTGCAGGCACAATAGAATCAAAGAAGCAAAAGATATTTTTGATTCAATGGTTCTGAAGGGCCCCAAACCTAACATTATCTCCTACTCTACCCTGCTTCATGGAATTGGCAGGTTGGATGATGCTCTGCACAAATTCAACCACATGGTTGATATTGGTGTACCACCGAGTGAGGCTGTTTACCGCTGTCTGATCCAGGGTTGTTGTAATCATGGTGAGTTGGTAAAAGCCAAGGAATTGATTTCTGAAATGATGAACAAGGATATTCCTCCTCCTGGTGTCAAGTATTTCAGTTCAATAATAAACAACCTGTGCAAAGAGGGAAGGGTAGCAGAAGGGAAAGATATCATGGACATGATGGTACAAACGGGGCAAAGGCCTAATGTTGTTACTTTTAATTCATTGATGGAGGGATATTGCTTAGTTGGTAATATGGAGGAGGCATTTGCATTACTTGATGCTATGGCATCAATTGGCATTGAACTGAATTGTTACATATATGGTACGCTTGTTGATGGCTATTGTAAAAATGGAAGGATTGATGATGCATTGACTGTATTCAGAGACATGTTGCACAAGGGAGTCAAGCCTACAAGTGTTTTATATAACATCATTCTCCATGGGTTATTTCAGGCCAGGAGGACAACTGCTGCAAAGAAAATGTTCCATGAGATGATTGAAAGTGGAACGACCGTGAGCATTCAGACATACGGTGTTGTGCTTGGTGGACTTTGTAGAAACAATTGCACCGATGAAGCAAATATGCTGTTGGAGAAATTATTTGCTATGAATGTAAAATTTGATATCATTACTTTCAATATTGTGATTAGTGCAATGCTCAAAGTTGGCAGAAGGCAAGAGGCTAAGGAATTGTTTGCTGCTATCTCAACTTATGGGTTGGTGCCTACCGTACATACCTACAACTTGATGATATCAAATCTTATAAAAGAAGAGTCATACGAAGAGGCTGACAATCTCTTTATATCAGTGGAGAAGAGTGGCCGTGCTCCTGACTCTCGTCTTCTTAATCATATCGTCAGGATGTTACTCAAGAAAGCTGAGGTTGCCAAAGCTAGTAATTATCTGTCTATAATTGACGAGAATAACCTCACTCTTGAAGCTTCAACTATTTCTTTACTGGCTTCTCTCTTCTCAAGGGAAGTAGAACTTGGTGCATACAGATCAGATGGCTATTCTTCTGTTGACGAGAACTCACTGCACTGA More
Protein seq		MSSRPRLSSIFAASTAASTTTTVAASPSRPLPPAYAAFQERLRSGTLGPDDARQLFDELLLRRDDPAPAPAPARAISDILAALARAPPSAACSDGPALAVELFKRMDRWACPHAAADALTIYTYNILIDCYRRMHRPELALAVFGRLLRTGLGPDVCSYNTLIDGFSKEGEVDKAYELFYKMIEQSVSPDVVTYNSLIDGLCKTKEMVKSERVLEQMVDAGIRPNNKTYNSLIYGYSTAGMWKESVRVFKEMSSSGLIPCVVNCNSFIHALCRHNRIKEAKDIFDSMVLKGPKPNIISYSTLLHGIGRLDDALHKFNHMVDIGVPPSEAVYRCLIQGCCNHGELVKAKELISEMMNKDIPPPGVKYFSSIINNLCKEGRVAEGKDIMDMMVQTGQRPNVVTFNSLMEGYCLVGNMEEAFALLDAMASIGIELNCYIYGTLVDGYCKNGRIDDALTVFRDMLHKGVKPTSVLYNIILHGLFQARRTTAAKKMFHEMIESGTTVSIQTYGVVLGGLCRNNCTDEANMLLEKLFAMNVKFDIITFNIVISAMLKVGRRQEAKELFAAISTYGLVPTVHTYNLMISNLIKEESYEEADNLFISVEKSGRAPDSRLLNHIVRMLLKKAEVAKASNYLSIIDENNLTLEASTISLLASLFSREVELGAYRSDGYSSVDENSLH
Function		Protein Rf1, mitochondrial [UniProtKB/Swiss-Prot:Q76C99]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsAzu_04g0009170	OsAzu_04g0009170.01	Chr04	15072947	15077190	+	NAM
CDS seq	ATGTCCTCCCGCCCCCGCCTCTCCTCCATCTTCGCCGCTTCCACCGCGGCGTCGACCACCACCACCGTCGCGGCATCGCCATCGCGCCCGCTCCCTCCTGCGTACGCCGCGTTCCAGGAGCGCCTGAGGTCGGGAACGCTCGGGCCCGACGACGCACGCCAACTGTTCGACGAATTGCTACTGCGCCGCGACGACCCTGCCCCTGCCCCCGCCCCCGCGCGCGCCATCAGCGACATCCTCGCTGCGCTCGCCCGCGCGCCGCCTTCCGCCGCCTGCAGTGATGGCCCCGCCCTGGCCGTCGAGCTGTTCAAACGGATGGACCGATGGGCATGCCCCCATGCGGCCGCTGATGCTCTCACCATCTACACCTACAACATCCTCATCGACTGCTACCGCCGAATGCACCGTCCAGAGCTAGCGCTTGCTGTCTTCGGCCGCTTGCTCAGGACGGGCCTGGGTCCGGATGTGTGTTCGTACAACACGCTCATCGACGGTTTCTCTAAGGAGGGCGAGGTGGACAAAGCTTACGAGTTGTTCTATAAGATGATAGAACAGTCCGTTTCGCCTGATGTGGTCACTTATAACTCACTCATCGATGGGCTCTGCAAGACAAAGGAAATGGTGAAGTCTGAGCGTGTTCTGGAGCAGATGGTTGATGCCGGTATTCGACCTAATAACAAGACATACAATAGCCTGATATATGGATATTCCACTGCGGGAATGTGGAAGGAGTCGGTTAGAGTGTTCAAAGAAATGTCAAGCTCCGGTCTCATACCATGTGTTGTTAATTGCAACTCCTTCATTCATGCTCTCTGCAGGCACAATAGAATCAAAGAAGCAAAAGATATTTTTGATTCAATGGTTCTGAAGGGCCCCAAACCTAACATTATCTCCTACTCTACCCTGCTTCATGGAATTGGCAGGTTGGATGATGCTCTGCACAAATTCAACCACATGGTTGATATTGGTGTACCACCGAGTGAGGCTGTTTACCGCTGTCTGATCCAGGGTTGTTGTAATCATGGTGAGTTGGTAAAAGCCAAGGAATTGATTTCTGAAATGATGAACAAGGATATTCCTCCTCCTGGTGTCAAGTATTTCAGTTCAATAATAAACAACCTGTGCAAAGAGGGAAGGGTAGCAGAAGGGAAAGATATCATGGACATGATGGTACAAACGGGGCAAAGGCCTAATGTTGTTACTTTTAATTCATTGATGGAGGGATATTGCTTAGTTGGTAATATGGAGGAGGCATTTGCATTACTTGATGCTATGGCATCAATTGGCATTGAACTGAATTGTTACATATATGGTACGCTTGTTGATGGCTATTGTAAAAATGGAAGGATTGATGATGCATTGACTGTATTCAGAGACATGTTGCACAAGGGAGTCAAGCCTACAAGTGTTTTATATAACATCATTCTCCATGGGTTATTTCAGGCCAGGAGGACAACTGCTGCAAAGAAAATGTTCCATGAGATGATTGAAAGTGGAACGACCGTGAGCATTCAGACATACGGTGTTGTGCTTGGTGGACTTTGTAGAAACAATTGCACCGATGAAGCAAATATGCTGTTGGAGAAATTATTTGCTATGAATGTAAAATTTGATATCATTACTTTCAATATTGTGATTAGTGCAATGCTCAAAGTTGGCAGAAGGCAAGAGGCTAAGGAATTGTTTGCTGCTATCTCAACTTATGGGTTGGTGCCTACCGTACATACCTACAACTTGATGATATCAAATCTTATAAAAGAAGAGTCATACGAAGAGGCTGACAATCTCTTTATATCAGTGGAGAAGAGTGGCCGTGCTCCTGACTCTCGTCTTCTTAATCATATCGTCAGGATGTTACTCAAGAAAGCTGAGGTTGCCAAAGCTAGTAATTATCTGTCTATAATTGACGAGAATAACCTCACTCTTGAAGCTTCAACTATTTCTTTACTGGCTTCTCTCTTCTCAAGGGAAGTAGAACTTGGTGCATACAGATCAGATGGCTATTCTTCTGTTGACGAGAACTCACTGCACTGA More
Protein seq	MSSRPRLSSIFAASTAASTTTTVAASPSRPLPPAYAAFQERLRSGTLGPDDARQLFDELLLRRDDPAPAPAPARAISDILAALARAPPSAACSDGPALAVELFKRMDRWACPHAAADALTIYTYNILIDCYRRMHRPELALAVFGRLLRTGLGPDVCSYNTLIDGFSKEGEVDKAYELFYKMIEQSVSPDVVTYNSLIDGLCKTKEMVKSERVLEQMVDAGIRPNNKTYNSLIYGYSTAGMWKESVRVFKEMSSSGLIPCVVNCNSFIHALCRHNRIKEAKDIFDSMVLKGPKPNIISYSTLLHGIGRLDDALHKFNHMVDIGVPPSEAVYRCLIQGCCNHGELVKAKELISEMMNKDIPPPGVKYFSSIINNLCKEGRVAEGKDIMDMMVQTGQRPNVVTFNSLMEGYCLVGNMEEAFALLDAMASIGIELNCYIYGTLVDGYCKNGRIDDALTVFRDMLHKGVKPTSVLYNIILHGLFQARRTTAAKKMFHEMIESGTTVSIQTYGVVLGGLCRNNCTDEANMLLEKLFAMNVKFDIITFNIVISAMLKVGRRQEAKELFAAISTYGLVPTVHTYNLMISNLIKEESYEEADNLFISVEKSGRAPDSRLLNHIVRMLLKKAEVAKASNYLSIIDENNLTLEASTISLLASLFSREVELGAYRSDGYSSVDENSLH More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.129175	0.0	0.000000

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_04g0349600	RBH	1.804112	1.796293	0.000000
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os04g28300	SBH	0.142335	0.280675	0.060394
Nipponbare \| IRGSP 1.0 \| RAP-db	Os04g0349600	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_04g0009270	SBH	0.068413	0.0	0.723975
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_04g0009950	RBH	0.376962	0.0	0.616493
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_04g0009740	RBH	0.562909	1.955666	0.987335
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_04g0009400	RBH	0.207296	0.045744	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_04g0009620	SBH	1.548575	0.0	0.779863
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_04G0265100	SBH	1.1930065	1.37742	0.501284
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_04g0008650	RBH	0.073570	0.000000	0.250776
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_04G0262800	SBH	0.248793	0.1167355	1.815949
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_04g0009190	RBH	0.137095	0.079411	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_04g0008820	RBH	0.945277	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_04g0008870	RBH	5.623301	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_04g0009380	RBH	0.129305	0.000000	0.149680
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_04g0009530	RBH	0.104267	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_04G008700	RBH	0.219173	0.974827	0.056668
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_04g0008730	RBH	1.335729	1.733793	1.706826

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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