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
OsZS97_02G0488900		OGI:02079950 \| 16/16			Zhenshan 97 \| ZS97RS3 \| HZAU			Chr02:29706266-29709923		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		OsbHLH049
DNA seq		GAACGAAGCACAGCTATAGTTTTGCTGCTCTAGCTCTCCCTCTCTCTACCGCTTGCATAGTTTCATTGCATGGCTGTCTGGGTGGCCGCACATCCCACCACTGTTGCTGTGCCTAAACCTTATCTTTTCCCCATATAACCAGCTCACACCGCTAGAGAGAAAGAAACATACGCATCCCACCAACGCGACGAGCTCAGAATCTCAGAAGTCAGCAGCAGCAAAGAGGCGATAAGTAGCCGCGGCTCACCGTTCGTTGCCCAAAACCACCCAAAAGCGTAGCGACACACGAGAAGCCACCAGCCAACGTAGTACGCGCCGAGAGCTGAGGCCATCCACGACACACGACCATGAGCACACTAGTAGACGCGCTGTGCGCTCCCTGCAGCGACACCGCGCTCATCTACGACACCTTCAACGCCTCCGCCGCCGCGAGCTTCCTCTTCGACAATGCCGCCGCCTTCTGCGACGCTGACATCCTCGGCGCCACGGCGACAGGGGAGAAGGAGGCGACGTCGTCGGCCGCGGCCGCGGCCGCGGACGCCGCCCCGCCGAGGAAGAAGCGGCGGCGGCGCGCGAAGAGCTGCAAGTCGCGGGAGGAGACGGAGACCCAGCGGATGACGCACATCGCCGTGGAGCGCAACCGCCGGCGCCAGATGAACGAGTACCTCGCCATCCTCCGGTCGCTCATGCCGGAGCCCTACGTCCAGAGGGTACGTCGTACTACGCGCGCCGGCACACGTCTCTCTCGCCCTCTCTGTTTTGGTTTTTTTTAGCAAACCGACATCGCTTCGTGTCAAGTGTTTCTACCCTCTTTTGTTCTGTATATCTGCGTTGCTCCCATTTGTCAAAGAGCAAGAAAGCGATGTCGGAGCAACCGGCGAGGAGAACGGCGATGAGAGAATGTTTGGCCGAAAGAGACTCCCCCGCCATGGCGCCATTGTCCGCCATTACTCATGGCGTATCGTCTCTTTACTGCTCAATCTCTTTTCATGAACAGAAGCATCCATTCTTTGCACAGAAACCTTCTGCCCATTAATGTGTCTCCCCTATCATTAATTCACTCGTACACAGAGAGAGTTGCCTGGATGGGCCTGTCATGTCAAATTTAATGCGTTCTTGATCATTTTTAAATGTTGTGTAGGGCGACCAGGCGTCCATTGTGGGAGGCGCAATCGAGTTCGTGAAGGAGCTCGAGCAGCAGCTGCAGTCGCTTGAGGCGCAGAAGCGAACGCTGCTCCCTCACCACAAGGCGAGATGCGACGACGCAACGCCGACGCATAACGCCAGCGGCAGCAACGTCGGGGCCGGCGGCTGCATGGAGCCCACGACGACAACGAGCAACTGCAGCAGCAGCGTCACCGAGGACGCGCCGTCCGCCGACGCGCCCCCGTTCGCGCAGTTCTTCGCGTACCCGCAGTACGTGTGGTGCCACTCGCCGCGCGACTCCACCACCACCACCACCGCGGCGTCTGCGTCGGCGTCGGCTTCGGCGTCGTCGTCGTCGCCGGCCACGGTGGCGGCGGCGCTCCAGTCCGAGCACCGCTCCGGGTTGGCCGACATCGAGGTGAGCCTGGTCGAGACGCACGCCAGCGTCCGTGTCATGTCACCGCGGCGGCCAGGGCAGCTGCTCAAGATGATCGCCGGCCTGCAGGCCCTCCGGCTCACCGTGCTGCACCTCAACGTCACCACGCTGGACTCCCTTGTGCTCTACACCCTCAGCGTCAAGGTACGCCTACGCCTATCGCCTGCGTCTGCAGCCGTGCACTGATTTCAGTTCTTTTTTCAACAAAAGTGCCTCAATTTTCGGCCACTGCATTTCACACGCATTTCGCGCTGAAACGCGCACCGATGCAGTAGCTAGCCAGGCGCTCAAACCGAGCGATACCACCAGCACAAACGTTTGTGCGTGTCTCCATGCATGGTTTGGGAATCATGAGGTCACTTCAACCGAGTTAATTAATCGGAGTAATCTGGGACGATTATTAGAGACGGTGTTTGATTGGTATAGCGTCTGAAAAGAAAACGTGTCAGATATTCTCCTGCCTGCACTGCACAGCACAGGCATAGGTCATCGCATCAAGGACGCAGTTGTGCAGGCCCCCAAACAGTATAATGAACAGAAACAAGAGATGAGCAGAGATGGAGATCGCTTCACCCATCGGCTTTCGATCAAGCATCATTGTTCGAGACGCATCAAAATTTCTCAGAATTTGATCGAATCCGATGGACCTGACTAGGAGCCTGAGTGCCTGGCCACCTGAGTCCTTTCCTGCTTCCCCTTCTCGCTTGTTGTTCGCTTTTGACCGGATACTCCGTAGGAGTATTTCAGTAGGAGTAGGCAGGTCGGGCCCCTGCAGCCAAAGGACTTGTCAAGTCCAAACGGTGAGTAGCGCACAGTACTACTAGTGGTCTGGTAGTCCTATGGGGTGTTTGGGAGAGAGGGGCTGTGCGTAGTGTGACGCTTCACGAAAAAGCTACTGCATCAGTCAGTCCAGATTGTGTAAGAAAAACGCTGCCACGGAGAATCCTTTCTGCTGAGCTGAGCCATGCTATAGATTTCGACTGGCATAGAGAACTGAGCAGAAAAGGCTATAGCTACAGTAGGCACAAGTATAGCGCTGGTGTTCAGCCATGATAGTGTGTGACAGTTCCCCGATGGAATCTGTGTGCGAGTAGTGCTAATCTACGGCATTTTTTTTGCGACTAGTGGCAGATTCCTTCGCTCCCTAACCGGCCATTGCACATGCACGCAATCTCATTAGTTCTCGTCTAATCCTAATCTTGTCTTTGCGTGGCCGTGTGCTGCACAGGTGGAGGAAGGATGCAGCCTGACGACGGTGGACGACATCGCGGCGGCGGTGCACCACGTGCTCTGCATCGTCGACGCGGAGGCGGCCGCCTCGGAGCATCTCCTCGCGGCGGGGCAACTGGCCACGACGGCGACGGCGGTGGCGAAGAGAGAACTCGCGACGTACATGTACTGAGCCGCTCCAAGTGCCTTACATGTCGTCGTTTGTGTGGTCGCGTGTACTGTATGCCGCGCTCCCGTTTTTCTCCCCTTTTTAGGCTCGTCACGTTTTTGCTGTGTAGTGGCCCGGCAGGTTAGATCTAGTTCTAGTTGTACTAGTAGATGCAAAATGCTATGTGTTCAGTAGTCCCAGCCTCTCGACGAGGGCGTACTTGTCTGTTTCTCGTTCTGAAAACAGAATGTTGTATTGCTGTACCTGTACAGTATCCTGCCTCGCCTTTCTGTAATAAGAGCGACTAGCGAGTAGCGACATTGGAAGGAACAGTTCGAGATTCGTATTATCCGAACCGGGCCTTATGAGGGTACTAGCTTACAATGGGCCATGTGAGTTACCACTGCTTCATGGCAAGGGCGGGCTTTAGCCCATCAACCGTGTGATTTGCTCGATTTGTGGGCCGTGATAAGGCCGAAGGCCAGCTTGCTGCCAAATCTCCAACCAGCCCCGCCGACCACCAGGAGCAAATCAACCCGTTTGACGGTTTGAAAAGTGGTCTATGCTGATATGGCATGTTGATTTGGTCCACCTGTGATGAATGAACTTTGTATGATTATATTTGTAGTACCACATCTATATCTATACCTAATATAAATATTCGGATTTTTTCTGTCGTCACATCCTTTTCACCAGCG More
CDS seq		ATGAGCACACTAGTAGACGCGCTGTGCGCTCCCTGCAGCGACACCGCGCTCATCTACGACACCTTCAACGCCTCCGCCGCCGCGAGCTTCCTCTTCGACAATGCCGCCGCCTTCTGCGACGCTGACATCCTCGGCGCCACGGCGACAGGGGAGAAGGAGGCGACGTCGTCGGCCGCGGCCGCGGCCGCGGACGCCGCCCCGCCGAGGAAGAAGCGGCGGCGGCGCGCGAAGAGCTGCAAGTCGCGGGAGGAGACGGAGACCCAGCGGATGACGCACATCGCCGTGGAGCGCAACCGCCGGCGCCAGATGAACGAGTACCTCGCCATCCTCCGGTCGCTCATGCCGGAGCCCTACGTCCAGAGGGGCGACCAGGCGTCCATTGTGGGAGGCGCAATCGAGTTCGTGAAGGAGCTCGAGCAGCAGCTGCAGTCGCTTGAGGCGCAGAAGCGAACGCTGCTCCCTCACCACAAGGCGAGATGCGACGACGCAACGCCGACGCATAACGCCAGCGGCAGCAACGTCGGGGCCGGCGGCTGCATGGAGCCCACGACGACAACGAGCAACTGCAGCAGCAGCGTCACCGAGGACGCGCCGTCCGCCGACGCGCCCCCGTTCGCGCAGTTCTTCGCGTACCCGCAGTACGTGTGGTGCCACTCGCCGCGCGACTCCACCACCACCACCACCGCGGCGTCTGCGTCGGCGTCGGCTTCGGCGTCGTCGTCGTCGCCGGCCACGGTGGCGGCGGCGCTCCAGTCCGAGCACCGCTCCGGGTTGGCCGACATCGAGGTGAGCCTGGTCGAGACGCACGCCAGCGTCCGTGTCATGTCACCGCGGCGGCCAGGGCAGCTGCTCAAGATGATCGCCGGCCTGCAGGCCCTCCGGCTCACCGTGCTGCACCTCAACGTCACCACGCTGGACTCCCTTGTGCTCTACACCCTCAGCGTCAAGGTGGAGGAAGGATGCAGCCTGACGACGGTGGACGACATCGCGGCGGCGGTGCACCACGTGCTCTGCATCGTCGACGCGGAGGCGGCCGCCTCGGAGCATCTCCTCGCGGCGGGGCAACTGGCCACGACGGCGACGGCGGTGGCGAAGAGAGAACTCGCGACGTACATGTACTGA More
Protein seq		MSTLVDALCAPCSDTALIYDTFNASAAASFLFDNAAAFCDADILGATATGEKEATSSAAAAAADAAPPRKKRRRRAKSCKSREETETQRMTHIAVERNRRRQMNEYLAILRSLMPEPYVQRGDQASIVGGAIEFVKELEQQLQSLEAQKRTLLPHHKARCDDATPTHNASGSNVGAGGCMEPTTTTSNCSSSVTEDAPSADAPPFAQFFAYPQYVWCHSPRDSTTTTTAASASASASASSSSPATVAAALQSEHRSGLADIEVSLVETHASVRVMSPRRPGQLLKMIAGLQALRLTVLHLNVTTLDSLVLYTLSVKVEEGCSLTTVDDIAAAVHHVLCIVDAEAAASEHLLAAGQLATTATAVAKRELATYMY
Function		Transcription factor bHLH96 [UniProtKB/Swiss-Prot:Q9C7T4]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsZS97_02G0488900	OsZS97_02T0488900.1	Chr02	29706266	29709923	+	makerRMon
CDS seq	ATGAGCACACTAGTAGACGCGCTGTGCGCTCCCTGCAGCGACACCGCGCTCATCTACGACACCTTCAACGCCTCCGCCGCCGCGAGCTTCCTCTTCGACAATGCCGCCGCCTTCTGCGACGCTGACATCCTCGGCGCCACGGCGACAGGGGAGAAGGAGGCGACGTCGTCGGCCGCGGCCGCGGCCGCGGACGCCGCCCCGCCGAGGAAGAAGCGGCGGCGGCGCGCGAAGAGCTGCAAGTCGCGGGAGGAGACGGAGACCCAGCGGATGACGCACATCGCCGTGGAGCGCAACCGCCGGCGCCAGATGAACGAGTACCTCGCCATCCTCCGGTCGCTCATGCCGGAGCCCTACGTCCAGAGGGGCGACCAGGCGTCCATTGTGGGAGGCGCAATCGAGTTCGTGAAGGAGCTCGAGCAGCAGCTGCAGTCGCTTGAGGCGCAGAAGCGAACGCTGCTCCCTCACCACAAGGCGAGATGCGACGACGCAACGCCGACGCATAACGCCAGCGGCAGCAACGTCGGGGCCGGCGGCTGCATGGAGCCCACGACGACAACGAGCAACTGCAGCAGCAGCGTCACCGAGGACGCGCCGTCCGCCGACGCGCCCCCGTTCGCGCAGTTCTTCGCGTACCCGCAGTACGTGTGGTGCCACTCGCCGCGCGACTCCACCACCACCACCACCGCGGCGTCTGCGTCGGCGTCGGCTTCGGCGTCGTCGTCGTCGCCGGCCACGGTGGCGGCGGCGCTCCAGTCCGAGCACCGCTCCGGGTTGGCCGACATCGAGGTGAGCCTGGTCGAGACGCACGCCAGCGTCCGTGTCATGTCACCGCGGCGGCCAGGGCAGCTGCTCAAGATGATCGCCGGCCTGCAGGCCCTCCGGCTCACCGTGCTGCACCTCAACGTCACCACGCTGGACTCCCTTGTGCTCTACACCCTCAGCGTCAAGGTGGAGGAAGGATGCAGCCTGACGACGGTGGACGACATCGCGGCGGCGGTGCACCACGTGCTCTGCATCGTCGACGCGGAGGCGGCCGCCTCGGAGCATCTCCTCGCGGCGGGGCAACTGGCCACGACGGCGACGGCGGTGGCGAAGAGAGAACTCGCGACGTACATGTACTGA More
Protein seq	MSTLVDALCAPCSDTALIYDTFNASAAASFLFDNAAAFCDADILGATATGEKEATSSAAAAAADAAPPRKKRRRRAKSCKSREETETQRMTHIAVERNRRRQMNEYLAILRSLMPEPYVQRGDQASIVGGAIEFVKELEQQLQSLEAQKRTLLPHHKARCDDATPTHNASGSNVGAGGCMEPTTTTSNCSSSVTEDAPSADAPPFAQFFAYPQYVWCHSPRDSTTTTTAASASASASASSSSPATVAAALQSEHRSGLADIEVSLVETHASVRVMSPRRPGQLLKMIAGLQALRLTVLHLNVTTLDSLVLYTLSVKVEEGCSLTTVDDIAAAVHHVLCIVDAEAAASEHLLAAGQLATTATAVAKRELATYMY More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsZS97_02G0488900	OsZS97_02T0488900.2	Chr02	29707123	29709923	+	makerRMon
CDS seq	ATGGCGTATCGTCTCTTTACTGCTCAATCTCTTTTCATGAACAGAAGCATCCATTCTTTGCACAGAAACCTTCTGCCCATTAATGGCGACCAGGCGTCCATTGTGGGAGGCGCAATCGAGTTCGTGAAGGAGCTCGAGCAGCAGCTGCAGTCGCTTGAGGCGCAGAAGCGAACGCTGCTCCCTCACCACAAGGCGAGATGCGACGACGCAACGCCGACGCATAACGCCAGCGGCAGCAACGTCGGGGCCGGCGGCTGCATGGAGCCCACGACGACAACGAGCAACTGCAGCAGCAGCGTCACCGAGGACGCGCCGTCCGCCGACGCGCCCCCGTTCGCGCAGTTCTTCGCGTACCCGCAGTACGTGTGGTGCCACTCGCCGCGCGACTCCACCACCACCACCACCGCGGCGTCTGCGTCGGCGTCGGCTTCGGCGTCGTCGTCGTCGCCGGCCACGGTGGCGGCGGCGCTCCAGTCCGAGCACCGCTCCGGGTTGGCCGACATCGAGGTGAGCCTGGTCGAGACGCACGCCAGCGTCCGTGTCATGTCACCGCGGCGGCCAGGGCAGCTGCTCAAGATGATCGCCGGCCTGCAGGCCCTCCGGCTCACCGTGCTGCACCTCAACGTCACCACGCTGGACTCCCTTGTGCTCTACACCCTCAGCGTCAAGGTGGAGGAAGGATGCAGCCTGACGACGGTGGACGACATCGCGGCGGCGGTGCACCACGTGCTCTGCATCGTCGACGCGGAGGCGGCCGCCTCGGAGCATCTCCTCGCGGCGGGGCAACTGGCCACGACGGCGACGGCGGTGGCGAAGAGAGAACTCGCGACGTACATGTACTGA More
Protein seq	MAYRLFTAQSLFMNRSIHSLHRNLLPINGDQASIVGGAIEFVKELEQQLQSLEAQKRTLLPHHKARCDDATPTHNASGSNVGAGGCMEPTTTTSNCSSSVTEDAPSADAPPFAQFFAYPQYVWCHSPRDSTTTTTAASASASASASSSSPATVAAALQSEHRSGLADIEVSLVETHASVRVMSPRRPGQLLKMIAGLQALRLTVLHLNVTTLDSLVLYTLSVKVEEGCSLTTVDDIAAAVHHVLCIVDAEAAASEHLLAAGQLATTATAVAKRELATYMY More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsZS97_02G0488900	OsZS97_02T0488900.3	Chr02	29706266	29709923	+	makerRMon
CDS seq	ATGAGCACACTAGTAGACGCGCTGTGCGCTCCCTGCAGCGACACCGCGCTCATCTACGACACCTTCAACGCCTCCGCCGCCGCGAGCTTCCTCTTCGACAATGCCGCCGCCTTCTGCGACGCTGACATCCTCGGCGCCACGGCGACAGGGGAGAAGGAGGCGACGTCGTCGGCCGCGGCCGCGGCCGCGGACGCCGCCCCGCCGAGGAAGAAGCGGCGGCGGCGCGCGAAGAGCTGCAAGTCGCGGGAGGAGACGGAGACCCAGCGGATGACGCACATCGCCGTGGAGCGCAACCGCCGGCGCCAGATGAACGAGTACCTCGCCATCCTCCGGTCGCTCATGCCGGAGCCCTACGTCCAGAGGGGCGACCAGGCGTCCATTGTGGGAGGCGCAATCGAGTTCGTGAAGGAGCTCGAGCAGCAGCTGCAGTCGCTTGAGGCGCAGAAGCGAACGCTGCTCCCTCACCACAAGGCGAGATGCGACGACGCAACGCCGACGCATAACGCCAGCGGCAGCAACGTCGGGGCCGGCGGCTGCATGGAGCCCACGACGACAACGAGCAACTGCAGCAGCAGCGTCACCGAGGACGCGCCGTCCGCCGACGCGCCCCCGTTCGCGCAGTTCTTCGCGTACCCGCAGTACGTGTGGTGCCACTCGCCGCGCGACTCCACCACCACCACCACCGCGGCGTCTGCGTCGGCGTCGGCTTCGGCGTCGTCGTCGTCGCCGGCCACGGTGGCGGCGGCGCTCCAGTCCGAGCACCGCTCCGGGTTGGCCGACATCGAGGTGAGCCTGGTCGAGACGCACGCCAGCGTCCGTGTCATGTCACCGCGGCGGCCAGGGCAGCTGCTCAAGATGATCGCCGGCCTGCAGGCCCTCCGGCTCACCGTGCTGCACCTCAACGTCACCACGCTGGACTCCCTTGTGCTCTACACCCTCAGCGTCAAGGTACGCCTACGCCTATCGCCTGCGTCTGCAGCCGTGCACTGA More
Protein seq	MSTLVDALCAPCSDTALIYDTFNASAAASFLFDNAAAFCDADILGATATGEKEATSSAAAAAADAAPPRKKRRRRAKSCKSREETETQRMTHIAVERNRRRQMNEYLAILRSLMPEPYVQRGDQASIVGGAIEFVKELEQQLQSLEAQKRTLLPHHKARCDDATPTHNASGSNVGAGGCMEPTTTTSNCSSSVTEDAPSADAPPFAQFFAYPQYVWCHSPRDSTTTTTAASASASASASSSSPATVAAALQSEHRSGLADIEVSLVETHASVRVMSPRRPGQLLKMIAGLQALRLTVLHLNVTTLDSLVLYTLSVKVRLRLSPASAAVH More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	4.379794	0.0894745	10.7906105

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_02g0691500	RBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os02g46560	RBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os02g0691500	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_02g0029740	RBH	0.0	0.0	0.0
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_02g0029810	RBH	0.0	0.0	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_02g0029670	RBH	0.268931	1.423666	0.414317
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_02g0029270	RBH	0.0	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_02g0029480	RBH	0.0	0.000000	0.0
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_02G0461000	RBH	2.333501	1.217656	1.6359215
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_02g0029280	RBH	0.0	0.000000	0.0
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_04G0475200	RBH	0.4767465	0.0508105	9.537774
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_02g0029580	RBH	0.0	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_02g0029320	RBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_02g0029630	RBH	0.0	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_02g0029470	RBH	0.0	0.0	0.0
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_02g0029150	RBH	0.0	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_02G029730	RBH	0.0	0.0	0.787011
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_02g0029500	RBH	0.0	0.0	0.000000

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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