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
LOC_Os04g45170		OGI:04080300 \| 16/16			Nipponbare \| IRGSP 1.0 \| MSU			Chr04:26703331-26708567		Homologues MicroCollinearity RGI-JBrowse RGAP Ricevarmap2
Gene Symbol		-
DNA seq		ATGGCGAGGCTGCTCGGAGTCTCCCTCCTCGTCGCGGGGCTCGGCTGCGCGCTGCTCGTCGCGCCCTCGGAATCAGCTGCAGATGACGGTATCAATTGCCCTTCCCATGTGTATTGTATGTATCTATTTTTCCATCTTTTGTGCCGTTCGTTTCTTGAGAAGTTGTTGCGTTGTTGTTGTTGTTGCGCAGTATCTGCGCTTCTTGCTTTCAAGAAGGCCATTTTCGAGGACCCTCTCGCCAAGCTGTCGGACTGGAACTCCAAGGATGAGAATCCTTGCGGCTGGACAGGGGTGGGGTGCTCGCCGTTCGACAGCCGCGTGGTGACTCTGTAAGAACTGGTTCCGCTTGTTCTCCTGTTGGTTTTTTTCTTTCTTTTCGTTGCATCACTTTAAAACATCATGCGGCTGAGATAGAACTTTAAGTTTTTGTTTAAGCAATCCACCATTTCTCGCGGAGTATTTGTGCATGCCCTGTTTTGGTTCATGTCTTGCACGGATGGAAGAAGTTTTTTCAGTCATAGGTTATCCTCTTTCAGAGTTTTTTAATTTTTTTTTAGAAATAATGGAATAACATTCCAGCTCTTTCAGAGCTTCTTGAACATGCACTTTCTCCTATGAAAATTAAAAACTGGCTGGAGGCCTCTCTATAACAACAGCAAGTCAGAATGATGCATGTTCTTTCAGAGAACAGTGGGCCTTAAGTTTTCTGGCTGCACCACAAGACATCCAGCTGGAAGCTATCATAGAGTTTTACCTTCTTTTATTTGTTTTCTCTTATGTTCAGTTGACTCAAGAAGCCCCAACAGGGAAAGAAGAGATTATGGATTTGTGGTCCCTAGGAACAAAAAAAAAAATCAATCCAACAGATTTCAGTTATCTATTACAATAAATATAATCCAAGTGGTGTTTATCCAAACACCAAAGTCAGATAAAATGAATATATAGTTTTATTTACACACGTTTTCTGTTCAAGTAAAAAATCACTAAATGTTCAGCATTGCAGAAATTTCAGTTGGTGTGTATTCCCTCGTCCCAAAATATAGCAACCTAGGACCGGATGGGACGTATCCTAGTACTACGAATCTGGACAGGGGACATGTCAAGATTCGTAGTACTAAAATACGTCCCATCCGGTACTAGTTTGCTATATTCTGGGACGGAGGAAGTACATTTTATTGTACATTTTATTGATAAACTTCCCTCTTCTCTATTGTAAAGTATCTTATTATTTACACGTTGTTATCCAGGGAATTGGCAAATTCATCGCTCAAAGGATTCCTGGCACTAGAGATTGAATCCCTGAGTTCTTTACAAAAACTGTATGTACTTATATGTCCATTTGATTCAATAATAAACTTGACCTGTTAGCCACTACTGAACTGATAGCAATCTTGGTGAACTTCTTGCAGCATATTGGATCACAATACACTCATGGGTCCAATACCAAAAGGAATTGGCAAGCTAAGAAATCTAATTATGTTGAACCTCAGCACCAATCAACTCGATGGGCCCATTCCCATTGAGATTGGTGACATGCCAAAAATCTCAAAAATGTACTGACCAAGAAGCTATAATCAACTTATATTTCTTCAGAATATGTTCAAAATTCATAACTCATCTATTGCCTTATGCCCTAGAGACCTTCGTGCGAATCGGTTGGATGGTGCTATCCCCCCTGAGATTGGTAATTTGACGAGCCTCACTGAGCTACAATTGAGCAATAATAGCCTTACAGGGACTATTCCTGGAAGTAATGATTCAAGCATGTAAGTAATACTTTTCAGAGTTCTCCAAATTCAAAGTCAAGTAACTGTTTTCAGCATGCATAAACTGGAAATGCATGGAAGAACCAAATAATGTTTCTTCTATAGGAAGGAATTAAAGTGATTTAGTTAAGAAGTAGACATCAATCAGGATTGACTCCATCCTGCAGTATTTACAGTAAAAGAAAGTATGAGTAGTTATGATTTATCATATACAAGCAAGTCTGATGAGATCAGAACCAATTATAATGCTGACAAACATTTGAATAAGCAATGTCACGCATCTTTCAGGGTATCCACCAACAGAGACGGTCAAATAGGATTGTGCCGATTAACTCAGCTAACTGATATGGACCTCTCTTATAACTATTTGGCTGGAGATGTTCCTACATGCTTCATGCAAATCCGAAGGTACACCTTGCTTTCTGTGGCTTGGATGGTTCAGTTTAGTCTTTCTGAACTTACCTGCTTTGCAGTATTTGAACAGATTAAGCTTGGTAGGAAATTGTTTCGAGAACAATGACACAACGAATCGTCCTGACAATCAATGTATGGCTATATTTCATTTTAACATGTTAATATCATTAATGCAGTTTAGTACTATTTTCAGCACTAAATTCAGCGCAAAGTTTTCTTACCGTTTGCCGCGATGTTCGATGTCATTTTCACAAGAGCGTATAAACATTATATATTTTTAGATTCACCTAACGGTTCATTTTTGCTGTCAAAATGTTACAGAAACGAAATTATTGTATGTATTACTTCTTAATAGGTAATATCCATGGCAACCTTGATAACTAAGGGACTACTGTCTACTTCCACCGGTTAGGCTAGGCTAATATGAAAACTGATGCACATCCATGTTCAAAAAAAAAAAAAGTTACACATCCATTTCTTCATTATTCAAAGTTAATTGAGTAATTTTTGGGTCCCGATAACATAGGTGGTGTATAGACCGTCCCAATTTACTAGCTGTAGCAAAGTAGGCCCTACGTTGTAAATGACATCATTAGTTTTTAATCACTAATGCTACTCATGGTGACTTAGGCATAGTGGAATCTTAGCTATCGTTGATAACATAAATAACTATACTTTGGCACTTTGTTTCCTTCCTTCTTGGACGTTATCTCTCACATTCTTCCTTTTGTCCTCCATGCTCTCTGTATGTCGGTATTTTATTTCTAAGTATTCAATTGTTCTGTTGGATTTTTATAATTCAGCACTGAACTGCCATGAATCAGGATTTAACCTATATTTGTGCATTTTCAAATACGACATGCACATACTTTTATGTTTGATATATGAGACCGCATGAGCCTTCTAAAGTAATTTATGAAACAACCAAACTAGAATGTTTATACTGCTTTAGTCAACTGATCAATGAGCAAGTGCATGTGCTGTAATTACAGGTGAAAACAGCCAGAAAGGAAATGAAAGCAGCCGTGTTGATGGAAACCAGCAGAAAAGCTTTCAACAACCACTTTGGCTTCTTATTCTAGAAGTCATTACAGCAATTTCATTGCTTACTGTGTTAACACTATGTACTATAGCTGGTCTCAGAAGATGCAAAGCTAGATCCTCCAGAAACAGTGGTACATGGACAAGGGCTATAAGCTGGAAGGAAAATACTGTAATTTCGATTGGTAAGTGTTTCTTTTTATTTGTGTGTGTGTGAGTGACTGGCGAAGTAAATATTGCACTTCCTTGGTTACAGAATGTTTGCTTGTGTAGATGATGACTTGCTGGCGAATGTGCCAAAAATAAGTCGGCAAGAGCTTGCAGAAGCCTGTGAAGACTTCAGCAATATCATTGGATCTACTCATGACACGGTGGTGTACAAAGGAACTATGAAGGATGGCAGTGAAATTGCTGTTGTGTCACTATCAGCTTCAGTACATTACTGGACGAGTTACGTTGAGCTGTACTTCCAGAAGGAGGCAAGAAGAACTCTGCATCTTGTGACTCGAAATTTCAAAAGGTGCAGCTATTTGCTTATATCTCATGGTACTTTTGAATTCTTCAGGTGGTAGAAATGGCCAGATTGAGTCATGAAAATGTTGCGAAGATGGTGGGATACAGCAAGGAGTCCGATCCATTTTCGAGAATGCTAGTCTTTCAGTACCCACCAAATGGGACACTCTATGAGCATCTTCATGGTAACCCAATGATCTCTCATCTTGTTGCCTTTCTGTTCAAAAGGTTGATACCACATGACATGGTGATAATAACTTAAATTTTGATGTATGCTATTTCTTGCAGATGGAGAAGGATATCAGCTATCTTGGCCCAGGCGGATGAAAATAGCACTCAGCATTGCTCGCGCCCTCAGATACCTGCACACTGAGATGCAGCCTCCATTTGCAGTTGCTGCACTGACATCAAGTTCAGTTTATCTAACTGAAGATTTCTCCCCAAAGGTCCGTCTCATCTGCTTGTGCCTTGTGACATGGCAATGAACATGGTGTCCTAGATTCGGTGCAGTCACACACAAATTGTCCTGTTCATGTAACAGCTTTTTTTTAGATAATGGATTAGATTAAACCCAGCCTCTACACCTTTGTGGGGTGTACACAGCTAAATGTAACAGCTGAAATGGTTTATGCGTTTGCAGATAATTGATTTTGAGAGATGGAGAGCTCTCCTGACAAAACCAGGGCTCAGCTCTGGCAGCATAGTGAACGGGTCATTCAACAACATCATAGACTCGCGGCACAGGCGTTTCATGGACATCCAGGCCAACACGTTTGCTTTCGGGGTGATTCTGCTGGAGCTGATAAGTGGAAGAGCCCCAGTTTCCAAAGATACAGGAGATCTTGTGGACTGGGTAAGTAACTTGGCCTGAATCATGATTTGACACCAGTAATTCCAGACATTGAATTATCAGATAAATGAAAACCGTGGCACTAGTCTGAAAGTCTGAAACTCTGCAATGTTGGTCCAACTTGGGGTCACAGGCAAGGAAGCACTTGGACCAGACCGAAGAATTCATCAAGCTGGTCGACCCGAAGCTGATGAACGCCAACCATGAGAACCTGGGCATCGTCTGCAACGTGGTGAACCTCTGCATCGACGCCGAGCCGTGCCGGAGACCGTCGATGAACATGATCACCGCCATTCTGGAGGAAGGCATCGACACGTCGCCGGCGACCGTCCTTCGGGACTCCTCCCTGGCATGGGCGGAGGCAGAGATTGCCATCTCGTAGTCGTAGACGGACATGCAATTTGCTGCTACTCGGACAGTAACTACAGAGACGCACACAGTGGTTTTGCCACAAAGGGCTTTTTAACCTTTTTTTTTTCTTTTTGATTCGTGGCTACTGCTTTACGTTTCCTCGGTGCCTTTTTGCCTCTCCCTCTCCCAGATCACATGAAAAATGTGTGGATATTTTGTGAGCGGATTTGATGTGTGATATGTCATATGTGATCTACCCAGGATTTACCTTTTCATTTTCGAAGTTTTAAAAAAAATGATCG More
CDS seq		ATGGCGAGGCTGCTCGGAGTCTCCCTCCTCGTCGCGGGGCTCGGCTGCGCGCTGCTCGTCGCGCCCTCGGAATCAGCTGCAGATGACGGTATCAATTGCCCTTCCCATGTGTATTTATCTGCGCTTCTTGCTTTCAAGAAGGCCATTTTCGAGGACCCTCTCGCCAAGCTGTCGGACTGGAACTCCAAGGATGAGAATCCTTGCGGCTGGACAGGGGTGGGGTGCTCGCCGTTCGACAGCCGCGTGGTGACTCTGGAATTGGCAAATTCATCGCTCAAAGGATTCCTGGCACTAGAGATTGAATCCCTGAGTTCTTTACAAAAACTCATATTGGATCACAATACACTCATGGGTCCAATACCAAAAGGAATTGGCAAGCTAAGAAATCTAATTATGTTGAACCTCAGCACCAATCAACTCGATGGGCCCATTCCCATTGAGATTGGTGACATGCCAAAAATCTCAAAAATAGACCTTCGTGCGAATCGGTTGGATGGTGCTATCCCCCCTGAGATTGGTAATTTGACGAGCCTCACTGAGCTACAATTGAGCAATAATAGCCTTACAGGGACTATTCCTGGAAGTAATGATTCAAGCATGGTATCCACCAACAGAGACGGTCAAATAGGATTGTGCCGATTAACTCAGCTAACTGATATGGACCTCTCTTATAACTATTTGGCTGGAGATGTTCCTACATGCTTCATGCAAATCCGAAGATTAAGCTTGGTAGGAAATTGTTTCGAGAACAATGACACAACGAATCGTCCTGACAATCAATGTGAAAACAGCCAGAAAGGAAATGAAAGCAGCCGTGTTGATGGAAACCAGCAGAAAAGCTTTCAACAACCACTTTGGCTTCTTATTCTAGAAGTCATTACAGCAATTTCATTGCTTACTGTGTTAACACTATGTACTATAGCTGGTCTCAGAAGATGCAAAGCTAGATCCTCCAGAAACAGTGGTACATGGACAAGGGCTATAAGCTGGAAGGAAAATACTGTAATTTCGATTGATGATGACTTGCTGGCGAATGTGCCAAAAATAAGTCGGCAAGAGCTTGCAGAAGCCTGTGAAGACTTCAGCAATATCATTGGATCTACTCATGACACGGTGGTGTACAAAGGAACTATGAAGGATGGCAGTGAAATTGCTGTTGTGTCACTATCAGCTTCAGTACATTACTGGACGAGTTACGTTGAGCTGTACTTCCAGAAGGAGGTGGTAGAAATGGCCAGATTGAGTCATGAAAATGTTGCGAAGATGGTGGGATACAGCAAGGAGTCCGATCCATTTTCGAGAATGCTAGTCTTTCAGTACCCACCAAATGGGACACTCTATGAGCATCTTCATGATGGAGAAGGATATCAGCTATCTTGGCCCAGGCGGATGAAAATAGCACTCAGCATTGCTCGCGCCCTCAGATACCTGCACACTGAGATGCAGCCTCCATTTGCAGTTGCTGCACTGACATCAAGTTCAGTTTATCTAACTGAAGATTTCTCCCCAAAGGTCCGTCTCATCTGCTTGTGCCTTGTGACATGGCAATGA More
Protein seq		MARLLGVSLLVAGLGCALLVAPSESAADDGINCPSHVYLSALLAFKKAIFEDPLAKLSDWNSKDENPCGWTGVGCSPFDSRVVTLELANSSLKGFLALEIESLSSLQKLILDHNTLMGPIPKGIGKLRNLIMLNLSTNQLDGPIPIEIGDMPKISKIDLRANRLDGAIPPEIGNLTSLTELQLSNNSLTGTIPGSNDSSMVSTNRDGQIGLCRLTQLTDMDLSYNYLAGDVPTCFMQIRRLSLVGNCFENNDTTNRPDNQCENSQKGNESSRVDGNQQKSFQQPLWLLILEVITAISLLTVLTLCTIAGLRRCKARSSRNSGTWTRAISWKENTVISIDDDLLANVPKISRQELAEACEDFSNIIGSTHDTVVYKGTMKDGSEIAVVSLSASVHYWTSYVELYFQKEVVEMARLSHENVAKMVGYSKESDPFSRMLVFQYPPNGTLYEHLHDGEGYQLSWPRRMKIALSIARALRYLHTEMQPPFAVAALTSSSVYLTEDFSPKVRLICLCLVTWQ
Function		Probable LRR receptor-like serine/threonine-protein kinase At1g63430 [UniProtKB/Swiss-Prot:C0LGH8]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
LOC_Os04g45170	LOC_Os04g45170.1	Chr04	26703331	26708567	+	MSU_osa1r7
CDS seq	ATGGCGAGGCTGCTCGGAGTCTCCCTCCTCGTCGCGGGGCTCGGCTGCGCGCTGCTCGTCGCGCCCTCGGAATCAGCTGCAGATGACGGTATCAATTGCCCTTCCCATGTGTATTTATCTGCGCTTCTTGCTTTCAAGAAGGCCATTTTCGAGGACCCTCTCGCCAAGCTGTCGGACTGGAACTCCAAGGATGAGAATCCTTGCGGCTGGACAGGGGTGGGGTGCTCGCCGTTCGACAGCCGCGTGGTGACTCTGGAATTGGCAAATTCATCGCTCAAAGGATTCCTGGCACTAGAGATTGAATCCCTGAGTTCTTTACAAAAACTCATATTGGATCACAATACACTCATGGGTCCAATACCAAAAGGAATTGGCAAGCTAAGAAATCTAATTATGTTGAACCTCAGCACCAATCAACTCGATGGGCCCATTCCCATTGAGATTGGTGACATGCCAAAAATCTCAAAAATAGACCTTCGTGCGAATCGGTTGGATGGTGCTATCCCCCCTGAGATTGGTAATTTGACGAGCCTCACTGAGCTACAATTGAGCAATAATAGCCTTACAGGGACTATTCCTGGAAGTAATGATTCAAGCATGGTATCCACCAACAGAGACGGTCAAATAGGATTGTGCCGATTAACTCAGCTAACTGATATGGACCTCTCTTATAACTATTTGGCTGGAGATGTTCCTACATGCTTCATGCAAATCCGAAGATTAAGCTTGGTAGGAAATTGTTTCGAGAACAATGACACAACGAATCGTCCTGACAATCAATGTGAAAACAGCCAGAAAGGAAATGAAAGCAGCCGTGTTGATGGAAACCAGCAGAAAAGCTTTCAACAACCACTTTGGCTTCTTATTCTAGAAGTCATTACAGCAATTTCATTGCTTACTGTGTTAACACTATGTACTATAGCTGGTCTCAGAAGATGCAAAGCTAGATCCTCCAGAAACAGTGGTACATGGACAAGGGCTATAAGCTGGAAGGAAAATACTGTAATTTCGATTGATGATGACTTGCTGGCGAATGTGCCAAAAATAAGTCGGCAAGAGCTTGCAGAAGCCTGTGAAGACTTCAGCAATATCATTGGATCTACTCATGACACGGTGGTGTACAAAGGAACTATGAAGGATGGCAGTGAAATTGCTGTTGTGTCACTATCAGCTTCAGTACATTACTGGACGAGTTACGTTGAGCTGTACTTCCAGAAGGAGGTGGTAGAAATGGCCAGATTGAGTCATGAAAATGTTGCGAAGATGGTGGGATACAGCAAGGAGTCCGATCCATTTTCGAGAATGCTAGTCTTTCAGTACCCACCAAATGGGACACTCTATGAGCATCTTCATGATGGAGAAGGATATCAGCTATCTTGGCCCAGGCGGATGAAAATAGCACTCAGCATTGCTCGCGCCCTCAGATACCTGCACACTGAGATGCAGCCTCCATTTGCAGTTGCTGCACTGACATCAAGTTCAGTTTATCTAACTGAAGATTTCTCCCCAAAGGTCCGTCTCATCTGCTTGTGCCTTGTGACATGGCAATGA More
Protein seq	MARLLGVSLLVAGLGCALLVAPSESAADDGINCPSHVYLSALLAFKKAIFEDPLAKLSDWNSKDENPCGWTGVGCSPFDSRVVTLELANSSLKGFLALEIESLSSLQKLILDHNTLMGPIPKGIGKLRNLIMLNLSTNQLDGPIPIEIGDMPKISKIDLRANRLDGAIPPEIGNLTSLTELQLSNNSLTGTIPGSNDSSMVSTNRDGQIGLCRLTQLTDMDLSYNYLAGDVPTCFMQIRRLSLVGNCFENNDTTNRPDNQCENSQKGNESSRVDGNQQKSFQQPLWLLILEVITAISLLTVLTLCTIAGLRRCKARSSRNSGTWTRAISWKENTVISIDDDLLANVPKISRQELAEACEDFSNIIGSTHDTVVYKGTMKDGSEIAVVSLSASVHYWTSYVELYFQKEVVEMARLSHENVAKMVGYSKESDPFSRMLVFQYPPNGTLYEHLHDGEGYQLSWPRRMKIALSIARALRYLHTEMQPPFAVAALTSSSVYLTEDFSPKVRLICLCLVTWQ More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.000000	0.206675	0.220219

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_04g0534200	RBH	0.000000	0.337661	0.876140
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os02g42370	SBH	0.435753	0.414834	0.511760
Nipponbare \| IRGSP 1.0 \| RAP-db	Os04g0534200	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_04g0021160	RBH	0.000000	9.996404	0.805691
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_04g0021920	RBH	0.134681	2.060713	0.102842
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_04g0021640	RBH	0.190048	11.336909	1.517212
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_04g0021390	RBH	0.000000	0.041310	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_04g0021570	RBH	0.000000	0.000000	2.558758
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_04G0420300	RBH	0.3483535	2.330302	0.2768125
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_04g0020370	RBH	0.108084	0.418379	0.000000
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_04G0420600	RBH	1.4627265	6.4065645	0.2615825
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_04g0020880	RBH	0.057315	0.063089	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_04g0020710	RBH	0.000000	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_04g0020790	RBH	0.0	6.657788	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_04g0021210	RBH	0.000000	0.677460	0.184198
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_04g0021380	RBH	0.0	4.670510	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_04G020640	RBH	0.0	0.407434	0.157704
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_04g0020570	RBH	0.0	9.218594	0.514410

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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