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
OsNip_09g0381400		OGI:09037990 \| 16/16			Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)			Chr09:12897572-12899549		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		GCGACTGAGTTTTCAAAGAAATACATTGTGAACTTGGTTCGAGGCAAGACAGCAAACATTAGAGTGCAGATTGCAGGTCGACCCTCAACAACTTAACATCAGGGTGGTTAGCTTTGCAGCAGCCAACAGCATCAACTTACACAATCTGCATCTTCCACTTTTATAGGACACAAGTCACCTCATGCTCACCATAGATGCTCTGTGAAAGTTACCTGCATCTTCAGTAGTCGCTGCTATTATCTACCCTGGAACAGCTACTATAATTCTCTCTATTATCCTTTGCTTGCGGTCTATCTAACTTCACTTGCTCAGTAAGCACGTGACCTATAACTGCTTATCATTGTCCTCAGCTCCTTTTGTTATTCATAAGCTGAGTGAACAATTAACCACTTTATGTACAAACAGCTGGCTTGTTATACTACAGGTTACTATGGTACTATTTGTTGTTTCTTTTTACCATATGCTTTTTAGCTTTTCTTAGTTAAGAGAACGTGTGCATCGCATCTTTCCATCGACCTGTCTACAGGCGGCGCGCCATTGGCGCGCCCCAGCCTCTAGTTCACATAGTTGTACGCGCGCAGCATGCATTTTATTTAGGCACGGTCCACAATTCATACATGTATAGTGGATACGTCTCGTCGGCAGACACTCACGGTATAGTAGGGTAGTCGTGTGTACAGTGATATAGTCATATCTGCGCGTCTTTTCATGCCGTTCGTTGACTTCGTTCACAGGGTCAGGGTCGGGTAGGCGATATCGAGTGTGACGCCACACAGGCCGGGGCCACCGACGTCGCGGAGAATCCGGATGTAGCCGCGCTCGCCCCATGACTGGCCCCATGAGTTCTTGATGGTCCAGTACTTGGCGCCGGAAGACGCGTCGGTGCCGTACCCGACGACGGTGACGGCGTGCGCTAGGCGCGTGCCGCACGGGCCCGTGTAAACGCCACCCTTGTAGAACTGCATCCCGCTACCGACCTCGATGGCCACAGCCACGGGCTGCCGAGCGACGGCGGCCTGCAACGCCGCCTCGTTCCGCGGCGGCACCTTCCCGAAGCCGGTGATCTTGGCGGCATGGTGCGCGGACTTGGCGCGGTTGCAGGGGCCCCGCCGCGCCGTGTACGGGTAGTCCGCCTCCGTGGTGAGGCCACCGTTCTCGACAACCCATTTGTACGCCCGCCCGTACGACCCTAAGTTGCAGCCGCCGTCATAGCTGTCGCAGTCCACCAGCTGCTGCTCCGACAGAGAGACCAGCTTCCCCGTCTTGATCATGTTCAGGCTCTCGATGGTCGCCGCTGTCACGAACGCCCAGCAGCTACCTGCAGGCGTACGTAACGTAGGTCCAATGCAATTAATAATTAATAATTAAGGTATATTTTACGTTTGAAATGGAACCATGTGTGAAATTTACACGTACTGCATGTTGACGTTTGGGACTTGGGAGGCACAACGGCGCCTTGGGCCCTCCAGTCGACACTGGCCGGAACGTCCACGCGGTAGGAGAAGCTGGCGTCGACGTCTCCGGCACCCGTCGTGATAACGGAGTCGTCCACGGGGCCATCGCCGGCGTAGTACCCGGTGTACGTGGCCAGGAACTCCTCCTCGGTGAGGTCTGCGAACTCGTTCTCGGCGAGCTGGTAAGTGAGGTCGCCGCGCAGGTTGACGGCGTCGATGAACTCCGCGTTGCGGCGGTACACATCGAACCGCTGCAGCGCCTCTTCTGCGCTCGGGTACGACCGGTTGTGAGCTCCCTGCCAAGCGCGGAACCTGTCCATCATCACCATGTCGCCGACGTCCAAGCAACTGCCCGCCGTCGCACGCGCCGGGAGCATGGAGGTGGCGAGAAGGGCACCGCACGACGCGAGCAGGGCCAGCGTGAGTACCGGTGGCGAGGCGCACGCCATGAATGGTGCCATGGCATGCACCTAACTTGTGGGTAAGTACGCGTTCCACCGTTCAATATTCCACTTCTGGTCGAC More
CDS seq		ATGGCACCATTCATGGCGTGCGCCTCGCCACCGGTACTCACGCTGGCCCTGCTCGCGTCGTGCGGTGCCCTTCTCGCCACCTCCATGCTCCCGGCGCGTGCGACGGCGGGCAGTTGCTTGGACGTCGGCGACATGGTGATGATGGACAGGTTCCGCGCTTGGCAGGGAGCTCACAACCGGTCGTACCCGAGCGCAGAAGAGGCGCTGCAGCGGTTCGATGTGTACCGCCGCAACGCGGAGTTCATCGACGCCGTCAACCTGCGCGGCGACCTCACTTACCAGCTCGCCGAGAACGAGTTCGCAGACCTCACCGAGGAGGAGTTCCTGGCCACGTACACCGGGTACTACGCCGGCGATGGCCCCGTGGACGACTCCGTTATCACGACGGGTGCCGGAGACGTCGACGCCAGCTTCTCCTACCGCGTGGACGTTCCGGCCAGTGTCGACTGGAGGGCCCAAGGCGCCGTTGTGCCTCCCAAGTCCCAAACGTCAACATGCAGTAGCTGCTGGGCGTTCGTGACAGCGGCGACCATCGAGAGCCTGAACATGATCAAGACGGGGAAGCTGGTCTCTCTGTCGGAGCAGCAGCTGGTGGACTGCGACAGCTATGACGGCGGCTGCAACTTAGGGTCGTACGGGCGGGCGTACAAATGGGTTGTCGAGAACGGTGGCCTCACCACGGAGGCGGACTACCCGTACACGGCGCGGCGGGGCCCCTGCAACCGCGCCAAGTCCGCGCACCATGCCGCCAAGATCACCGGCTTCGGGAAGGTGCCGCCGCGGAACGAGGCGGCGTTGCAGGCCGCCGTCGCTCGGCAGCCCGTGGCTGTGGCCATCGAGGTCGGTAGCGGGATGCAGTTCTACAAGGGTGGCGTTTACACGGGCCCGTGCGGCACGCGCCTAGCGCACGCCGTCACCGTCGTCGGGTACGGCACCGACGCGTCTTCCGGCGCCAAGTACTGGACCATCAAGAACTCATGGGGCCAGTCATGGGGCGAGCGCGGCTACATCCGGATTCTCCGCGACGTCGGTGGCCCCGGCCTGTGTGGCGTCACACTCGATATCGCCTACCCGACCCTGACCCTGTGA More
Protein seq		MAPFMACASPPVLTLALLASCGALLATSMLPARATAGSCLDVGDMVMMDRFRAWQGAHNRSYPSAEEALQRFDVYRRNAEFIDAVNLRGDLTYQLAENEFADLTEEEFLATYTGYYAGDGPVDDSVITTGAGDVDASFSYRVDVPASVDWRAQGAVVPPKSQTSTCSSCWAFVTAATIESLNMIKTGKLVSLSEQQLVDCDSYDGGCNLGSYGRAYKWVVENGGLTTEADYPYTARRGPCNRAKSAHHAAKITGFGKVPPRNEAALQAAVARQPVAVAIEVGSGMQFYKGGVYTGPCGTRLAHAVTVVGYGTDASSGAKYWTIKNSWGQSWGERGYIRILRDVGGPGLCGVTLDIAYPTLTL
Function		Senescence-specific cysteine protease SAG12 [UniProtKB/Swiss-Prot:Q9FJ47]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNip_09g0381400	OsNip_09t0381400-01	Chr09	12897572	12899549	-	RAP2018-11-26
CDS seq	ATGGCACCATTCATGGCGTGCGCCTCGCCACCGGTACTCACGCTGGCCCTGCTCGCGTCGTGCGGTGCCCTTCTCGCCACCTCCATGCTCCCGGCGCGTGCGACGGCGGGCAGTTGCTTGGACGTCGGCGACATGGTGATGATGGACAGGTTCCGCGCTTGGCAGGGAGCTCACAACCGGTCGTACCCGAGCGCAGAAGAGGCGCTGCAGCGGTTCGATGTGTACCGCCGCAACGCGGAGTTCATCGACGCCGTCAACCTGCGCGGCGACCTCACTTACCAGCTCGCCGAGAACGAGTTCGCAGACCTCACCGAGGAGGAGTTCCTGGCCACGTACACCGGGTACTACGCCGGCGATGGCCCCGTGGACGACTCCGTTATCACGACGGGTGCCGGAGACGTCGACGCCAGCTTCTCCTACCGCGTGGACGTTCCGGCCAGTGTCGACTGGAGGGCCCAAGGCGCCGTTGTGCCTCCCAAGTCCCAAACGTCAACATGCAGTAGCTGCTGGGCGTTCGTGACAGCGGCGACCATCGAGAGCCTGAACATGATCAAGACGGGGAAGCTGGTCTCTCTGTCGGAGCAGCAGCTGGTGGACTGCGACAGCTATGACGGCGGCTGCAACTTAGGGTCGTACGGGCGGGCGTACAAATGGGTTGTCGAGAACGGTGGCCTCACCACGGAGGCGGACTACCCGTACACGGCGCGGCGGGGCCCCTGCAACCGCGCCAAGTCCGCGCACCATGCCGCCAAGATCACCGGCTTCGGGAAGGTGCCGCCGCGGAACGAGGCGGCGTTGCAGGCCGCCGTCGCTCGGCAGCCCGTGGCTGTGGCCATCGAGGTCGGTAGCGGGATGCAGTTCTACAAGGGTGGCGTTTACACGGGCCCGTGCGGCACGCGCCTAGCGCACGCCGTCACCGTCGTCGGGTACGGCACCGACGCGTCTTCCGGCGCCAAGTACTGGACCATCAAGAACTCATGGGGCCAGTCATGGGGCGAGCGCGGCTACATCCGGATTCTCCGCGACGTCGGTGGCCCCGGCCTGTGTGGCGTCACACTCGATATCGCCTACCCGACCCTGACCCTGTGA More
Protein seq	MAPFMACASPPVLTLALLASCGALLATSMLPARATAGSCLDVGDMVMMDRFRAWQGAHNRSYPSAEEALQRFDVYRRNAEFIDAVNLRGDLTYQLAENEFADLTEEEFLATYTGYYAGDGPVDDSVITTGAGDVDASFSYRVDVPASVDWRAQGAVVPPKSQTSTCSSCWAFVTAATIESLNMIKTGKLVSLSEQQLVDCDSYDGGCNLGSYGRAYKWVVENGGLTTEADYPYTARRGPCNRAKSAHHAAKITGFGKVPPRNEAALQAAVARQPVAVAIEVGSGMQFYKGGVYTGPCGTRLAHAVTVVGYGTDASSGAKYWTIKNSWGQSWGERGYIRILRDVGGPGLCGVTLDIAYPTLTL More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNip_09g0381400	OsNip_09t0381400-02	Chr09	12899148	12899542	-	RAP2018-11-26
CDS seq	ATGGCACCATTCATGGCGTGCGCCTCGCCACCGGTACTCACGCTGGCCCTGCTCGCGTCGTGCGGTGCCCTTCTCGCCACCTCCATGCTCCCGGCGCGTGCGACGGCGGGCAGTTGCTTGGACGTCGGCGACATGGTGATGATGGACAGGTTCCGCGCTTGGCAGGGAGCTCACAACCGGTCGTACCCGAGCGCAGAAGAGGCGCTGCAGCGGTTCGATGTGTACCGCCGCAACGCGGAGTTCATCGACGCCGTCAACCTGCGCGGCGACCTCACTTACCAGCTCGCCGAGAACGAGTTCGCAGACCTCACCGAGGAGGAGTTCCTGGCCACGTACACC More
Protein seq	MAPFMACASPPVLTLALLASCGALLATSMLPARATAGSCLDVGDMVMMDRFRAWQGAHNRSYPSAEEALQRFDVYRRNAEFIDAVNLRGDLTYQLAENEFADLTEEEFLATYT

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNip_09g0381400	OsNip_09t0381400-03	Chr09	12898143	12899539	-	IsoSeq
CDS seq	ATGTGTACCGCCGCAACGCGGAGTTCATCGACGCCGTCAACCTGCGCGGCGACCTCACTTACCAGCTCGCCGAGAACGAGTTCGCAGACCTCACCGAGGAGGAGTTCCTGGCCACGTACACCGGGTACTACGCCGGCGATGGCCCCGTGGACGACTCCGTTATCACGACGGGTGCCGGAGACGTCGACGCCAGCTTCTCCTACCGCGTGGACGTTCCGGCCAGTGTCGACTGGAGGGCCCAAGGCGCCGTTGTGCCTCCCAAGTCCCAAACGTCAACATGCAGTAGCTGCTGGGCGT More
Protein seq	MCTAATRSSSTPSTCAATSLTSSPRTSSQTSPRRSSWPRTPGTTPAMAPWTTPLSRRVPETSTPASPTAWTFRPVSTGGPKAPLCLPSPKRQHAVAAGR

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.618085	0.000000	118.546928

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_11g0425100	RBH	0.031731	0.065084	3.320534
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os09g21370	RBH	0.000000	0.0	19.603275
Nipponbare \| IRGSP 1.0 \| RAP-db	Os09g0381400	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_09g0008570	RBH	0.000000	1.218259	57.389248
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_09g0008550	RBH	0.000000	0.000000	45.210125
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_09g0008780	RBH	0.000000	0.000000	66.125084
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_09g0008590	RBH	0.000000	0.000000	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_09g0008790	RBH	0.000000	3.163757	137.700363
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_09G0218900	RBH	0	0.0253665	0
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_09g0008730	RBH	0.000000	0.000000	15.246854
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_09G0200300	RBH	0.0140735	0.095089	0.1352445
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_09g0008710	RBH	0.0	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_09g0008520	RBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_09g0008430	RBH	0.000000	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_09g0008470	RBH	0.0	0.0	11.474059
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_09g0008470	RBH	0.000000	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_09G009000	RBH	0.000000	0.000000	24.822929
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_09g0008770	RBH	0.000000	3.021610	161.688568

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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