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
OsPr106_08g0016670		OGI:08060540 \| 16/16			PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)			Chr08:21896964-21903022		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		gacgtggttgtagaagcttgtacacacaaaagagaggaatttgagggagagagagtgagagagaagcctagctagctagcaagcacacaccacacacatctccaaattaagcacaagaggaaacaacacacaagccacctcgatctctctccttcctctcgatcccaagaagcccaaggaagcttcctatacgtttagtggttagcgcgctcgctcgccgccgcgccgcggcgaaggagggacgacgacggacatggcgtcggcgacgtcgacgacgcccgacctgtcgctgcacatcagcctgccgagcggtggcgcggcggtggggacgacggcgccgccggggctggggaacggcggtgcggttggtggtgccggcggcggcaaggcggcgGGTggtggtgacccgtggcggaggctggatggctccacggcgtcgacggagctgtcgctgtcgacgccgcagcagcagcaggagggcagtacatcggcggccgatgtgctgccgtggcggctgcggcagccgacggcggcggcggcgtccgtgccggtgacactgccgacgataccgatggatggttcggcggcggcggcgcgcgcgccgatccgtggggtgcctgtgtatagcggcggcgccggcggtggccacccgttcctcggaggcggcggcggcgaccaccggcacaaccggctctacaacccctaccactccacggcatggccctcgtcgtcgctgtgctcgacgtcgccggctccggctcctcctCCCCcaccagcagctctcgacccgacgacgtcgtcgctgctgtcgccgtccgcgtaccaccggatgctctccagcacggggcgcctccacggcgtgctcgccgacaccctccgcggctacgccggcgccgctgcggtggcgggctccatcggctacggctccgcggccgccgccgccgccgccatgggcggctacggcggcgccggcgccggcggcgggttcgcctcctcccgcttcatgccgcgcctcctcccggcgtcccgccgcagcatgcgcgccccgcggatgcggtggacgagctccctccacgcccgcttcgtccacgccgtcgagcttCtcggcggccacgagcgtgaggccccatctaaacatggatcatttcatgcgaaaataagctcaaaaaatctcatctcgcgctctaatttgatgcaggagcgacgcccaaatcggtgctagagctgatggacgtcaaggatctgaccctagctcatgtgaagagccatctgcaggtgatgatgatgatgatgagatcgatgccctacctatcaacaacaccaacaactcctccttcttggaaatttccatatcatatcaccacatcgccatggccatgatcgagctaagctactacaaagcttgggaaaattgcagctgatttcccttcaaaatccgcactgctcacgcgcactgtttcttcttgttcttgctcggacactgcaccgtacgtacatggggggagagagagagagaaatcgagagagtaccaggcacagattccgatgagaactccatgagagagagaaatcgaggagccctagagagagagattgtgtgtgtgtggagaagatcgatgcgtgtgggggtgtgtgcgagaaaaagttgccatcattatgcaataatgcattctgtgtgtgtcctgaccagagcacttcactcactcactcagctagggaacagaatcccagccaagaagagagagagagtgaagctgagcagcaagtgcagtaaaatttttctcaattctttcttgaggtgttctcgtgatggagtagtatttggtttgtccatttcttggtgtttttttgctttgcttttggctgccatgatctccagcttgatccatcatgttttgctgtcttttactatcctcactctgaatactccgattgataatctatttatccatcccaagaagatgcatatatatctttctttgcagctttgctttgtgcattgctttctcggtgcatgattcttttcttgctgcgctttctgcagatgtataggaccgtgaagagcactgacaagccagcagcagcctcaggtaattaacctcgaccatttcagatcatcaatCcccaattaaccaattccccattgccaaattaacttcaattaacttcactaaattcattgccttattaattaaatcatcacattgtgtacacTAttatttgtgtgcttactagcaaacagatatgggactgaacattattacttgtgatattattgtcttcagggccgatggacggcagcggctccggctccggctccggcgacgacgagctcctggccggcgatggaaggcaggcgacgtcatcgggcgccgatgcggaccggcggatgtcgttcaccgagcaccggtcctcctccgagggagcggcgagccatgccggcggtggcggcgacggcgactgctcctcctctgccgtcaactccgacaccatcagagcgcgcagcaattcgccgaggtatgcacacaaaatttggtgactaatttcgttgtttgtttgtttgtttttcagtgctttagttttgtgttaTTtttcctagtacatcaatagaaacttgggattgtgtttggtgctgttcgttaaaagaaaagtcttagtttggacagtaacatacatagcttaagagcaaagataacccaaacaggaagttaatcaagttgtgaacacaagctactacagtataatctggttattttggtagtggctaaagctcaaaaagatgtttggccctacacaaatcacacacaaaaagaaggagagagagagataaggataggagggcctctcccatgcatttgacttgatcagtgcatgcatgcacagccatggcctcctccttcaagatgaagaTGtgtgtgtttttcttgtgctttgcaatgtcctcttcttcctcctagttcttctctctccagtggtaatagatctgcTttttttaccttttcttatcaatgcatggctgcctgtgtgtgtgtgtccagggggctgtgggctttgacctcagacctgatactagctgacatcctagaaatgtgtaaccaagggcctcttcctgtgttgctttgtcctttactttccttgccattactcccagtgtctactgatactgtagcagatatactgaggttcaataataggagaaatttatgtattgggcatcaaacattgtttttttAaaaaaaaaaacatgatatgaaatgctgtttatatattgacacagaaaaactctctccatcctgaaaactgacttttgtagcttgataaagctctttcaaatttgaaaattatgtaatattttgggttgttcactaaaaatgtgttccatttccatgatcatctataatctacgatgcatttatcgcctaataaatttctcaagattttaattatctcttttaagtttgtcttaagatttctgtaatgttgaccatttttatactactgcatttttttttgaaaaaaaaatggagcacaaaagtaaaaaaaagaattgcataatttcatttttacatattttccaaactatatagcttgtgttagccattggtacgaaacatttgaatgtagggttttttttggaatgaatatttaaatgtaggttttgcctactataaacaataaattaaagggctcatatataatcccccccaacatgcacacgcaaaggaaaaaatgaattacatccattttgagtacaacaagaacaattacaatttttagtgtctcgacctttagagtttcgtttctcagaattttctcttctcggttttctatgcataaatcttgtagagaaaaatcatattggagtgcgcacattggtaaatatagcaagggtagtatcattcactactagagaactgatctttgctgggtcagacgaaaaccacattagccccagttccaataacaaccgggactaaaggtcccgaattcttggtcccggactatagagggttacaatCcgggacaaataagggtttctccaccagtgatttatggtgtgaaccaacttttgtatgtttttgttaaaatattacataaatagaatatattgtgggattttttaacagtttaattattaaaagcagtcttagttgaaaaataaataaaatatctaaaaatagcgatgggtttaaaagtgtatgaataatttattaatggaggagaccttcatatgcatcgtcaatgagagaaatatctagtccatgttagtaactaaatgccaatTAtaaagtatgccatctatataactatcctagaaagAaataatacagtgtacaatagaatatttgtctagtatgaacttaacaaaagataattagtaccttttctgacataattgagctaataggtttttcaagcTttttaatgtagagaagcttgttttagtgtgcatttgtgcccgcgccaGTTatatgcagcatggtttacatatctatgagtaacttctttctctctctgtgacagtactgtgcatgcacacatttgtaccaacacaacatataaatctttttaatggcatgttgcctagagctagagagctttgtagccagcaaacctatggctaggttcacaattttcatgattgccggtaatatgtactacaagttactactgttccaaattaaaagcattgcaaaggtagggattaattaattgggacaccaaattaaagtgctttggcctacagtgtacagtccagtcctaggctggaaatctagggttaagcatatgggcaaataaaaccatgagatcactactacAaaaaaaaaaattgtagccacaaaaaaatcacttgtaataataacagggagctcctatgatctaaacccgcttccgaaaaacaattgtcaaggcggctgtcaattttcacatcaatgtccgtaatatgtatagcgaggttgcatttatttggaagcaattaatttaatttatctcaaatttagactttatttccaaataatttgcttttaggtctctattcctacctatatatgtgtgtgcaaatatgcatgtacttaattactaaaaaagttgaaagaacacttggtacataaaaaaggttaattagtactatggtgtatattgctaataaacttcactctgcactagtaacaattttgccaaacttctgttcagagatctatggctttcatcgagcgtgtgcaatatggatcctcaacatttggttacagttgaggtatggatactcatcagattgacctccctgtattctttccttaatatactacactgactgaccgtgtacggatatatccgtgttagatgtataggccgggtttcaatccatcatccaaaaaaacatatactacactgacatgcagtttaatttctttcctttataacttacgtggtatatattactgttttataaactacactgacacacataaatttgtacaattggatcaggacatggagccttgtagatcaagcagcttgcaagtatccagccatgaactgagcagccctagcctcgagttcacgctaggaagaccgagctggcacagcatagatcatgactagctagctagcaagctcttgcttgcttgcttgctatatatatggacccatgaattgcacattcagatatactgtttatgaccatactcagatcgatacctgcgtcgccgcgatatcagcaatgcgcgatgaaacaagacatggatgaaaaaaaattaattaggagtggtttgtttgttttgtcgaaacaacacgatagtcccctctttcactttgctctcttttttcttagtttttcattacatttttgtatttattctcaatgtgtaagtgcagtagattatattctcatgcactacatgacactaggggtgcttgaaagttgtaatgcctctttgcaacttggtgaccggtgtaatgtatcatttgcacatgAaaaaaaaaacagagaaaatatctaacctgacaatgattatattcttcttgtgatgcatatatataagtatgtgtcttctcca More
CDS seq		atggcgtcggcgacgtcgacgacgcccgacctgtcgctgcacatcagcctgccgagcggtggcgcggcggtggggacgacggcgccgccggggctggggaacggcggtgcggttggtggtgccggcggcggcaaggcggcgGGTggtggtgacccgtggcggaggctggatggctccacggcgtcgacggagctgtcgctgtcgacgccgcagcagcagcaggagggcagtacatcggcggccgatgtgctgccgtggcggctgcggcagccgacggcggcggcggcgtccgtgccggtgacactgccgacgataccgatggatggttcggcggcggcggcgcgcgcgccgatccgtggggtgcctgtgtatagcggcggcgccggcggtggccacccgttcctcggaggcggcggcggcgaccaccggcacaaccggctctacaacccctaccactccacggcatggccctcgtcgtcgctgtgctcgacgtcgccggctccggctcctcctCCCCcaccagcagctctcgacccgacgacgtcgtcgctgctgtcgccgtccgcgtaccaccggatgctctccagcacggggcgcctccacggcgtgctcgccgacaccctccgcggctacgccggcgccgctgcggtggcgggctccatcggctacggctccgcggccgccgccgccgccgccatgggcggctacggcggcgccggcgccggcggcgggttcgcctcctcccgcttcatgccgcgcctcctcccggcgtcccgccgcagcatgcgcgccccgcggatgcggtggacgagctccctccacgcccgcttcgtccacgccgtcgagcttCtcggcggccacgagcgagcgacgcccaaatcggtgctagagctgatggacgtcaaggatctgaccctagctcatgtgaagagccatctgcagatgtataggaccgtgaagagcactgacaagccagcagcagcctcagggccgatggacggcagcggctccggctccggctccggcgacgacgagctcctggccggcgatggaaggcaggcgacgtcatcgggcgccgatgcggaccggcggatgtcgttcaccgagcaccggtcctcctccgagggagcggcgagccatgccggcggtggcggcgacggcgactgctcctcctctgccgtcaactccgacaccatcagagcgcgcagcaattcgccgagagatctatggctttcatcgagcgtgtgcaatatggatcctcaacatttggttacagttgaggacatggagccttgtagatcaagcagcttgcaagtatccagccatgaactgagcagccctagcctcgagttcacgctaggaagaccgagctggcacagcatagatcatgactag More
Protein seq		MASATSTTPDLSLHISLPSGGAAVGTTAPPGLGNGGAVGGAGGGKAAGGGDPWRRLDGSTASTELSLSTPQQQQEGSTSAADVLPWRLRQPTAAAASVPVTLPTIPMDGSAAAARAPIRGVPVYSGGAGGGHPFLGGGGGDHRHNRLYNPYHSTAWPSSSLCSTSPAPAPPPPPAALDPTTSSLLSPSAYHRMLSSTGRLHGVLADTLRGYAGAAAVAGSIGYGSAAAAAAAMGGYGGAGAGGGFASSRFMPRLLPASRRSMRAPRMRWTSSLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTVKSTDKPAAASGPMDGSGSGSGSGDDELLAGDGRQATSSGADADRRMSFTEHRSSSEGAASHAGGGGDGDCSSSAVNSDTIRARSNSPRDLWLSSSVCNMDPQHLVTVEDMEPCRSSSLQVSSHELSSPSLEFTLGRPSWHSIDHD
Function		Probable transcription factor RL9 [UniProtKB/Swiss-Prot:Q0J235]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_08g0016670	OsPr106_08g0016670.01	Chr08	21896964	21903022	+	NAM
CDS seq	atggcgtcggcgacgtcgacgacgcccgacctgtcgctgcacatcagcctgccgagcggtggcgcggcggtggggacgacggcgccgccggggctggggaacggcggtgcggttggtggtgccggcggcggcaaggcggcgGGTggtggtgacccgtggcggaggctggatggctccacggcgtcgacggagctgtcgctgtcgacgccgcagcagcagcaggagggcagtacatcggcggccgatgtgctgccgtggcggctgcggcagccgacggcggcggcggcgtccgtgccggtgacactgccgacgataccgatggatggttcggcggcggcggcgcgcgcgccgatccgtggggtgcctgtgtatagcggcggcgccggcggtggccacccgttcctcggaggcggcggcggcgaccaccggcacaaccggctctacaacccctaccactccacggcatggccctcgtcgtcgctgtgctcgacgtcgccggctccggctcctcctCCCCcaccagcagctctcgacccgacgacgtcgtcgctgctgtcgccgtccgcgtaccaccggatgctctccagcacggggcgcctccacggcgtgctcgccgacaccctccgcggctacgccggcgccgctgcggtggcgggctccatcggctacggctccgcggccgccgccgccgccgccatgggcggctacggcggcgccggcgccggcggcgggttcgcctcctcccgcttcatgccgcgcctcctcccggcgtcccgccgcagcatgcgcgccccgcggatgcggtggacgagctccctccacgcccgcttcgtccacgccgtcgagcttCtcggcggccacgagcgagcgacgcccaaatcggtgctagagctgatggacgtcaaggatctgaccctagctcatgtgaagagccatctgcagatgtataggaccgtgaagagcactgacaagccagcagcagcctcagggccgatggacggcagcggctccggctccggctccggcgacgacgagctcctggccggcgatggaaggcaggcgacgtcatcgggcgccgatgcggaccggcggatgtcgttcaccgagcaccggtcctcctccgagggagcggcgagccatgccggcggtggcggcgacggcgactgctcctcctctgccgtcaactccgacaccatcagagcgcgcagcaattcgccgagagatctatggctttcatcgagcgtgtgcaatatggatcctcaacatttggttacagttgaggacatggagccttgtagatcaagcagcttgcaagtatccagccatgaactgagcagccctagcctcgagttcacgctaggaagaccgagctggcacagcatagatcatgactag More
Protein seq	MASATSTTPDLSLHISLPSGGAAVGTTAPPGLGNGGAVGGAGGGKAAGGGDPWRRLDGSTASTELSLSTPQQQQEGSTSAADVLPWRLRQPTAAAASVPVTLPTIPMDGSAAAARAPIRGVPVYSGGAGGGHPFLGGGGGDHRHNRLYNPYHSTAWPSSSLCSTSPAPAPPPPPAALDPTTSSLLSPSAYHRMLSSTGRLHGVLADTLRGYAGAAAVAGSIGYGSAAAAAAAMGGYGGAGAGGGFASSRFMPRLLPASRRSMRAPRMRWTSSLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTVKSTDKPAAASGPMDGSGSGSGSGDDELLAGDGRQATSSGADADRRMSFTEHRSSSEGAASHAGGGGDGDCSSSAVNSDTIRARSNSPRDLWLSSSVCNMDPQHLVTVEDMEPCRSSSLQVSSHELSSPSLEFTLGRPSWHSIDHD More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_08g0016670	OsPr106_08g0016670.02	Chr08	21896985	21902985	+	IsoSeq
CDS seq	atggttcggcggcggcggcgcgcgcgccgatccgtggggtgcctgtgtatagcggcggcgccggcggtggccacccgttcctcggaggcggcggcggcgaccaccggcacaaccggctctacaacccctaccactccacggcatggccctcgtcgtcgctgtgctcgacgtcgccggctccggctcctcctCCCCcaccagcagctctcgacccgacgacgtcgtcgctgctgtcgccgtccgcgtaccaccggatgctctccagcacggggcgcctccacggcgtgctcgccgacaccctccgcggctacgccggcgccgctgcggtggcgggctccatcggctacggctccgcggccgccgccgccgccgccatgggcggctacggcggcgccggcgccggcggcgggttcgcctcctcccgcttcatgccgcgcctcctcccggcgtcccgccgcagcatgcgcgccccgcggatgcggtggacgagctccctccacgcccgcttcgtccacgccgtcgagcttCtcggcggccacgagcgagcgacgcccaaatcgg More
Protein seq	MVRRRRRARRSVGCLCIAAAPAVATRSSEAAAATTGTTGSTTPTTPRHGPRRRCARRRRLRLLLPHQQLSTRRRRRCCRRPRTTGCSPARGASTACSPTPSAATPAPLRWRAPSATAPRPPPPPPWAATAAPAPAAGSPPPASCRASSRRPAAACAPRGCGGRAPSTPASSTPSSFSAATSERRPNR

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
RI	Chr08	21898162	21899053	+	OsPr106_08g0016670.02	OsPr106_08g0016670.01,OsPr106_08g0016670.02	All

Expression

	Leaf	Root	Panicle
FPKM	1.479942	0.0	3.776894

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_08g0426866	RBH	0.000000	0.000000	0.000000
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os08g33050	RBH	0.085491	0.000000	0.067607
Nipponbare \| IRGSP 1.0 \| RAP-db	Os08g0426866	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_08g0016690	RBH	0.338326	0.0	0.000000
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_08g0016540	RBH	0.000000	0.0	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_08g0016510	RBH	0.200355	0.0	1.139014
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_08g0016850	RBH	0.066505	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_09g0009440	RBH	0.0	0.0	0.000000
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_08G0327600	RBH	3.865936	0.2100275	6.9177545
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_08g0016570	RBH	0.183881	0.0	0.174067
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_08G0349300	RBH	3.952112	0.511476	13.1284935
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_08g0015930	RBH	0.059244	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_08g0016210	RBH	0.350614	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_08g0016000	RBH	0.000000	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_08g0016820	RBH	0.087649	0.0	0.295270
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_08g0016220	RBH	0.000000	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_08G016340	RBH	0.074552	0.0	0.365347
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_08g0016470	RBH	0.448978	0.0	1.458338

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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