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
OsNaBo_12g0005240		OGI:12010290 \| 12/16			NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)			Chr12:3993097-4000082		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		RPP30S, OsRpp30-S, CHS31, OsCHS31, -
DNA seq		gtcaaatacaatgataacagggtacgagttttgcataaaagtgataaaacttttcattaccacattgcttttgacatgataacataatttgatctcattttattattttagatcattcatgttaatctcacccaagagtctcctaagcttcttgaagctggtaagaaattggacatgacatattcagtgaagtggttacaaacagatgtgacctttgcacgccgctttgaagtatacctggattatcctttctttgagcaccaggtaatattttcccactccaaagAaaaaaaaactatgcgtaacatgcagctctcagcttgcttacttatgtgaaagagaaaaaatgttaattgtaacaacagggagctgaatcgtcctgttctttttgaaagttgttcaaaggttctgacttctatgcaaatttctaatgttcagattcattggttctccattttcaattctttcatgatggttattttcctcactggtttggtttcaatgatattgatgcggacattgagaaatgactatgcaaagtatgctcgtgaagatgatgatctggagtcactggtatatctaccttttgtttaattgtattcttagctctagcatctaagttggatttgttttcacctagtgccactcgattgggacctcaagtcttgatattccttttgttaggagagagatgttaatgaggaatctggatggaagcttgttcatggtgatgtatttcgccctcctcgaagtttggcctttctttctgcagttgttggcatcggcactcagctggcagctcttatccttcttgttattgtattggccattgttggcatgctatatgttgggtaagcaaccccccatccccaaaatctccttgcacatacaatgcatagtttggaatacctgagttgctgaccaatgaaactaccatattactcaatagatgaaagaaagaagatagggaatacctgaacttgttaggttcccaccacatgttttttgaaagctgtccaggaaccttccatgtcctgtactttacctggaaaatcttgattctgcagtaatcaatttcaataatgaagaattgttctgaatctaacatgcataatagacaattttgttaaaatgtcttggattaaattttctgcatctggttggtatgacttaaaactactgggaactggctcaccactcaccagtcgtctgaacctgagaaacaacggcacataggttgttaagtgcagataacattttggtcaaacgactatttcttgtttatgtcctaaccatgctgaaaagaactaagaaaagaaaggaactgtaccttttcattgtccaaaaattgccttgtattgtgtttctcactttactggttggagtggtggaatgtctgccttctgttaaaaatgcacacatccattagcccaaatccctaaggcctgtgattgtatgaatcctaaagatataaaattcctatattattttgaaaacagctttaagtttttttcttttttttagcatttcacattttgtgcatggatttgcttttctaacttatatagcgcgcgatatttgtcaggcgagggtctatcatcacaaccttcattgtgtgctatgctcttacatcttttatttctggctatgtcagtggtggcctctactcaaggaatggtggtatggttctttccttttggaattgcattattttcttgtattatttgtctgtgcaattcaatctcttctcaaggttctgtttcatagtttcctcctgtcattccTttttttttttttgaagtttctagaatttgcatgttgtcatatattatattttcccacttcatgatgtatggTtttttgaaccgtaatttccttacatggcaggtaaaaactggataaaggctatgatccttacagcatccctatttccattcttgtgctttgcaattggctttgttctgaatacaattgctatcttctaccgatcattagcggcaataccattcggcacaatggttgtcatgttcgttctttgggccttcatttcttttccgctggtgcttctgggaactgttgttggtaggaactggagtggtgctcctaacaatccctgccgagtaaagactattccacggcctattccagagaagaagtggtaccttacaccttctgttatctcattgatgggtgggctgcttccctttggcagtatcttcattgagatgtactttgtgttcacgtcattctggaactacaaggtaaacagtttaacttaagtatccaagtttgttttggaacagaagtagtgcctatggtgtactggtgttcaacctcttatatggctgcttcataaattacacaatttattttttgaatgaactcttggtggatttctaatatgtctgcttcatacatctgtctatgcactttgtttaaTtttaataatatggataatttgatcgtgacaattcgtttgacttccttggcaggtttattatgtctacggcttcatgctgctggtctttgtcatccttctaatagttacaatctgtgtcactattgtgggtacttatttcttgctgaatgctgagaactatcactggcaatggacttcatttctctctgctgcatcaactgcgttatatgtgtatctatattccatctactactatcatgtaaagacaaagatgtcaggTtttttccagacgagtttctacttcggttacacattgatgttctgccttggtctaggcatactttgtggtaagatcttaatttctactagtaccttctaatccgtgacactttatcattatgatgtttttgttttgacatctgttttggcgattcaggtgctattggctatctagggtcaactctttttgtgaggagaatctacagaaacatcaaatgtgattagatgatcgcagtttggaagacatagcagatcacatgttgtcactggaactgtggtagagaggccaagaagtggattaatgctagatgctgattaagttttttgagccacagaccgaaggggggccatgatctcctaacttaatataaatacattcatacgcctactctcttttttgactatgtcgccctgattatgcatacctgtggtagttgaggatttggttggttttttaatcagaagtaggatgtaacattgtaacatgtgaaatattcatgcggcactagatttcttctcttcgtatggattggaccgggggcttgtggattccaattcaaggctgtcattttaccacgagcacactgtggttatatgtattgcaacattgttatagccattaagctttatacatgggtttatctacatttaatctttggacacatgtttcgaggtacaaatttagtatatttctctttaatttatactgttattatgtgcaaacagttgaattaactaacctgaatattcgaatttacgcatgtccttcgtatggcaggtttacatgattaaatgttgtcattgttggcagtagggaatgagctagatatcgtggttttgtatgatctgttgtaaaatctgattgctgcttgggatcttattgaccaagctataaacactactttctgctagtccagttgccgtcaacaatccataacaaaaaatcatgatccagatgctgaatatataaaagctaaaatgtagatcaaaactcatgatcgatcgatgtagatggtccgatctttcatagcggaagaatgaacaatgtgtaactatttaagtagcaaccaaaattgcaatatctgagatggattggaatgtggtacaagagaattgtgttctcgctctcaagaacaaacaaaaaatttacctattcttcagacaatacacaagtcataagacttcactctgctaacttgcacaggcccttcttgagtttcaactgggaataggatttcgttgccatggcttaactgctcttgctgctcgacaaagagggactcatcaccatcataaggtaaatgcagtagttcaatcatcttcattggcagaaggttctggatttatatcaagagattgtggttctcctttgtaagctggcaattccaaagatagcagatctacttcatgaggcataggatcccaactaatccagtcagcaagcttgaagtctgctgaattcaactgcttatttggtaacagcctgtcgattctaatggtttccttgtagaagtgctttttcctcagagccttggaaaccagtgacctgagaatgaacatatggcttagaatacatggcacggcatcatgattcatgctaaactgcctagctttctaaaataagctacggatatcatataagagacgtgcaagtgacctgcagttgacggatagagcagctttggctcgttgggtagaaaggccaagcaaataagaagataagtttatggcatcatagggtcctctaatttcagaagcagtgtgagcagcacttgatatgatgagattctttcctttagtccactccaccaagagctgaaaaaaggtgaaaggttttggttactaaggaactgagtaatacaagagctgaaaaaagatgaaaaggttttggttactaaggaactgagtattagtattacgatatgcaaaggcaataaggaagagcaagagatggccaaccttggcttcggctatggcctgtctccttgaagcggcatcagcgatgaggggagaataggcgatctccaagtgcaggcccttctgcagtgcaagcttgagcatggggagcttgaggcggaaggacagcttgtgggaaaagtcgatggagacaatatcgaggtggtcaaatgtggcctgacagaggtggtcgaaggcggcttgggtgagcggccgcgcggcgacgatgtcataggtgcgaaggaggcgagcggcagagggggccagggcggaggcgcaggcggcagcggagtcgagggagagggtgatgcgcgtgtattgtaggaagggatgtcgacggcggtggagggaggcggagggtgacacccggagagaggaggcaataggtgcatgggagtcagtgagtaggccacggtgagggtgatcaagcgcgaccgcggagtagccgaggtcaagggcacgggcgactacgctagtgttggtggtggtagatttggagtcgtcggggaggatgctgaggtcgaagaagccggcaggcgccatggcaaacagtggtgtagctaggaatttttccttgggtagtcctacttcaaaattgcaggttaacatcacataccaaaattttatacacaagttcaaagttagtgaaagggctatacaaaattagaaatataacaatagagtcttataacaacaatagtcagctaacttaacaagcaagttaaaatatgcaaatattatagagattttctcccatccttggagaggtatatacctccttgtatttgagatatacctatccataaaacaagtcttgtgccaactcagtctctctctctatctctccctctctgctactagtgtgtgtgttctaacgaaatttagggcgaccaactatgttccttcctAaaaatgggaaaagttgtgttccttccttgtcagggacaagccaatgattttgaggttaggtattcgaaatgtgaaggaataagaaaattttacaacccaaagcctaattttgatatgtttaatttcatgtagttctaaactactattagataatatatagcagatataagtataatttcataaattcataaaattggctataaattgaatgtgcttaacatatgaaagtaggaaacttctaactggcaatgcttcacaaggttcaaattgggagtttgggagttgggacaaggttcaaaactgaaagttcaattgttcaaatatactagcaatcaatcagccatcccaggcttcaaatgaaagagatgttcctaatccaaaatcacagcaccacagcagcagacaacaattaccttgggcttctcggactctcggggcagcgcagagggcgtcggcggcggcggcggcggcaccgcgcgacggcgcgaagctggccgggcttggctatttggcgtcgggcgcggcggcgactgcggctctcgcctctcggcttctcaaggcgacgcgattgcacgaggcgggagcaaggcgcgaaggcgggcgggggttggcgagttggcggacagcggctcggcgcgaccgcgagaccgcgtctgatcggcgggcggctgcggctgcggcggcggcggcggcgacgcgacggcctgagagagagatgacgcagttggtgggtacggacagagggacagacggaaaccctcccggcttttcacagcgaaaagagcgagagaaaaaaagAaaaaaatagcacaggaaaaaaagtaccaaaaaatagcacaagaatttttcgctttcaatcaaaagcacagacttccgtcgggtttggaattaacagagttagattaaagtatagaaaatttttgttggacccatttgcccttcatcttccttgccgtaatctcccattgtgtcatctcgttctcttcattctttctctttaccaaaccctagctctcactcccatccgattggacaccatgtggaagacagggtttttgacgggggctctcgggttggtgcccacgatgacggcgctggcgccgcggccaaacagcgacgcggcgacgagggtgtcgaggtgggcctcgtcgggggcgacgggcgctatgaggaagaccttcgcgcaggccacgagcacgcgcgcaccgtgggtgttgtcggcgatgtccttggcgaggcggagcagccgtgcatgtagaggatggcgcgctggacggaggccgaggagcgccgcaagccgctcgtcggcgccaggggtgtgggcgccggcgttggtggaggtgacgagatgggtgatgtccgtggcagggtggtcccactcagcgattgccctcgccgcggtgaccatggccagctccggcat More
CDS seq		atgccggagctggccatggtcaccgcggcgagggcaatcgctgagtgggaccaccctgccacggacatcacccatctcgtcacctccaccaacgccggcgcccacacccctggcgccgacgagcggcttgcggcgctcctcggcctccgtccagcgcgccatcctctacatgcacggctgctccgcctcgccaaggacatcgccgacaacacccacggtgcgcgcgtgctcgtggcctgcgcgaaggtcttcctcatagcgcccgtcgcccccgacgaggcccacctcgacaccctcgtcgccgcgtcgctgtttggccgcggcgccagcgccgtcatcgccgtcgcgtcgccgccgccgccgccgcagccgcagccgcccgccgatcagacgcggtctcgcggtcgcgccgagccgctgtccgccaactcgccaacccccgcccgccttcgcgccttgctcccgcctcccgagaggcgagagccgcagtcgccgccgcgcccgacgccaaatagccaagcccggccagcttcgcgccgtcgcgcggtgccgccgccgccgccgccgacgccctctgcgctgccccgagagtccgagaagcccaagctcttggtggagtggactaaaggaaagaatctcatcatatcaagtgctgctcacactgcttctgaaattagaggaccctatgatgccataaacttatcttcttatttgcttggcctttctacccaacgagccaaagctgctctatccgtcaactgcagaatcaagattttccaggtaaagtacaggacatggaaggttcctggacagctttcaaaaaacatgtggtgggaacctaacaagttcagattttggggatggggggttgcttacccaacatatagcatgccaacaatggccaatacaataacaagaaggataagagctgccagctga More
Protein seq		MPELAMVTAARAIAEWDHPATDITHLVTSTNAGAHTPGADERLAALLGLRPARHPLHARLLRLAKDIADNTHGARVLVACAKVFLIAPVAPDEAHLDTLVAASLFGRGASAVIAVASPPPPPQPQPPADQTRSRGRAEPLSANSPTPARLRALLPPPERREPQSPPRPTPNSQARPASRRRAVPPPPPPTPSALPRESEKPKLLVEWTKGKNLIISSAAHTASEIRGPYDAINLSSYLLGLSTQRAKAALSVNCRIKIFQVKYRTWKVPGQLSKNMWWEPNKFRFWGWGVAYPTYSMPTMANTITRRIRAAS
Function		Chalcone synthase 8 [UniProtKB/Swiss-Prot:O23731]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNaBo_12g0005240	OsNaBo_12g0005240.02	Chr12	3999031	4000082	-	NAM
CDS seq	atgccggagctggccatggtcaccgcggcgagggcaatcgctgagtgggaccaccctgccacggacatcacccatctcgtcacctccaccaacgccggcgcccacacccctggcgccgacgagcggcttgcggcgctcctcggcctccgtccagcgcgccatcctctacatgcacggctgctccgcctcgccaaggacatcgccgacaacacccacggtgcgcgcgtgctcgtggcctgcgcgaaggtcttcctcatagcgcccgtcgcccccgacgaggcccacctcgacaccctcgtcgccgcgtcgctgtttggccgcggcgccagcgccgtcatcgccgtcgcgtcgccgccgccgccgccgcagccgcagccgcccgccgatcagacgcggtctcgcggtcgcgccgagccgctgtccgccaactcgccaacccccgcccgccttcgcgccttgctcccgcctcccgagaggcgagagccgcagtcgccgccgcgcccgacgccaaatagccaagcccggccagcttcgcgccgtcgcgcggtgccgccgccgccgccgccgacgccctctgcgctgccccgagagtccgagaagcccaaggtaattgttgtctgctgctgtggtgctgtgattttggattag More
Protein seq	MPELAMVTAARAIAEWDHPATDITHLVTSTNAGAHTPGADERLAALLGLRPARHPLHARLLRLAKDIADNTHGARVLVACAKVFLIAPVAPDEAHLDTLVAASLFGRGASAVIAVASPPPPPQPQPPADQTRSRGRAEPLSANSPTPARLRALLPPPERREPQSPPRPTPNSQARPASRRRAVPPPPPPTPSALPRESEKPKVIVVCCCGAVILD More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNaBo_12g0005240	OsNaBo_12g0005240.01	Chr12	3993097	4000082	-	NAM
CDS seq	atgccggagctggccatggtcaccgcggcgagggcaatcgctgagtgggaccaccctgccacggacatcacccatctcgtcacctccaccaacgccggcgcccacacccctggcgccgacgagcggcttgcggcgctcctcggcctccgtccagcgcgccatcctctacatgcacggctgctccgcctcgccaaggacatcgccgacaacacccacggtgcgcgcgtgctcgtggcctgcgcgaaggtcttcctcatagcgcccgtcgcccccgacgaggcccacctcgacaccctcgtcgccgcgtcgctgtttggccgcggcgccagcgccgtcatcgccgtcgcgtcgccgccgccgccgccgcagccgcagccgcccgccgatcagacgcggtctcgcggtcgcgccgagccgctgtccgccaactcgccaacccccgcccgccttcgcgccttgctcccgcctcccgagaggcgagagccgcagtcgccgccgcgcccgacgccaaatagccaagcccggccagcttcgcgccgtcgcgcggtgccgccgccgccgccgccgacgccctctgcgctgccccgagagtccgagaagcccaagctcttggtggagtggactaaaggaaagaatctcatcatatcaagtgctgctcacactgcttctgaaattagaggaccctatgatgccataaacttatcttcttatttgcttggcctttctacccaacgagccaaagctgctctatccgtcaactgcagaatcaagattttccaggtaaagtacaggacatggaaggttcctggacagctttcaaaaaacatgtggtgggaacctaacaagttcagattttggggatggggggttgcttacccaacatatagcatgccaacaatggccaatacaataacaagaaggataagagctgccagctga More
Protein seq	MPELAMVTAARAIAEWDHPATDITHLVTSTNAGAHTPGADERLAALLGLRPARHPLHARLLRLAKDIADNTHGARVLVACAKVFLIAPVAPDEAHLDTLVAASLFGRGASAVIAVASPPPPPQPQPPADQTRSRGRAEPLSANSPTPARLRALLPPPERREPQSPPRPTPNSQARPASRRRAVPPPPPPTPSALPRESEKPKLLVEWTKGKNLIISSAAHTASEIRGPYDAINLSSYLLGLSTQRAKAALSVNCRIKIFQVKYRTWKVPGQLSKNMWWEPNKFRFWGWGVAYPTYSMPTMANTITRRIRAAS More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.000000	0.000000	0.681745

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_12g0175900	RBH	0.432496	0.879727	1.074523
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os12g07690	RBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os12g0175900	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_12g0005040	RBH	0.000000	0.000000	0.000000
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_12g0005250	RBH	0.000000	1.299432	0.724802
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_12g0005300	RBH	0.000000	4.056070	2.353904
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_12g0005120	RBH	0.043495	0.088196	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_12g0005230	RBH	0.000000	0.000000	1.887099
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_12G0064500	RBH	0.542732	2.166142	0.537992
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_12g0005210	RBH	0.000000	0.000000	0.174032
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_12G0068800	RBH	0.4063805	1.751596	0.815976
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_12g0005040	RBH	0.144909	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_12g0005290	RBH	0.110723	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_12g0005230	RBH	0.000000	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_12g0005200	RBH	0.000000	0.0	0.047529
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_12g0005170	RBH	0.000000	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_12G005050	RBH	0.000000	0.000000	0.204158
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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