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
OsARC_08g0013891		OGI:01056340 \| 16/16			ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)			Chr08:18027342-18032198		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		AtpB
DNA seq		tttcttggattatttacaagcggtattcaagctcttatttttgcaatgttagccgcagcctatataggtgaatccatggagggtcatcattgaattgactagttttcaaaatagtcttttttttagcttaactcaattcatgcatggttgcggaaaattcgcttggttggaaaacaaaatagttagaattgcgtatgaatatacaatctagagttgtagaagagagaataggctatattatggaattgccaaacaaagtatataggcattagggaggggcagagtcaggctagatctatatcctttatgtctataagttcagtcatcttttgtatgggtttccactttaaggaattttttttgaatccgattcaatagaaaatgagaaaatacacaaacaaaatagaagaatcaaattgatatgggatattatatattcccaagttagattcattatctaatccgatatatggaatcggattccatatccaattcgatgcagcatattgttatcaattggatatcttgatttaattcctattggatctggattaggtcgatttccataggggttcttcctctatttcactttttattatgaattagatgataggggaaaaaatagaaactcaaggatatcgaagaggaaagaaagaaggatggaatgaaagatcagttggttagaaagaaagagaaatagaataatgagtacacaaacctctaatgattagaaactaaaaaggagatctcgaagcagttcggagaattcagattatcgtttcaatttgtactttttagttacttctgtccaatagagcttagaaatatgaatttcttggttgattgtatccttaaccatttcttttttttgacacgaggaactcatcatgaatccactaattgctgctgcttccgttattgctgctggattggccataggtcttgcttctattgggcctggagttggtcaaggtactgctgcaggacaagctgtagaaggtattgcgagacagccagaagcagaaggtaaaatacgcggtactttattgcttagtctagcttttatggaagctttaacaatttatgaactagttgtggcactggcgtttttatttgcgaacccttttgtttaatcctaaaaaaaacgagtcctttagattagatactttcttctttttttagtaaattggtatttgcttctgcaattccaattatatcaatactttactcctaatttattactcctagagttttctatttatggggacagacaataccccaccccaggaatagctgatttgaggatgatcaatttagaggatatgttcgccgtcttgcttcccgccctttgtttagggcagtggaaagtatttttccttttattttaggaattttgggaacatttcaacaaaggaggtctttcacaggtcaaacgagatctaagacttaatctaaaagaaattactaaattgaatctatttctattaaaaaaattgcattAaaaaaaccgatcaaaaagggcaagcgaagtaagtgatcgaaaaactttgttctttgttcgtcctatctataagaggagagcatatgaaaaatgtaacccatttctttcgtttttttagctcactggccatccgctgggagtttcgggcttaataccgatattttagcaacaaatctaataaatctaactgtagtggttggtgtattgatttattttggaaagggagtgtgtgcgagttgtctatttcaagaatagattggatctatccggctgcactttagaatattttttagtatttttcgaataaataagaaaagggtgcacgatctcgacgaattacttctgaataaatgcagaaatcatatgaaagaaccatagcatttcgcgacctattggtaaatcaaatcaactttgattctctatagaccaataatatgagaccattaacacggttaaagctaaactgcttgaaatctaggcaaaagggggtactctttctacaactatattagtattagtaccaaatgctttaaacaggaaatagctaatgtagaatttatctgatatagaacactcatatcgataaaatggtttgaactatttactagaaggggcaccctgcccttttttatccaatgccgaatcgacgacctatgtataaaaaaggagaaagtttttggatgtgaagaaaaaggtaggaattctatccattttcattttccatttttctatttagtttttcttaatgaaattgacaattttaactaaagggcaaatacaaataaaaaaacaactttgctgcccacgatagatttttatctaggcggaagagtcctcttaatatttatctagtcttatatgagtttcggtatattgaaatatAaacagaaaagagagggtaggggataggctcattacattaaaaaaatatggaagtagccatagcaaaaaaagaaaaaagggagcgtgagagccaaatgaatcgaaagattcatgtttggttcgggaagagatcataaagttgtaaacttaatagcaaggtaatctactttcattaaaagttttattagataatcgaaaacagaggatcttgagtactattcgaaatttagaagaattgcgtagaggaaccattgagcagctcgaaaaagctcgaattcgattacagaaagtcgaactagaagcggatgagtatcgaatgaatggatactctgagatagaacgagaaaaagcaaatttgattaatgccacttctattagtttggaacaattagaaaagtctaaaaacgaatccctttattttgaaaaacaaagggcgatgaatcaggtccgacaacgggttttccaacaagccgtacaaggagctctaggaactctgaatagttgtttgaataccgagttacatttccgtacgattcgtgctaatattagcattctcggggccatggaatggaagagttaaattaattagtccttgaacttctactttcctttagaatttaggcattatttttccccttgcttccgaaaaaaaaatagtaaagaaacactgatggcaacccttcgagtcgacgaaattcataaaattctccgcgaacgtattgaacaatataatagaaaagtagggattgagaatatcggtcgcgtagttcaagtgggggatgggattgctcttattataggtcttggtgaaataatgtcaggcaaattagtcgaatttgcacaagcgactaggggtattgctctgaattttgaatccaaaaatgttgggattgtattaatgggcgatgggttgatgatacatgagggcagttttgtaaaagcaacaggaagaattgctcagatacccgtgagcgaggcttacttgggtcgtgttataaatgctctagctaaacctattgatgggagaggcgaaattgtagcttcggaatctcgcttaattgaatctcctgctccgggtataatttccaggcattctgtatatgaaccccttcaaacggggcttattgctatcgattcgatgattcctattgggcgcggtcagcgagagttaattattggggacagacaaaccagcaaaacagtagtagctaccgatacaattctgaatcaaaaagggcaagatgtaatatgtgcttatgtagctatcggtcaaagagcatcctccgtagctcaagtagtaactactttccatgaatagggggccatggaatacactattgtagtagctgaaatggcggattcccctactacattataaaacctcgctccttatacaggagcagccctggctgagtattttatgtaccgcgaatggcatactttaataatttatgatgatctctccaaacaggaacaagcttatcaccaaatgtcccttttattaagaagaccccctggccgtgaagcttacctaggggatgttttttatttgcattcacgccttttagaaagagccgctaaattaaattctcttttaggggaaggaagtatgactgctttaccaatagttgagactcaatctggagacgtttccgcctatattcctactaatgtaatctccattacagatggacaaatattcttatccgcagatctattcaatgccggaattcggcctgctattaatgtgggtatttccgtttccagagtaggatccgcggctcaaattaaagccatgaaacaagtagctcgcaaatcaaaattggaattagctcaattcgcagagttaaaagcctttgcacaattcgcctctgctcttgataaaacaagtcagaatcaattggcaaggggccgacgattacgagaattgcttaaacaattccaagcaaatcctcttccagtggaagagcagatagctactatttatatcggaacaagaggatatcttgattccttagaaattggacaggtaaagaaatttttggatgagttacgtaaacacctaaaagatactaaacctcaattccaagaaattatatcttctagcaagacattcaccgaggaagcggaaatccttttgaaggaagctattcaggaacaactcgaacggttttcccttcaggaacaaacataaattttgcacgtctactcttgttagtagaagtagtagaggagaaatcgttgaggaagatttttcatttgaatcatgcAaaaaaAGTTTTCTTAGTTTTTAGTATAGTTATTTAAAGAATAGATAAAAATAAGATTGCGTCCAATAGGATTTGAACCTATACCAAAGGTTTAGAAGACCTGTCCTATCCATTAGACAATGGACGCTTTTTTCATATTTTCTTCTTTCTTTTCATTTTTTATCGGACCAAGAGAAAAAACTGTTAGACCAAAACTCTTTTAGG More
CDS seq		atgtaccgcgaatggcatactttaataatttatgatgatctctccaaacaggaacaagcttatcaccaaatgtcccttttattaagaagaccccctggccgtgaagcttacctaggggatgttttttatttgcattcacgccttttagaaagagccgctaaattaaattctcttttaggggaaggaagtatgactgctttaccaatagttgagactcaatctggagacgtttccgcctatattcctactaatgtaatctccattacagatggacaaatattcttatccgcagatctattcaatgccggaattcggcctgctattaatgtgggtatttccgtttccagagtaggatccgcggctcaaattaaagccatgaaacaagtagctcgcaaatcaaaattggaattagctcaattcgcagagttaaaagcctttgcacaattcgcctctgctcttgataaaacaagtcagaatcaattggcaaggggccgacgattacgagaattgcttaaacaattccaagcaaatcctcttccagtggaagagcagatagctactatttatatcggaacaagaggatatcttgattccttagaaattggacaggtaaagaaatttttggatgagttacgtaaacacctaaaagatactaaacctcaattccaagaaattatatcttctagcaagacattcaccgaggaagcggaaatccttttgaaggaagctattcaggaacaactcgaacggttttcccttcaggaacaa More
Protein seq		MYREWHTLIIYDDLSKQEQAYHQMSLLLRRPPGREAYLGDVFYLHSRLLERAAKLNSLLGEGSMTALPIVETQSGDVSAYIPTNVISITDGQIFLSADLFNAGIRPAINVGISVSRVGSAAQIKAMKQVARKSKLELAQFAELKAFAQFASALDKTSQNQLARGRRLRELLKQFQANPLPVEEQIATIYIGTRGYLDSLEIGQVKKFLDELRKHLKDTKPQFQEIISSSKTFTEEAEILLKEAIQEQLERFSLQEQ
Function		ATP synthase subunit alpha, chloroplastic [UniProtKB/Swiss-Prot:P0C2Z6]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.18	Chr08	18029294	18029531	+	IsoSeq
CDS seq	ttaaagctaaactgcttgaaatctaggcaaaagggggtactctttctacaacta
Protein seq	LKLNCLKSRQKGVLFLQL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.15	Chr08	18028184	18032198	+	IsoSeq
CDS seq	atgtaccgcgaatggcatactttaataatttatgatgatctctccaaacaggaacaagcttatcaccaaatgtcccttttattaagaagaccccctggccgtgaagcttacctaggggatgttttttatttgcattcacgccttttagaaagagccgctaaattaaattctcttttaggggaaggaagtatgactgctttaccaatagttgagactcaatctggagacgtttccgcctatattcctactaatgtaatctccattacagatggacaaatattcttatccgcagatctattcaatgccggaattcggcctgctattaatgtgggtatttccgtttccagagtaggatccgcggctcaaattaaagccatgaaacaagtagctcgcaaatcaaaattggaattagctcaattcgcagagttaaaagcctttgcacaattcgcctctgctcttgataaaacaagtcagaatcaattggcaaggggccgacgattacgagaattgcttaaacaattccaagcaaatcctcttccagtggaagagcagatagctactatttatatcggaacaagaggatatcttgattccttagaaattggacaggtaaagaaatttttggatgagttacgtaaacacctaaaagatactaaacctcaattccaagaaattatatcttctagcaagacattcaccgaggaagcggaaatccttttgaaggaagctattcaggaacaactcgaacggttttcccttcaggaacaa More
Protein seq	MYREWHTLIIYDDLSKQEQAYHQMSLLLRRPPGREAYLGDVFYLHSRLLERAAKLNSLLGEGSMTALPIVETQSGDVSAYIPTNVISITDGQIFLSADLFNAGIRPAINVGISVSRVGSAAQIKAMKQVARKSKLELAQFAELKAFAQFASALDKTSQNQLARGRRLRELLKQFQANPLPVEEQIATIYIGTRGYLDSLEIGQVKKFLDELRKHLKDTKPQFQEIISSSKTFTEEAEILLKEAIQEQLERFSLQEQ More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.14	Chr08	18028184	18030369	+	IsoSeq
CDS seq	atggaagtagccatagcaaaaaaagaaaaaagggagcgtgagagccaaatgaatcgaaagattcatgtttggttcgggaagaga
Protein seq	MEVAIAKKEKRERESQMNRKIHVWFGKR

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.17	Chr08	18029073	18030300	+	IsoSeq
CDS seq	atggaagtagccatagcaaaaaaagaaaaaagggagcgtgagagccaaatgaatcgaaagattcatgtttggttcgggaagaga
Protein seq	MEVAIAKKEKRERESQMNRKIHVWFGKR

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.16	Chr08	18029071	18029615	+	IsoSeq
CDS seq	gtgcgagttgtctatttcaagaatagattggatctatccggctgcactttagaatattttttagtatttttc
Protein seq	VRVVYFKNRLDLSGCTLEYFLVFF

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.11	Chr08	18028184	18031994	+	IsoSeq
CDS seq	atgtaccgcgaatggcatactttaataatttatgatgatctctccaaacaggaacaagcttatcaccaaatgtcccttttattaagaagaccccctggccgtgaagcttacctaggggatgttttttatttgcattcacgccttttagaaagagccgctaaattaaattctcttttaggggaaggaagtatgactgctttaccaatagttgagactcaatctggagacgtttccgcctatattcctactaatgtaatctccattacagatggacaaatattcttatccgcagatctattcaatgccggaattcggcctgctattaatgtgggtatttccgtttccagagtaggatccgcggctcaaattaaagccatgaaacaagtagctcgcaaatcaaaattggaattagctcaattcgcagagttaaaagcctttgcacaattcgcctctgctcttgataaaacaagtcagaatcaattggcaaggggccgacgattacgagaattgcttaaacaattccaagcaaatcctcttccagtggaagagcagatagctactatttatatcggaacaagaggatatcttgattccttagaaattggacaggtaaagaaatttttggatgagttacgtaaacacctaaaagatactaaacctcaattccaagaaattatatcttctagcaagacattcaccgaggaagcggaaatccttttgaaggaagctattcaggaacaactcgaacggttttcccttcaggaacaa More
Protein seq	MYREWHTLIIYDDLSKQEQAYHQMSLLLRRPPGREAYLGDVFYLHSRLLERAAKLNSLLGEGSMTALPIVETQSGDVSAYIPTNVISITDGQIFLSADLFNAGIRPAINVGISVSRVGSAAQIKAMKQVARKSKLELAQFAELKAFAQFASALDKTSQNQLARGRRLRELLKQFQANPLPVEEQIATIYIGTRGYLDSLEIGQVKKFLDELRKHLKDTKPQFQEIISSSKTFTEEAEILLKEAIQEQLERFSLQEQ More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.10	Chr08	18028184	18029929	+	IsoSeq
CDS seq	atgatcaatttagaggatatgttcgccgtcttgcttcccgccctttgtttagggcagtggaaagtatttttcctttta
Protein seq	MINLEDMFAVLLPALCLGQWKVFFLL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.13	Chr08	18028184	18030068	+	IsoSeq
CDS seq	atggaagtagccatagcaaaaaaagaaaaaagggagcgtgagagccaaatgaatcgaaagattcatgtttggttcgggaagaga
Protein seq	MEVAIAKKEKRERESQMNRKIHVWFGKR

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.12	Chr08	18028184	18029859	+	IsoSeq
CDS seq	atgatcaatttagaggatatgttcgccgtcttgcttcccgccctttgtttagggcagtggaaagtatttttcctttta
Protein seq	MINLEDMFAVLLPALCLGQWKVFFLL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.05	Chr08	18027547	18029762	+	IsoSeq
CDS seq	atgatcaatttagaggatatgttcgccgtcttgcttcccgccctttgtttagggcagtggaaagtatttttcctttta
Protein seq	MINLEDMFAVLLPALCLGQWKVFFLL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.04	Chr08	18027547	18028827	+	IsoSeq
CDS seq	atgatcaatttagaggatatgttcgccgtcttgcttcccgccctttgtttagggcagtggaaagtatttttcctttta
Protein seq	MINLEDMFAVLLPALCLGQWKVFFLL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.07	Chr08	18027639	18028023	+	IsoSeq
CDS seq	atatcctttatgtctataagttcagtcatcttttgtatgggtttccactttaaggaattttttttgaatccgatt
Protein seq	ISFMSISSVIFCMGFHFKEFFLNPI

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.06	Chr08	18027573	18028478	+	IsoSeq
CDS seq	gctatattatggaattgccaaacaaagtatataggcattagggaggggcagagtcaggctagatctatatcctttatgtctataagttcagtcatcttttgtatgggtttccactttaaggaattttttttgaatccgatt
Protein seq	AILWNCQTKYIGIREGQSQARSISFMSISSVIFCMGFHFKEFFLNPI

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.01	Chr08	18027342	18027727	+	IsoSeq
CDS seq	atgaatatacaatctagagttgtagaagagagaataggctatattatggaattgccaaacaaagtatatagg
Protein seq	MNIQSRVVEERIGYIMELPNKVYR

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.03	Chr08	18027539	18030369	+	IsoSeq
CDS seq	atgatcaatttagaggatatgttcgccgtcttgcttcccgccctttgtttagggcagtggaaagtatttttcctttta
Protein seq	MINLEDMFAVLLPALCLGQWKVFFLL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.02	Chr08	18027409	18029788	+	IsoSeq
CDS seq	gtgaatccatggagggtcatcattgaattgactagttttcaaaatagtcttttttttagcttaactcaattcatgcatggttgcggaaaattcgcttggttggaaaacaaaatagttagaattgcgtatgaatataca
Protein seq	VNPWRVIIELTSFQNSLFFSLTQFMHGCGKFAWLENKIVRIAYEYT

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.09	Chr08	18028184	18028794	+	IsoSeq
CDS seq	atgatcaatttagaggatatgttcgccgtcttgcttcccgccctttgtttagggcagtggaaagtatttttcctttta
Protein seq	MINLEDMFAVLLPALCLGQWKVFFLL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_08g0013891	OsARC_08g0013891.08	Chr08	18027711	18027988	+	IsoSeq
CDS seq	tcaatagaaaatgagaaaatacacaaacaaaatagaagaatcaaattgatatgggatattatatattcccaagttagattcatt
Protein seq	SIENEKIHKQNRRIKLIWDIIYSQVRFI

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	280.727295	11.331708	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os04g16740	RBH	366.193787	344.205444	44.800987
Nipponbare \| IRGSP 1.0 \| RAP-db	NA	NA	NA	NA	NA
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_08g0013710	SBH	0.000000	5.991801	7.182114
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_10g0018220	SBH	726.383789	85.930038	597.339661
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_08g0013620	SBH	17.790222	0.000000	21.770741
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_08g0013910	RBH	0.479764	0.062354	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0017970	RBH	1652.038818	120.820091	1315.958740
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0300300	RBH	4539.07959	422.9936675	612.403595
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA
Zhenshan 97 \| ZS97RS3 \| HZAU	NA	NA	NA	NA	NA
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_01g0017990	SBH	747.249451	6.285062	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0017940	RBH	218.670197	62.714031	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0018190	RBH	4714.895508	360.585022	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_Ung0019590	RBH	428.789459	0.0	177.504990
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0017850	RBH	436.983917	80.464249	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_10G017790	RBH	286.852173	78.991211	447.335388
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_04g0004650	SBH	2354.627930	984.945374	3754.520264

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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