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
OsLima_01g0006010		OGI:01016130 \| 16/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr01:4547675-4552667		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		OsWD40-7
DNA seq		ggttccccgccacaagcccacaaatatTAtgcgagagagagagcacccgttaccgcctccctcacctcacgctgacgatcgccaccgcctcccccgcaaaaccgtcgcgccgactcactctcgccgccgccgccgccgccgccgccgcgagatccgatcgccatgacgatctcctcgtccctcgcctcccgcctcggccccggcggccccacgaggtggagcccctacgcccgggcccccgatcccggccacggggcggggaggagctccgttcctcccggtggtggtggtaactcacgccctcccctccgcgtcgcccccgccacggcgaggctcctcggccaccccgcgcggaagggggccgcggcgccgcccggatcgaggtgccgcgcggaggcggaggcggaggccacagccgcctccgatgctgcctgccctaacccgccgcggcgtgggtgcgaagagacgaacccgaacccgaaccctaagagaaaccctaagccggcggagagaggggaggagccgcccgtccgcgccgtcggctgcggcggattcgccttcctctgcgccctcgctggccacaccgaggtgattattgtctccccccactcaactattttctgcgatgaatttgcgtcgattctataacctaatcatatgatgagtgaggattttgctatattctatataacctaatcatctgacgagtgaggaatttggtcgattctataacctaatcatctgatgagtgaggaatttgctcgattctataacctaatcatctgatgagtgaggaatttgctcgattctataacctaatcatctgattgagaggaatttgcgtcgattctataacctaatcttctgatgagtaattgtccaacgctgcaggctatcagtgggatctctctgcctgtgggttccgacaagctttactccggcagcgctgacggctccgtccgcgtctgggactgcaactctggcaaggtagctgggctctccgctctcggcactcccttcaggctctttacgcatgattcaagttgagtaaattcaagttgggggttgcatctgcgtcgattcctccgttgattgtggcggtctttgaagtgcttccatgagatcaattggggagtactatctgattgcttcctgtggtcagacatattggtaccaaatcagttttttctttgcaAGattgGGGTTatCGGCatgccggaccgaattgttacgggaatcttttcgcctgcttgtgtactgttgatcagtatatcagggtcagtttgcgagcaaggcaatgaggctggtttggctgataagcaaggggctctctggaattacattacagttctctctggctgatggtccatacatggttttgtcaaaaaaaaaaagtagtgaaaaaaagaaagagaaagtaaaaaaaaaaGaaaaaaaaagatgtgagatgattgatgattatattttcttggaaagagaagactgaacaaggaggaaaagataggtgtctggctgataaaaaaattctaatatttattacattgcattgttttcttaatgtttctgtcatagtgcgttgatgccatcaagatgggaggcaagattggttgcatgattacccatggcccatggatatttgttggaatcacgaagtccgtggaggtaatattttaatttcgttgatttttttttgtgggagtagtccattttgtgttacatattgcgatgttactattgtgcattgaactgttgatattgatccctacaacgaattgtaggcatggaacacacaaacagggatgaagtccagtctccatggaccttctggtctggtttgttccatgactatcaaggatgagatgttgtttgctggtaccggagatggtcgcatcatggcttggaaaattcctgacaagaagggtgactctggaccagtggcaatcctcagtggccatgagcgccaagtgatttcgctcggtgtctcagcaacaaggctttactctggctcacttgacaagaccatcaaagtatggtaatgctgcaaaacttgtgcaaacttgtgcttctgtgttggctactaaggaatattatgttagtactagtatttggccataaaactctattcatcaggtatgggaccttaaaactctgcagtgtgtccaaacactctctgagcacaaagctgctgtaacatctgtgctttgttgggatgaaaaactattatcttgctctctggacaagactgtaaagatctgggctgcttcaaagtctggagaccttcaagtgatatatacccattctgaggagcatgtaagttctactctggcctgcatcctctgtagcaatggttgcacaagttttatagcattgaaatttcaggcacaaatttatttagctacttaaccagttaaaatagtcaataagatgacatttttgtgtatctaaactgcatattaggttgacatgttttttgactggagggagtactattgtgcgtattttcttgtgttgaacgttactattctccaacactcaaatagtttctggctgctaaatcacttagggcatttttatttcagatgatgtagtaactaaattaaacttagtttaagagttaagtcacattactttctgtttttaaactgcatttcaatgctaatgcagttatactatgttgaatgggagcactacgtagcttttgcacaattaaaaaaaagacactatgttgaaaccTttttttttttggggtggtcgtgcctagcaccaaatatggtatataaactgcactgtttactatctactttacttttctatcttttatttatataaagtttttcttggcgtgttctatgcattgagcagctccttcctgttgtcgaatggcagcaaaatcccttcataagcacaattagttctcttaattgacttggaagatctttgctcaagagtagttttgttgccgcaattggtcttgtgttatttatgtctattaatgagtccatcttcattcagtcaagcaagggtaccttcaatatgtaggatttcagtgttctagacttattctgtactgtatgtaGgggtggaaacgagccgaggctcggcttgcagtggctcgcaaaaaacttggcttggctcggcttggttagggaaacaagctaaaacttaagctcggctcggctcgtttcctgactcgagccagctcgagctggcttgcaagccttcttgttgaaacacctcttcatatatAttttgtaattattaaaaaaagtaaaaacaaatcatcaacatgtaaaatttaaataagtttttatattcaattcttcaaaatcttgatgataaatttcaagttgacaaataataacactatataaagtaaaataatcaatataaacacacgatggcctaggctcgcgagctaaaacaagcggctcgcgagctagctcggctcagctcatttcagcaacgagctaaaaaggaggcttgggcttggcttgtttggcttacgagctgagccaagccaaccaagctcgagccaagcccgagctgagctcacgagcccgagctttttttccacccctaactgtatgggtggttcagtgttcttggttagctggtagtgaagagtgaacttataatgatcagcatatttcattgtggcatcaagaccaaggagagaccctctacccgttttctatttaatccttgtaattaatctccatattaatcggcttggagaaacgaaacgacgttactgctgctgcatgattgcacaggcaaggaatgttccatgctgcatgcagctcaaaaatcgcatggcctactcgatctccgtgataactagttaatccatccaacatgcacatgctaccagcgttaatatgctgatcaaatcggaatatctccactttcgttatgcgctgatcattatggaatggagggagtaataatttggttggctggtagtgaagagtgaacttaaagtaataaggactaaacatccgcttgggaaactttagaaggctgctcagttcatctggttcccttgaaagagtatcaataagggagtatgatgtaattgaggaagctattgatggaagtgtctcaggctctcagcaacaattgaatgatttgtacaatctgcatcaaagcatgaacaaatggggtcgtgaattgtcaattcttagttctggatattcttcttgcttttctgcccagtattgctaccaaccctctatatccaagtattctttaatccttttcaagatactgctctagaatctgttgatcgctttgggtgtttttgttgtggagaaacattctgtatttattgtggtgcatggttatggaaaccatgtaagttcaatgctagtgtccagtttgcaagttcagttttctttggatgagaatgctctgcttctgaaccttactcctttcaacagtcttcagttgttcccctgttgctaaacatgcacttctgttgcagggagtacgcacgctctttggcatgcaccgtgttggaaagacgccagttctgttctgctccctccacaacagcaactgcatacgtctgttcgacctgccatcgtaagtgcataaaaaatctgtaggccatcgaagaacgtactgctcccttactggaagtctcaaaaatggtttggtcttggtctttcaggttcgacgagatgggcaagcttttctccaagaaggaagtgaggaccatcgagctcgcagccggcggcctcctcttcaccggcgacggcgccggcgagctgaaggtgtggaggtgggcgcccgaggaggagcctgcaaccccggcgctcgtgaaatcatcaatgtagaagcactgtagcgtcgttgagtaaagatagcagctcctgcgaattgtcgtgagctccatctcagaatccatgtagtaataacttatgacaatgctgatgtaaatatatttgcccaatcctgaggcctgattagcaatattatgttccattctccc More
CDS seq		atgacgatctcctcgtccctcgcctcccgcctcggccccggcggccccacgaggtggagcccctacgcccgggcccccgatcccggccacggggcggggaggagctccgttcctcccggtggtggtggtaactcacgccctcccctccgcgtcgcccccgccacggcgaggctcctcggccaccccgcgcggaagggggccgcggcgccgcccggatcgaggtgccgcgcggaggcggaggcggaggccacagccgcctccgatgctgcctgccctaacccgccgcggcgtgggtgcgaagagacgaacccgaacccgaaccctaagagaaaccctaagccggcggagagaggggaggagccgcccgtccgcgccgtcggctgcggcggattcgccttcctctgcgccctcgctggccacaccgaggctatcagtgggatctctctgcctgtgggttccgacaagctttactccggcagcgctgacggctccgtccgcgtctgggactgcaactctggcaagtgcgttgatgccatcaagatgggaggcaagattggttgcatgattacccatggcccatggatatttgttggaatcacgaagtccgtggaggcatggaacacacaaacagggatgaagtccagtctccatggaccttctggtctggtttgttccatgactatcaaggatgagatgttgtttgctggtaccggagatggtcgcatcatggcttggaaaattcctgacaagaagggtgactctggaccagtggcaatcctcagtggccatgagcgccaagtgatttcgctcggtgtctcagcaacaaggctttactctggctcacttgacaagaccatcaaagtatgggaccttaaaactctgcagtgtgtccaaacactctctgagcacaaagctgctgtaacatctgtgctttgttgggatgaaaaactattatcttgctctctggacaagactgtaaagatctgggctgcttcaaagtctggagaccttcaagtgatatatacccattctgaggagcatggagtacgcacgctctttggcatgcaccgtgttggaaagacgccagttctgttctgctccctccacaacagcaactgcatacgtctgttcgacctgccatcgttcgacgagatgggcaagcttttctccaagaaggaagtgaggaccatcgagctcgcagccggcggcctcctcttcaccggcgacggcgccggcgagctgaaggtgtggaggtgggcgcccgaggaggagcctgcaaccccggcgctcgtgaaatcatcaatgtag More
Protein seq		MTISSSLASRLGPGGPTRWSPYARAPDPGHGAGRSSVPPGGGGNSRPPLRVAPATARLLGHPARKGAAAPPGSRCRAEAEAEATAASDAACPNPPRRGCEETNPNPNPKRNPKPAERGEEPPVRAVGCGGFAFLCALAGHTEAISGISLPVGSDKLYSGSADGSVRVWDCNSGKCVDAIKMGGKIGCMITHGPWIFVGITKSVEAWNTQTGMKSSLHGPSGLVCSMTIKDEMLFAGTGDGRIMAWKIPDKKGDSGPVAILSGHERQVISLGVSATRLYSGSLDKTIKVWDLKTLQCVQTLSEHKAAVTSVLCWDEKLLSCSLDKTVKIWAASKSGDLQVIYTHSEEHGVRTLFGMHRVGKTPVLFCSLHNSNCIRLFDLPSFDEMGKLFSKKEVRTIELAAGGLLFTGDGAGELKVWRWAPEEEPATPALVKSSM
Function		Zinc finger CCCH domain-containing protein 17 [UniProtKB/Swiss-Prot:Q0DYP5]

Transcripts

sorry

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_01g0006010	OsLima_01g0006010.01	Chr01	4547675	4552667	+	NAM
CDS seq	atgacgatctcctcgtccctcgcctcccgcctcggccccggcggccccacgaggtggagcccctacgcccgggcccccgatcccggccacggggcggggaggagctccgttcctcccggtggtggtggtaactcacgccctcccctccgcgtcgcccccgccacggcgaggctcctcggccaccccgcgcggaagggggccgcggcgccgcccggatcgaggtgccgcgcggaggcggaggcggaggccacagccgcctccgatgctgcctgccctaacccgccgcggcgtgggtgcgaagagacgaacccgaacccgaaccctaagagaaaccctaagccggcggagagaggggaggagccgcccgtccgcgccgtcggctgcggcggattcgccttcctctgcgccctcgctggccacaccgaggctatcagtgggatctctctgcctgtgggttccgacaagctttactccggcagcgctgacggctccgtccgcgtctgggactgcaactctggcaagtgcgttgatgccatcaagatgggaggcaagattggttgcatgattacccatggcccatggatatttgttggaatcacgaagtccgtggaggcatggaacacacaaacagggatgaagtccagtctccatggaccttctggtctggtttgttccatgactatcaaggatgagatgttgtttgctggtaccggagatggtcgcatcatggcttggaaaattcctgacaagaagggtgactctggaccagtggcaatcctcagtggccatgagcgccaagtgatttcgctcggtgtctcagcaacaaggctttactctggctcacttgacaagaccatcaaagtatgggaccttaaaactctgcagtgtgtccaaacactctctgagcacaaagctgctgtaacatctgtgctttgttgggatgaaaaactattatcttgctctctggacaagactgtaaagatctgggctgcttcaaagtctggagaccttcaagtgatatatacccattctgaggagcatggagtacgcacgctctttggcatgcaccgtgttggaaagacgccagttctgttctgctccctccacaacagcaactgcatacgtctgttcgacctgccatcgttcgacgagatgggcaagcttttctccaagaaggaagtgaggaccatcgagctcgcagccggcggcctcctcttcaccggcgacggcgccggcgagctgaaggtgtggaggtgggcgcccgaggaggagcctgcaaccccggcgctcgtgaaatcatcaatgtag More
Protein seq	MTISSSLASRLGPGGPTRWSPYARAPDPGHGAGRSSVPPGGGGNSRPPLRVAPATARLLGHPARKGAAAPPGSRCRAEAEAEATAASDAACPNPPRRGCEETNPNPNPKRNPKPAERGEEPPVRAVGCGGFAFLCALAGHTEAISGISLPVGSDKLYSGSADGSVRVWDCNSGKCVDAIKMGGKIGCMITHGPWIFVGITKSVEAWNTQTGMKSSLHGPSGLVCSMTIKDEMLFAGTGDGRIMAWKIPDKKGDSGPVAILSGHERQVISLGVSATRLYSGSLDKTIKVWDLKTLQCVQTLSEHKAAVTSVLCWDEKLLSCSLDKTVKIWAASKSGDLQVIYTHSEEHGVRTLFGMHRVGKTPVLFCSLHNSNCIRLFDLPSFDEMGKLFSKKEVRTIELAAGGLLFTGDGAGELKVWRWAPEEEPATPALVKSSM More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_01g0006010	OsLima_01g0006010.03	Chr01	4548567	4552667	+	NAM
CDS seq	atgaggctggtttggctgataagcaaggggctctctggaattacattacagttctctctggctgatggtccatacatgtgcgttgatgccatcaagatgggaggcaagattggttgcatgattacccatggcccatggatatttgttggaatcacgaagtccgtggaggcatggaacacacaaacagggatgaagtccagtctccatggaccttctggtctggtttgttccatgactatcaaggatgagatgttgtttgctggtaccggagatggtcgcatcatggcttggaaaattcctgacaagaagggtgactctggaccagtggcaatcctcagtggccatgagcgccaagtgatttcgctcggtgtctcagcaacaaggctttactctggctcacttgacaagaccatcaaagtatgggaccttaaaactctgcagtgtgtccaaacactctctgagcacaaagctgctgtaacatctgtgctttgttgggatgaaaaactattatcttgctctctggacaagactgtaaagatctgggctgcttcaaagtctggagaccttcaagtgatatatacccattctgaggagcatggagtacgcacgctctttggcatgcaccgtgttggaaagacgccagttctgttctgctccctccacaacagcaactgcatacgtctgttcgacctgccatcgttcgacgagatgggcaagcttttctccaagaaggaagtgaggaccatcgagctcgcagccggcggcctcctcttcaccggcgacggcgccggcgagctgaaggtgtggaggtgggcgcccgaggaggagcctgcaaccccggcgctcgtgaaatcatcaatgtag More
Protein seq	MRLVWLISKGLSGITLQFSLADGPYMCVDAIKMGGKIGCMITHGPWIFVGITKSVEAWNTQTGMKSSLHGPSGLVCSMTIKDEMLFAGTGDGRIMAWKIPDKKGDSGPVAILSGHERQVISLGVSATRLYSGSLDKTIKVWDLKTLQCVQTLSEHKAAVTSVLCWDEKLLSCSLDKTVKIWAASKSGDLQVIYTHSEEHGVRTLFGMHRVGKTPVLFCSLHNSNCIRLFDLPSFDEMGKLFSKKEVRTIELAAGGLLFTGDGAGELKVWRWAPEEEPATPALVKSSM More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_01g0006010	OsLima_01g0006010.02	Chr01	4547733	4552667	+	NAM
CDS seq	atgacgatctcctcgtccctcgcctcccgcctcggccccggcggccccacgaggtggagcccctacgcccgggcccccgatcccggccacggggcggggaggagctccgttcctcccggtggtggtggtaactcacgccctcccctccgcgtcgcccccgccacggcgaggctcctcggccaccccgcgcggaagggggccgcggcgccgcccggatcgaggtgccgcgcggaggcggaggcggaggccacagccgcctccgatgctgcctgccctaacccgccgcggcgtgggtgcgaagagacgaacccgaacccgaaccctaagagaaaccctaagccggcggagagaggggaggagccgcccgtccgcgccgtcggctgcggcggattcgccttcctctgcgccctcgctggccacaccgaggctatcagtgggatctctctgcctgtgggttccgacaagctttactccggcagcgctgacggctccgtccgcgtctgggactgcaactctggcaaggtagctgggctctccgctctcggcactcccttcaggctctttacgcatgattcaagttga More
Protein seq	MTISSSLASRLGPGGPTRWSPYARAPDPGHGAGRSSVPPGGGGNSRPPLRVAPATARLLGHPARKGAAAPPGSRCRAEAEAEATAASDAACPNPPRRGCEETNPNPNPKRNPKPAERGEEPPVRAVGCGGFAFLCALAGHTEAISGISLPVGSDKLYSGSADGSVRVWDCNSGKVAGLSALGTPFRLFTHDSS

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
RI	Chr01	4548566	4549336	+	OsLima_01g0006010.02	OsLima_01g0006010.01,OsLima_01g0006010.02	All
A5	Chr01	4548661	4549247	+	OsLima_01g0006010.03	OsLima_01g0006010.01,OsLima_01g0006010.03	All

Expression

	Leaf	Root	Panicle
FPKM	0.159580	0.118016	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0187500	RBH	1.593069	1.290906	2.164315
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os01g09252	RBH	1.046536	0.843435	0.544385
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0187500	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0006600	RBH	0.263695	3.695562	5.912740
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_01g0006240	RBH	0.295995	1.143075	3.619409
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0006550	RBH	0.195700	1.708816	3.103149
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0006070	RBH	0.099323	0.053953	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0006260	RBH	4.750277	6.413085	15.447327
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0079900	RBH	2.7927765	5.477164	7.9023565
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0006210	RBH	0.566588	0.104805	1.352865
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0080200	RBH	3.5346815	11.047866	11.270938
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0006220	RBH	0.121806	2.793710	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0006270	RBH	0.000000	5.819687	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0006220	RBH	0.192152	0.110933	0.213595
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0006180	RBH	0.301167	0.640094	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G006220	RBH	0.284849	0.403314	4.376122
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0006120	RBH	1.236629	7.628105	4.085769

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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