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_01g0042250		OGI:01115110 \| 16/16			PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)			Chr01:39925053-39928463		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		OsSTA40
DNA seq		ccgcggaaagcttctccatcgatcgatctctcctctctctcccgcgggggctctccggcgcacggtgccctctcgtgcctcggagaccccgatccgccgccgccgccgccgccgccgtgcctgagtagtacagtcttgttgtcgaggtgaggtgagtggtgggaggagaaatggacaccgggatgagggtggcgctgcaccggcaggtgtcgtcggggtcgctgaaggagagcggggagctccggcggcagtcgtcgctggagtctccccggacggggagggcggcgacgaggttcctgttcgggaggcagtcgtcgatggacccgaaccggcggcgcgggcggagccagagccccgtcggcctcgccgaggacctgaccgtgccggacaacctcgacgccaccatgcagctgctcttcctggcctgccacggcgacgccgccggcgtcgaggccctgctccgcggcggcgtcgacgtcaacagcatcaacctcgacggccgcaccgcgctgcacatcgcctcctgcgagggccaccccgacgtcgtccgcgtgctgctcacctggaaggccaacatcgacgcccgcgaccggtggggcagcacggtcagtgaccagtgttcgcaatttcggttctatcggaccctatacgatatagttttggccgaaatttttaatttttttcattttttcatgaatttggtaatattttattcaaatttgatcaaattttattaaaaattcgtaaaatttcggaccgaaatttcataaattttggtatttcggccatccatgatagaaatcatcaaaccgaaacattaaaccctgtcagtgactcgtccaagacaagactcgatcaacatcaagattttcgttacattttttggttcagaaattcagattctgatttgattcgtttcttcctcgaatcgcaggctgtagctgatgccaagtgttatggccacacggaggtgtacaatcttctcaaggctcgtggtgcaaagatcccggtatctttctgcatgaacaaactgaaaattttgtcatttgctctcaattcattcggttcgtcagtttcgaagaatttgaggtttatttggtggtctttgtttctttttttgttcagagaaacaggaggacaccgatgatggtgtcgaatcctggggacgtaccagagtacgaattgaaccctagtgagctccaattcaagaaaggggatgaggtggtcaaggtaaaaactctctgtcccaattgcgttccagtgaagttggttgaagaaacattatagataagcagaaaattaatgttctaatgacgtgcgtgcatcgtacagggcgtgtaccaagttgccaaatggaatggaaccaaggttcatgttaagatacttgatagagaatgctactgcgatcaggaagtcatgtaagaagcaaatcccaaaagtcagtttcaaagtgtgcagtgaactgacctgacaagaaactaacacttgttttgttacagaaactctttcaggcatgagctgaccgtattggagaaggtccggcacccgaatgttgttcagttcgtcggagccgtcactcagaacatacctatgatgattatttctgaatacctcccaaatgtaacaagatcactgtcttttacttctgaaaaaaaaagtgttattaacaaacagtctgaataaggcactgtataccttacacacagggtgatttatcaagctgtattccgaggaaaggaaagctacatggtcagaaggttctaaaatatggccttgagatcgccaggtaaatctaccttctgagatgtggaattaaacacacttgatataatctgtaatctttttgttccacaaaacaatgatgtttaatgccaaattttgcatcagtactagttagatgctgacttgaatgccttctattgagacaacaatgcttctttgaatgttcaggggcatgacttatcttcaccagtgcaagccagaccccatcatccactgcgacctaaagccaaagtaagatgaggaaatgaagcaagcactagacttgcatacttttgagtttcattcttgtgctacaaactgctagcagttggatgctctctttcaaggttgtgccgtactttactatttgaatcttggtaaggtgccagaaatatcttcctggatagtggaggccaactgaaaatcgcaggattcggtctgacgaggctgtcgaaaatctctcctggcagagtgaaactggccgatcatgagtccatggttgacagcttcagtgagtaaaattttagtacaatgaaatgagataagaaaaaagaagacatcagtaaagtttttactgacaaactgatcttgcctcttttttggtttgttttaggtcactacactgcacctgagctgtacagaaacgaaatattcgacgcaagcgtcgacgccttctcatttggtttcatcctctatgaggtcagtgacattcatactctggtttctgaacatgatacattgttctgatgagcaattgatacattgttctgatgagcaatctctgtaaggagactagtcattctaatgagaattaactctttgtggtatactcagatggttgaaggaacacacactgtacatgggaagtcatcagaggaatctggccacacaattcgatatgatgggatgcgtccatcgctgaagaacaagctcaggggatatcctccagatttcaaagcgtgagttctgaaaaaacaagagcatgagatatcttgtgcatcgttgtgcaaactagtaaataaacattcatcagcttctgttcagtaacatgttaaaaactagataatcagagtgtggaaactaaattgcaggctgatcgaagaatgctgggatactcagggtatagcaaggccaacattttcagagataatcatcaggctcgacaagatatacgcccagtgcatgaagcaagggacctggaaggactcgctaaagatttggtccgtatctcggcgatttaagaatatcagatctaagcatttcagaaccaaaaagagagtccatgtcgcaatgtgaaaacataattggagatggtatgtcatcatattgtttcatgggattaattagcgactgaaacatttcttctgcattgcatttgcacttcttttttctacaggaaatgacacgtgtgggctaagctgcatgaacgccttcttgtgtacatatcactgcgaagcaaatgcgtcactctctgtgaagaagaagcctgagctagcactcactcgtctggaggaggatgacacgacgtaccgacaaatttgtgtacgtgttgtaaaaggcccggcgaaaaaaaaagtacttgtaaaagatcaatttgagttaaattggaagtaacaaagcttaattattactacgttgtgtattgttttc More
CDS seq		atggacaccgggatgagggtggcgctgcaccggcaggtgtcgtcggggtcgctgaaggagagcggggagctccggcggcagtcgtcgctggagtctccccggacggggagggcggcgacgaggttcctgttcgggaggcagtcgtcgatggacccgaaccggcggcgcgggcggagccagagccccgtcggcctcgccgaggacctgaccgtgccggacaacctcgacgccaccatgcagctgctcttcctggcctgccacggcgacgccgccggcgtcgaggccctgctccgcggcggcgtcgacgtcaacagcatcaacctcgacggccgcaccgcgctgcacatcgcctcctgcgagggccaccccgacgtcgtccgcgctgtagctgatgccaagtgttatggccacacggaggtgtacaatcttctcaaggctcgtggtgcaaagatcccgagaaacaggaggacaccgatgatggtgtcgaatcctggggacgtaccagagtacgaattgaaccctagtgagctccaattcaagaaaggggatgaggtggtcaagggcgtgtaccaagttgccaaatggaatggaaccaaggttcatgttaagatacttgatagagaatgctactgcgatcaggaagtcataaactctttcaggcatgagctgaccgtattggagaaggtccggcacccgaatgttgttcagttcgtcggagccgtcactcagaacatacctatgatgattatttctgaatacctcccaaatggtgatttatcaagctgtattccgaggaaaggaaagctacatggtcagaaggttctaaaatatggccttgagatcgccaggggcatgacttatcttcaccagtgcaagccagaccccatcatccactgcgacctaaagccaaaaaatatcttcctggatagtggaggccaactgaaaatcgcaggattcggtctgacgaggctgtcgaaaatctctcctggcagagtgaaactggccgatcatgagtccatggttgacagcttcagtcactacactgcacctgagctgtacagaaacgaaatattcgacgcaagcgtcgacgccttctcatttggtttcatcctctatgagatggttgaaggaacacacactgtacatgggaagtcatcagaggaatctggccacacaattcgatatgatgggatgcgtccatcgctgaagaacaagctcaggggatatcctccagatttcaaagcgctgatcgaagaatgctgggatactcagggtatagcaaggccaacattttcagagataatcatcaggctcgacaagatatacgcccagtgcatgaagcaagggacctggaaggactcgctaaagatttggtccgtatctcggcgatttaagaatatcagatctaagcatttcagaaccaaaaagagagtccatgtcgcaatgtga More
Protein seq		MDTGMRVALHRQVSSGSLKESGELRRQSSLESPRTGRAATRFLFGRQSSMDPNRRRGRSQSPVGLAEDLTVPDNLDATMQLLFLACHGDAAGVEALLRGGVDVNSINLDGRTALHIASCEGHPDVVRAVADAKCYGHTEVYNLLKARGAKIPRNRRTPMMVSNPGDVPEYELNPSELQFKKGDEVVKGVYQVAKWNGTKVHVKILDRECYCDQEVINSFRHELTVLEKVRHPNVVQFVGAVTQNIPMMIISEYLPNGDLSSCIPRKGKLHGQKVLKYGLEIARGMTYLHQCKPDPIIHCDLKPKNIFLDSGGQLKIAGFGLTRLSKISPGRVKLADHESMVDSFSHYTAPELYRNEIFDASVDAFSFGFILYEMVEGTHTVHGKSSEESGHTIRYDGMRPSLKNKLRGYPPDFKALIEECWDTQGIARPTFSEIIIRLDKIYAQCMKQGTWKDSLKIWSVSRRFKNIRSKHFRTKKRVHVAM
Function		Integrin-linked protein kinase 1 [UniProtKB/Swiss-Prot:F4IS56]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_01g0042250	OsPr106_01g0042250.02	Chr01	39925223	39928448	+	NAM
CDS seq	atggacaccgggatgagggtggcgctgcaccggcaggtgtcgtcggggtcgctgaaggagagcggggagctccggcggcagtcgtcgctggagtctccccggacggggagggcggcgacgaggttcctgttcgggaggcagtcgtcgatggacccgaaccggcggcgcgggcggagccagagccccgtcggcctcgccgaggacctgaccgtgccggacaacctcgacgccaccatgcagctgctcttcctggcctgccacggcgacgccgccggcgtcgaggccctgctccgcggcggcgtcgacgtcaacagcatcaacctcgacggccgcaccgcgctgcacatcgcctcctgcgagggccaccccgacgtcgtccgcgctgtagctgatgccaagtgttatggccacacggaggtgtacaatcttctcaaggctcgtggtgcaaagatcccgagaaacaggaggacaccgatgatggtgtcgaatcctggggacgtaccagagtacgaattgaaccctagtgagctccaattcaagaaaggggatgaggtggtcaagggcgtgtaccaagttgccaaatggaatggaaccaaggttcatgttaagatacttgatagagaatgctactgcgatcaggaagtcataaactctttcaggcatgagctgaccgtattggagaaggtccggcacccgaatgttgttcagttcgtcggagccgtcactcagaacatacctatgatgattatttctgaatacctcccaaatggtgatttatcaagctgtattccgaggaaaggaaagctacatggtcagaaggttctaaaatatggccttgagatcgccaggggcatgacttatcttcaccagtgcaagccagaccccatcatccactgcgacctaaagccaaaaaatatcttcctggatagtggaggccaactgaaaatcgcaggattcggtctgacgaggctgtcgaaaatctctcctggcagagtgaaactggccgatcatgagtccatggttgacagcttcagtcactacactgcacctgagctgtacagaaacgaaatattcgacgcaagcgtcgacgccttctcatttggtttcatcctctatgagatggttgaaggaacacacactgtacatgggaagtcatcagaggaatctggccacacaattcgatatgatgggatgcgtccatcgctgaagaacaagctcaggggatatcctccagatttcaaagcgctgatcgaagaatgctgggatactcagggtatagcaaggccaacattttcagagataatcatcaggctcgacaagatatacgcccagtgcatgaagcaagggacctggaaggactcgctaaagatttggaaatga More
Protein seq	MDTGMRVALHRQVSSGSLKESGELRRQSSLESPRTGRAATRFLFGRQSSMDPNRRRGRSQSPVGLAEDLTVPDNLDATMQLLFLACHGDAAGVEALLRGGVDVNSINLDGRTALHIASCEGHPDVVRAVADAKCYGHTEVYNLLKARGAKIPRNRRTPMMVSNPGDVPEYELNPSELQFKKGDEVVKGVYQVAKWNGTKVHVKILDRECYCDQEVINSFRHELTVLEKVRHPNVVQFVGAVTQNIPMMIISEYLPNGDLSSCIPRKGKLHGQKVLKYGLEIARGMTYLHQCKPDPIIHCDLKPKNIFLDSGGQLKIAGFGLTRLSKISPGRVKLADHESMVDSFSHYTAPELYRNEIFDASVDAFSFGFILYEMVEGTHTVHGKSSEESGHTIRYDGMRPSLKNKLRGYPPDFKALIEECWDTQGIARPTFSEIIIRLDKIYAQCMKQGTWKDSLKIWK More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_01g0042250	OsPr106_01g0042250.03	Chr01	39925223	39928448	+	NAM
CDS seq	atggacaccgggatgagggtggcgctgcaccggcaggtgtcgtcggggtcgctgaaggagagcggggagctccggcggcagtcgtcgctggagtctccccggacggggagggcggcgacgaggttcctgttcgggaggcagtcgtcgatggacccgaaccggcggcgcgggcggagccagagccccgtcggcctcgccgaggacctgaccgtgccggacaacctcgacgccaccatgcagctgctcttcctggcctgccacggcgacgccgccggcgtcgaggccctgctccgcggcggcgtcgacgtcaacagcatcaacctcgacggccgcaccgcgctgcacatcgcctcctgcgagggccaccccgacgtcgtccgcgctgtagctgatgccaagtgttatggccacacggaggtgtacaatcttctcaaggctcgtggtgcaaagatcccgagaaacaggaggacaccgatgatggtgtcgaatcctggggacgtaccagagtacgaattgaaccctagtgagctccaattcaagaaaggggatgaggtggtcaagggcgtgtaccaagttgccaaatggaatggaaccaaggttcatgttaagatacttgatagagaatgctactgcgatcaggaagtcataaactctttcaggcatgagctgaccgtattggagaaggtccggcacccgaatgttgttcagttcgtcggagccgtcactcagaacatacctatgatgattatttctgaatacctcccaaatggtgatttatcaagctgtattccgaggaaaggaaagctacatggtcagaaggttctaaaatatggccttgagatcgccaggggcatgacttatcttcaccagtgcaagccagaccccatcatccactgcgacctaaagccaaaaaatatcttcctggatagtggaggccaactgaaaatcgcaggattcggtctgacgaggctgtcgaaaatctctcctggcagagtgaaactggccgatcatgagtccatggttgacagcttcagtgagtaa More
Protein seq	MDTGMRVALHRQVSSGSLKESGELRRQSSLESPRTGRAATRFLFGRQSSMDPNRRRGRSQSPVGLAEDLTVPDNLDATMQLLFLACHGDAAGVEALLRGGVDVNSINLDGRTALHIASCEGHPDVVRAVADAKCYGHTEVYNLLKARGAKIPRNRRTPMMVSNPGDVPEYELNPSELQFKKGDEVVKGVYQVAKWNGTKVHVKILDRECYCDQEVINSFRHELTVLEKVRHPNVVQFVGAVTQNIPMMIISEYLPNGDLSSCIPRKGKLHGQKVLKYGLEIARGMTYLHQCKPDPIIHCDLKPKNIFLDSGGQLKIAGFGLTRLSKISPGRVKLADHESMVDSFSE More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_01g0042250	OsPr106_01g0042250.01	Chr01	39925223	39928463	+	NAM
CDS seq	atggacaccgggatgagggtggcgctgcaccggcaggtgtcgtcggggtcgctgaaggagagcggggagctccggcggcagtcgtcgctggagtctccccggacggggagggcggcgacgaggttcctgttcgggaggcagtcgtcgatggacccgaaccggcggcgcgggcggagccagagccccgtcggcctcgccgaggacctgaccgtgccggacaacctcgacgccaccatgcagctgctcttcctggcctgccacggcgacgccgccggcgtcgaggccctgctccgcggcggcgtcgacgtcaacagcatcaacctcgacggccgcaccgcgctgcacatcgcctcctgcgagggccaccccgacgtcgtccgcgctgtagctgatgccaagtgttatggccacacggaggtgtacaatcttctcaaggctcgtggtgcaaagatcccgagaaacaggaggacaccgatgatggtgtcgaatcctggggacgtaccagagtacgaattgaaccctagtgagctccaattcaagaaaggggatgaggtggtcaagggcgtgtaccaagttgccaaatggaatggaaccaaggttcatgttaagatacttgatagagaatgctactgcgatcaggaagtcataaactctttcaggcatgagctgaccgtattggagaaggtccggcacccgaatgttgttcagttcgtcggagccgtcactcagaacatacctatgatgattatttctgaatacctcccaaatggtgatttatcaagctgtattccgaggaaaggaaagctacatggtcagaaggttctaaaatatggccttgagatcgccaggggcatgacttatcttcaccagtgcaagccagaccccatcatccactgcgacctaaagccaaaaaatatcttcctggatagtggaggccaactgaaaatcgcaggattcggtctgacgaggctgtcgaaaatctctcctggcagagtgaaactggccgatcatgagtccatggttgacagcttcagtcactacactgcacctgagctgtacagaaacgaaatattcgacgcaagcgtcgacgccttctcatttggtttcatcctctatgagatggttgaaggaacacacactgtacatgggaagtcatcagaggaatctggccacacaattcgatatgatgggatgcgtccatcgctgaagaacaagctcaggggatatcctccagatttcaaagcgctgatcgaagaatgctgggatactcagggtatagcaaggccaacattttcagagataatcatcaggctcgacaagatatacgcccagtgcatgaagcaagggacctggaaggactcgctaaagatttggtccgtatctcggcgatttaagaatatcagatctaagcatttcagaaccaaaaagagagtccatgtcgcaatgtga More
Protein seq	MDTGMRVALHRQVSSGSLKESGELRRQSSLESPRTGRAATRFLFGRQSSMDPNRRRGRSQSPVGLAEDLTVPDNLDATMQLLFLACHGDAAGVEALLRGGVDVNSINLDGRTALHIASCEGHPDVVRAVADAKCYGHTEVYNLLKARGAKIPRNRRTPMMVSNPGDVPEYELNPSELQFKKGDEVVKGVYQVAKWNGTKVHVKILDRECYCDQEVINSFRHELTVLEKVRHPNVVQFVGAVTQNIPMMIISEYLPNGDLSSCIPRKGKLHGQKVLKYGLEIARGMTYLHQCKPDPIIHCDLKPKNIFLDSGGQLKIAGFGLTRLSKISPGRVKLADHESMVDSFSHYTAPELYRNEIFDASVDAFSFGFILYEMVEGTHTVHGKSSEESGHTIRYDGMRPSLKNKLRGYPPDFKALIEECWDTQGIARPTFSEIIIRLDKIYAQCMKQGTWKDSLKIWSVSRRFKNIRSKHFRTKKRVHVAM More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_01g0042250	OsPr106_01g0042250.04	Chr01	39925053	39928442	+	IsoSeq
CDS seq	atgagtccatggttgacagcttcagtcactacactgcacctgagctgtacagaaacgaaatattcgacgcaagcgtcgacgccttctcatttggtttcatcctctatgagatggttgaaggaacacacactgtacatgggaagtcatcagaggaatctggccacacaattcgatatgatgggatgcgtccat
Protein seq	MSPWLTASVTTLHLSCTETKYSTQASTPSHLVSSSMRWLKEHTLYMGSHQRNLATQFDMMGCVH

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
RI	Chr01	39927203	39927512	+	OsPr106_01g0042250.03	OsPr106_01g0042250.03,OsPr106_01g0042250.01,OsPr106_01g0042250.04,OsPr106_01g0042250.02	All
RI	Chr01	39927648	39928033	+	OsPr106_01g0042250.03	OsPr106_01g0042250.03,OsPr106_01g0042250.02	All
A5	Chr01	39925603	39925987	+	OsPr106_01g0042250.04	OsPr106_01g0042250.04,OsPr106_01g0042250.03,OsPr106_01g0042250.02,OsPr106_01g0042250.01	All
A5	Chr01	39928033	39928210	+	OsPr106_01g0042250.04	OsPr106_01g0042250.04,OsPr106_01g0042250.03,OsPr106_01g0042250.02	All

Expression

	Leaf	Root	Panicle
FPKM	0.0	0.0	12.097238

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0892800	RBH	0.070043	0.273335	5.473732
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os01g66860	RBH	0.082925	0.173160	1.147719
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0892800	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0043260	RBH	0.0	1.414408	3.463333
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_01g0042860	RBH	0.0	0.000000	4.931595
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0043200	RBH	0.0	0.0	9.873382
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0042660	RBH	0.0	0.096522	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0042160	SBH	0.800334	0.0	1.293878
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0639400	RBH	1.6997265	8.962563	0
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0041880	RBH	0.0	0.0	8.153606
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0640200	RBH	0.8966315	1.423505	0.014337
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_01g0042220	RBH	0.0	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0042170	RBH	0.0	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0042440	RBH	0.0	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0042380	RBH	0.0	0.000000	0.949311
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0042230	RBH	0.0	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G042650	RBH	0.0	0.0	2.322269
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0042350	RBH	0.0	1.917060	15.689843

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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