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
LOC_Os01g23370		OGI:01038920 \| 14/16			Nipponbare \| IRGSP 1.0 \| MSU			Chr01:13137848-13141064		Homologues MicroCollinearity RGI-JBrowse RGAP Ricevarmap2
Gene Symbol		OsSTA13
DNA seq		ATGGCGTCCACTGAAACTATCAAAGAATTCTTCAACGTCAATGGCCAGATAATCGGCGCCGCCGTGCTTGCCGTGCTCGCTATGGTAGTGGTGGCGCTCGGCACGTACGGCCGTCATTGCAGCCACCCGGCGCTCCGCCTCTTCGTGTGGGGCGCCTCCACCGTCTTCCTCCTGCTCTCCACCTCCATCATCTCCAATTTGCTCAAGGGGGTCCAGGTGGACAAGTGCAGCAATGCCTCTCCCCAAGCTTCCGGTGGCGTCCAGCAGAAGGACAAGCCGGATATTAGGAAGATGTGGATAATCCTCCTGTGGTCGGCACTCATCCTCATCATCAAGGGCAAGTCCGACACGTCGGCGACCGCCCGTTAACATGGCCTCGTCGTCGCCGTCGTCCGGCGACGTTAGCGTCGACGGGCAGAAGGTCCGGCCACCGCTGGAGTATCTGCTGAAGTACATATGGCTGATCTATCTGATTGTGGTGTGCTATCCACTGGAGGACTGGGTGGGCACTACCAGGAGGAACATCTTCGTCGCGTTCTGCATGCTCGGCCTCGCCAAGTTGCTGCTCAACCTGTTCGCGTCATGGCGGGCGAGCAGCTCGTTCGCCGTTGGCAAGAACGCCCGGCTTGTCTCCGGCTACATGGAGCAGCTCGAGGAAGAGGGCGACGAGGTCGGCGGCCATGACCAGGTGCCCCGTTACATAGTGACGGGGGGGAAGGAGGAGCACGTCGCCACGGGCGCCCGCGGATACCGCATCAGGCGGGACGCCCTGGACGATGAGTCCAGCAGCCTCGTGACGCTGGACCGCGTGTGGCGGATGGCGGAGCACGGCGATGTCAACGGCCTCCTCGCCAAGCGGCCCGAGCTCAGGGACCTCTGCCTCTCCTTCTCCCTGTTCAAGAGCCTTCGCCGGCAGCTGTCAGGCTATCCCCTGGACGACGCGGGCTCTACCAAGGCCCTTGAGTTCGTGCTGCGAGGCATGAACGCCGCCGGCTCTGCCTGTGCCGTCAACGCCGACCGAGTGTTCCATGTTCTCGTCGACGAGCTCTCGTTTGCCAGCGACTTCTACTTCGCTGGGCTTCCGCTGTGCACTTACAGCGGGTGGTGCGCCGCCCTGAACTACATCTTCTCCGTCCTAATCGTTGTCGGAGCCACCGCCGTGGGAACAATATATAAAGTGGAAAAGGTGATCATATTCTAACAAGTGCTAAAGAGAGACACCTTTCTTTCCAAAAAAAAAAAGCTACCAGTACACTCAATATCTATATATTTTTTTTCTTCTTAGAGAAGTTTCTCTTAAATTATTCATCCGATTACACCGTTGTGTTCGTAACAATTAAATCTTTACAATAAGATCTCACATGATTATATTTTGATGAAAAATCACAAATTACTTTTATGATATGTCTAAATTACTTCTAGATTTCACTAAGTTACTTCTTACACATATAAAAGTAAATTCAGTAAACCTTAAAAGTAATTTACATATATTATAGAAGTAACTTATAACAAAAAGAAAGTAACTTTAATTTAGAACTATATCTAGATTCATTTACATCTATATAAATAAGGGCAATGCTAAAGTGACTTATATTATGAAACGGGGGGAGTAACTATCTGTAGTAGAAATAATTATATTGTGAGTAAGCTGAAATAAGAAACTACGTAGAGTACAATTTGCAAGTAAAGTGTAGAGAAGATTTATAAAGTCCACAAAATATAGAATTAACTAAAAATAATCAACTTAGAGCATTATGAATGTATAAAAGTAATTTAGTCAAATCTAAAAGTAACATATATATATATATATATATATATATATATATATATATATATATATATATATATAGTAAAAGTAACTTACGTATATAATTAAAGTAATTTATAAATATAAATATTTTTTCATCGTAATATAATTATGTAAGATCTTGTTGTAAATATTTAATTGCAACGAATGTAATGGTGTAATCAGATTGTAGATTGGATAAGTAATTTGAGAGAAAACTTTATAAAAAAGAAAAGGACATGCATATCTAAGAGGGAAAAAAGCATGCACGTGTAGTAGTACTTCTTCTCATAATTGGTTGGTCGCTAGTTAACACTAAATCAAGAGGCTTCTCGGTTTAGATTTTGCCATTCAAAGAAGGGAAGCCTAACTTTGTCGTCACGTTCGCCCTCCTGGTGGCGGTGGCGCTCGTCGAGGTATGGGACATCGTCGCCGGCGTGTGCTCCAATTGGAGTAAGATGGCCATGCTCGGCCACTACATCAGGCACGAGCCACAGTGGCGTCGGTGTCGCCGCGCCCACGCGGCGCTCGACGCCGTGCTGCGGTTCAGGCCCGCGAGGCGGTGGCGCAACAAGATCGGGCAGAACTCGGTGCTGGAGCCCCGCCGCTTCTGCCGGCGGTCCGGCCTCCTCTCCGAGAAGCTCTACGGCCGCGCCGGGCTCATGAGGTCGGTGGAAGTCTCGCCGGCGGTGAAGGACGCGGTTCTCAGGTCCTTGATGAGCAGCTACGGCAGGTCGAGCAGAGGACGCGCGGCGGAGCGGCGAGTCGGCAGCAAGGTCGACTGGCTGTGGTACGGCTCCCGAAAGAGCTGGGCGTCCGACGACGGCGACGGCTGCGTCAGCACCACCGACATCATCCTCGCGTGGCACGTCGCCACGAGGCTCTACGAGATGAGATGCTCGCTGCACGCTTCGTCTCCGACGCCGTCGGCATCATCGTCGGACATGGCCGCCGCGTGCCACCTCTCCAACTACTGCGCGTACCTGGCGTCGGCCGCGCCGGAGCTGCTGCCGGACATCGCCACGTGGACCGAGAAACGGTACAGGGAGGTGACGGCCGACGTCACCGCGGGCGCTGGGCAAGGACAGCGCCGCCGGTGAGACGACGACGGCGCAGCAGAGGTACGAGCGGCTCGTGGCGACGCTGAGCGCCGGCGCGCGCGACAAGGCGCTGCGTCGCGGCGCGGAGATCGCGCGCCGCCTTGCGGAGGAGTACACGACCGCCGCCGAGGACGACGACGAGGCGTCGGCGTGGCTGTTCCTGGCGGATTTCTGGTCGGAGATGATGCTCTACGTGGCGCCGTCGGAGAACGTCAAGGGGCACGTGGAGGCCATGGCGCGCGGCGGCGAGTTCGTCACGCTGCTCTGGGCGCTGCTCCTGCACGCCGGCATCACCGCTAGGCCTGAGGCGCCAAGCCGTATTATCCCGTAG More
CDS seq		ATGGCGTCCACTGAAACTATCAAAGAATTCTTCAACGTCAATGGCCAGATAATCGGCGCCGCCGTGCTTGCCGTGCTCGCTATGGTAGTGGTGGCGCTCGGCACGTACGGCCGTCATTGCAGCCACCCGGCGCTCCGCCTCTTCGTGTGGGGCGCCTCCACCGTCTTCCTCCTGCTCTCCACCTCCATCATCTCCAATTTGCTCAAGGGGGTCCAGGTGGACAAGTGCAGCAATGCCTCTCCCCAAGCTTCCGGTGGCGTCCAGCAGAAGGACAAGCCGGATATTAGGAAGATGGCAAGTCCGACACGTCGGCGACCGCCCGTTAACATGGCCTCGTCGTCGCCGTCGTCCGGCGACGTTAGCGTCGACGGGCAGAAGGTCCGGCCACCGCTGGAGTATCTGCTGAAGTACATATGGCTGATCTATCTGATTGTGGTGTGCTATCCACTGGAGGACTGGGTGGGCACTACCAGGAGGAACATCTTCGTCGCGTTCTGCATGCTCGGCCTCGCCAAGTTGCTGCTCAACCTGTTCGCGTCATGGCGGGCGAGCAGCTCGTTCGCCGTTGGCAAGAACGCCCGGCTTGTCTCCGGCTACATGGAGCAGCTCGAGGAAGAGGGCGACGAGGTCGGCGGCCATGACCAGGTGCCCCGTTACATAGTGACGGGGGGGAAGGAGGAGCACGTCGCCACGGGCGCCCGCGGATACCGCATCAGGCGGGACGCCCTGGACGATGAGTCCAGCAGCCTCGTGACGCTGGACCGCGTGTGGCGGATGGCGGAGCACGGCGATGTCAACGGCCTCCTCGCCAAGCGGCCCGAGCTCAGGGACCTCTGCCTCTCCTTCTCCCTGTTCAAGAGCCTTCGCCGGCAGCTGTCAGGCTATCCCCTGGACGACGCGGGCTCTACCAAGGCCCTTGAGTTCGTGCTGCGAGGCATGAACGCCGCCGGCTCTGCCTGTGCCGTCAACGCCGACCGAGTGTTCCATGTTCTCGTCGACGAGCTCTCGTTTGCCAGCGACTTCTACTTCGCTGGGCTTCCGCTGTGCACTTACAGCGGGTGGTGCGCCGCCCTGAACTACATCTTCTCCGTCCTAATCGTTGTCGGAGCCACCGCCGTGGGAACAATATATAAAGTGGAAAAGATTTTGCCATTCAAAGAAGGGAAGCCTAACTTTGTCGTCACGTTCGCCCTCCTGGTGGCGGTGGCGCTCGTCGAGGTATGGGACATCGTCGCCGGCGTGTGCTCCAATTGGAGTAAGATGGCCATGCTCGGCCACTACATCAGGCACGAGCCACAGTGGCGTCGGTGTCGCCGCGCCCACGCGGCGCTCGACGCCGTGCTGCGGTTCAGGCCCGCGAGGCGGTGGCGCAACAAGATCGGGCAGAACTCGGTGCTGGAGCCCCGCCGCTTCTGCCGGCGGTCCGGCCTCCTCTCCGAGAAGCTCTACGGCCGCGCCGGGCTCATGAGGTCGGTGGAAGTCTCGCCGGCGGTGAAGGACGCGGTTCTCAGGTCCTTGATGAGCAGCTACGGCAGGTCGAGCAGAGGACGCGCGGCGGAGCGGCGAGTCGGCAGCAAGGTCGACTGGCTGTGGTACGGCTCCCGAAAGAGCTGGGCGTCCGACGACGGCGACGGCTGCGTCAGCACCACCGACATCATCCTCGCGTGGCACGTCGCCACGAGGCTCTACGAGATGAGATGCTCGCTGCACGCTTCGTCTCCGACGCCGTCGGCATCATCGTCGGACATGGCCGCCGCGTGCCACCTCTCCAACTACTGCGCGTACCTGGCGTCGGCCGCGCCGGAGCTGCTGCCGGACATCGCCACGTGGACCGAGAAACGGTACAGGGAGGACAGCGCCGCCGGTGAGACGACGACGGCGCAGCAGAGGTACGAGCGGCTCGTGGCGACGCTGAGCGCCGGCGCGCGCGACAAGGCGCTGCGTCGCGGCGCGGAGATCGCGCGCCGCCTTGCGGAGGAGTACACGACCGCCGCCGAGGACGACGACGAGGCGTCGGCGTGGCTGTTCCTGGCGGATTTCTGGTCGGAGATGATGCTCTACGTGGCGCCGTCGGAGAACGTCAAGGGGCACGTGGAGGCCATGGCGCGCGGCGGCGAGTTCGTCACGCTGCTCTGGGCGCTGCTCCTGCACGCCGGCATCACCGCTAGGCCTGAGGCGCCAAGCCGTATTATCCCGTAG More
Protein seq		MASTETIKEFFNVNGQIIGAAVLAVLAMVVVALGTYGRHCSHPALRLFVWGASTVFLLLSTSIISNLLKGVQVDKCSNASPQASGGVQQKDKPDIRKMASPTRRRPPVNMASSSPSSGDVSVDGQKVRPPLEYLLKYIWLIYLIVVCYPLEDWVGTTRRNIFVAFCMLGLAKLLLNLFASWRASSSFAVGKNARLVSGYMEQLEEEGDEVGGHDQVPRYIVTGGKEEHVATGARGYRIRRDALDDESSSLVTLDRVWRMAEHGDVNGLLAKRPELRDLCLSFSLFKSLRRQLSGYPLDDAGSTKALEFVLRGMNAAGSACAVNADRVFHVLVDELSFASDFYFAGLPLCTYSGWCAALNYIFSVLIVVGATAVGTIYKVEKILPFKEGKPNFVVTFALLVAVALVEVWDIVAGVCSNWSKMAMLGHYIRHEPQWRRCRRAHAALDAVLRFRPARRWRNKIGQNSVLEPRRFCRRSGLLSEKLYGRAGLMRSVEVSPAVKDAVLRSLMSSYGRSSRGRAAERRVGSKVDWLWYGSRKSWASDDGDGCVSTTDIILAWHVATRLYEMRCSLHASSPTPSASSSDMAAACHLSNYCAYLASAAPELLPDIATWTEKRYREDSAAGETTTAQQRYERLVATLSAGARDKALRRGAEIARRLAEEYTTAAEDDDEASAWLFLADFWSEMMLYVAPSENVKGHVEAMARGGEFVTLLWALLLHAGITARPEAPSRIIP
Function		-

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
LOC_Os01g23370	LOC_Os01g23370.1	Chr01	13137848	13141064	+	MSU_osa1r7
CDS seq	ATGGCGTCCACTGAAACTATCAAAGAATTCTTCAACGTCAATGGCCAGATAATCGGCGCCGCCGTGCTTGCCGTGCTCGCTATGGTAGTGGTGGCGCTCGGCACGTACGGCCGTCATTGCAGCCACCCGGCGCTCCGCCTCTTCGTGTGGGGCGCCTCCACCGTCTTCCTCCTGCTCTCCACCTCCATCATCTCCAATTTGCTCAAGGGGGTCCAGGTGGACAAGTGCAGCAATGCCTCTCCCCAAGCTTCCGGTGGCGTCCAGCAGAAGGACAAGCCGGATATTAGGAAGATGGCAAGTCCGACACGTCGGCGACCGCCCGTTAACATGGCCTCGTCGTCGCCGTCGTCCGGCGACGTTAGCGTCGACGGGCAGAAGGTCCGGCCACCGCTGGAGTATCTGCTGAAGTACATATGGCTGATCTATCTGATTGTGGTGTGCTATCCACTGGAGGACTGGGTGGGCACTACCAGGAGGAACATCTTCGTCGCGTTCTGCATGCTCGGCCTCGCCAAGTTGCTGCTCAACCTGTTCGCGTCATGGCGGGCGAGCAGCTCGTTCGCCGTTGGCAAGAACGCCCGGCTTGTCTCCGGCTACATGGAGCAGCTCGAGGAAGAGGGCGACGAGGTCGGCGGCCATGACCAGGTGCCCCGTTACATAGTGACGGGGGGGAAGGAGGAGCACGTCGCCACGGGCGCCCGCGGATACCGCATCAGGCGGGACGCCCTGGACGATGAGTCCAGCAGCCTCGTGACGCTGGACCGCGTGTGGCGGATGGCGGAGCACGGCGATGTCAACGGCCTCCTCGCCAAGCGGCCCGAGCTCAGGGACCTCTGCCTCTCCTTCTCCCTGTTCAAGAGCCTTCGCCGGCAGCTGTCAGGCTATCCCCTGGACGACGCGGGCTCTACCAAGGCCCTTGAGTTCGTGCTGCGAGGCATGAACGCCGCCGGCTCTGCCTGTGCCGTCAACGCCGACCGAGTGTTCCATGTTCTCGTCGACGAGCTCTCGTTTGCCAGCGACTTCTACTTCGCTGGGCTTCCGCTGTGCACTTACAGCGGGTGGTGCGCCGCCCTGAACTACATCTTCTCCGTCCTAATCGTTGTCGGAGCCACCGCCGTGGGAACAATATATAAAGTGGAAAAGATTTTGCCATTCAAAGAAGGGAAGCCTAACTTTGTCGTCACGTTCGCCCTCCTGGTGGCGGTGGCGCTCGTCGAGGTATGGGACATCGTCGCCGGCGTGTGCTCCAATTGGAGTAAGATGGCCATGCTCGGCCACTACATCAGGCACGAGCCACAGTGGCGTCGGTGTCGCCGCGCCCACGCGGCGCTCGACGCCGTGCTGCGGTTCAGGCCCGCGAGGCGGTGGCGCAACAAGATCGGGCAGAACTCGGTGCTGGAGCCCCGCCGCTTCTGCCGGCGGTCCGGCCTCCTCTCCGAGAAGCTCTACGGCCGCGCCGGGCTCATGAGGTCGGTGGAAGTCTCGCCGGCGGTGAAGGACGCGGTTCTCAGGTCCTTGATGAGCAGCTACGGCAGGTCGAGCAGAGGACGCGCGGCGGAGCGGCGAGTCGGCAGCAAGGTCGACTGGCTGTGGTACGGCTCCCGAAAGAGCTGGGCGTCCGACGACGGCGACGGCTGCGTCAGCACCACCGACATCATCCTCGCGTGGCACGTCGCCACGAGGCTCTACGAGATGAGATGCTCGCTGCACGCTTCGTCTCCGACGCCGTCGGCATCATCGTCGGACATGGCCGCCGCGTGCCACCTCTCCAACTACTGCGCGTACCTGGCGTCGGCCGCGCCGGAGCTGCTGCCGGACATCGCCACGTGGACCGAGAAACGGTACAGGGAGGACAGCGCCGCCGGTGAGACGACGACGGCGCAGCAGAGGTACGAGCGGCTCGTGGCGACGCTGAGCGCCGGCGCGCGCGACAAGGCGCTGCGTCGCGGCGCGGAGATCGCGCGCCGCCTTGCGGAGGAGTACACGACCGCCGCCGAGGACGACGACGAGGCGTCGGCGTGGCTGTTCCTGGCGGATTTCTGGTCGGAGATGATGCTCTACGTGGCGCCGTCGGAGAACGTCAAGGGGCACGTGGAGGCCATGGCGCGCGGCGGCGAGTTCGTCACGCTGCTCTGGGCGCTGCTCCTGCACGCCGGCATCACCGCTAGGCCTGAGGCGCCAAGCCGTATTATCCCGTAG More
Protein seq	MASTETIKEFFNVNGQIIGAAVLAVLAMVVVALGTYGRHCSHPALRLFVWGASTVFLLLSTSIISNLLKGVQVDKCSNASPQASGGVQQKDKPDIRKMASPTRRRPPVNMASSSPSSGDVSVDGQKVRPPLEYLLKYIWLIYLIVVCYPLEDWVGTTRRNIFVAFCMLGLAKLLLNLFASWRASSSFAVGKNARLVSGYMEQLEEEGDEVGGHDQVPRYIVTGGKEEHVATGARGYRIRRDALDDESSSLVTLDRVWRMAEHGDVNGLLAKRPELRDLCLSFSLFKSLRRQLSGYPLDDAGSTKALEFVLRGMNAAGSACAVNADRVFHVLVDELSFASDFYFAGLPLCTYSGWCAALNYIFSVLIVVGATAVGTIYKVEKILPFKEGKPNFVVTFALLVAVALVEVWDIVAGVCSNWSKMAMLGHYIRHEPQWRRCRRAHAALDAVLRFRPARRWRNKIGQNSVLEPRRFCRRSGLLSEKLYGRAGLMRSVEVSPAVKDAVLRSLMSSYGRSSRGRAAERRVGSKVDWLWYGSRKSWASDDGDGCVSTTDIILAWHVATRLYEMRCSLHASSPTPSASSSDMAAACHLSNYCAYLASAAPELLPDIATWTEKRYREDSAAGETTTAQQRYERLVATLSAGARDKALRRGAEIARRLAEEYTTAAEDDDEASAWLFLADFWSEMMLYVAPSENVKGHVEAMARGGEFVTLLWALLLHAGITARPEAPSRIIP More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.0	0.0	0.000000

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0335600	SBH	0.0	0.0	0.478521
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os01g23440	RBH	0.0	0.0	0.251920
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0335600	SBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0015420	RBH	0.0	0.0	0.0
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_01g0015190	RBH	0.0	0.0	0.476381
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0015440	RBH	0.0	0.0	0.000000
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0014930	RBH	0.0	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0014980	RBH	0.0	0.0	0.0
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0215700	RBH	0.012476	0.075286	0.0220775
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0014880	RBH	0.0	0.0	0.311324
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0212000	RBH	0.0155685	0.0382135	0.0387935
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_01g0014880	RBH	0.0	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0015140	SBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0014880	RBH	0.0	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0014990	RBH	0.0	0.0	0.000000
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0014690	SBH	0.0	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G015080	RBH	0.0	0.0	0.450563
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0014900	RBH	0.0	0.0	0.335720

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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