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
OsLiXu_01g0031310		OGI:01091020 \| 15/16			LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)			Chr01:31830224-31835581		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		atggaggaggtgaggaggcatcatcacttcatcaaggtcatggtcggcgagttcgcccgccgcctcgtgagtgctctctctccctctctccctctctcctgcctacccgtaggggccccccaaacattgacatatggagtactagtatggttgcaaaaattgtggcatcttatctggcggagattgataatggatgatgcattaattaacatatacatgcatctaTttttagccaaccatatgctatgctcattgataatggatgatgcatttggtgtcatatatttgtggtctttgttctaatagacgagatggatattggtaaatatataaagggggaaatagttttgtagtgtctgataacatgattatatttgtatactaactgttgtactccctccgttccgtttcaggttataagacgttttgattttgatcaaagtcaaactactataagtttgactaactctgtagAaaaaaatagtaatatttataacaccaacatagtttcattaaatttataattgaataaattttcataatatatttgtcttgggttaaaaaaattacaacttttttctaccAaattagtcaaacttaagtagtttgactttgactaaagtcaaaacatcttataccttgaaacggatgagtattaggcaaGaaaaataaattgttggtggcatactaacattcatttccttgtgcatgcatgatgcatgtggtcagataatgcaattcgagcttcagattacgagcattgatattatgcttgtgcgactgtgcgtattatacaagtacccctactatatgtgaacaatttactgaaagcacacagagttgcatcttgcatttgcatttcatctcctctcagcaatggctttgacggccaaggtgctatctcgaatcatgcagaaacggctcaaaatatgccctaactcctaaagcctctatatgtaggagatacctcaaggcttccttattcacattccagaggtggaccacagtacttttgatgcttcattaccatcatctgccaaaggcacgcttcagaattcagaagggaagacttggcctgttgagctagagaaacttgatggccatgtatttctgaccactggatgggcgaagtttgtggaggacaattctttgagggaatatgagttccttctcttcagatatgatgataacatgcatttcatggttttgccatttggtctgaatgcttgtgagaaagtaattcggtcttcaggaagtccacaaggaaaacttccatgtgatatattctgctgtactaagaggggtcgggatggtgatagactaacagaggcagccaacagtctcacgcctagtcattcacaggtaggttgagataacaaatggatccgttatgaggtaatattatagtgtaatctcaaataattaaatcagtttcatacaggtcgttttttttgcctgtattttttttaaactattttttttgcctatacacagttcatatggaatcactttgtttgaaaatagctttacatttgatttttcaagtctgttagaatcaatatggaataccagaatacctgactatctctaaaaacacaataaaactactgttcacttgggaatcttaaggtgcagaacaattatttcaagtaactttaggaggtttgacgttttgaaataactattcctaacttgattttttccgtttaataagttccaccttgggaacaggcaggatatgaattataaaattgttggtttgtaccttagtagtgatgttgtctccttgaactgaaaattttatacaacttttaggtattgcaaaggacaactcaaggccatgagcttatttcaccacaaagtttccctgatcaacatgaagtatgcggctcgaaagatgggttagatgaacacttatcactgaacgggccaatggaggatgataaagctaatgcgatagctgaagtaatgagcatattggatgttgacaaagtgacagttgaattattctgtgcaatgcttgttttctataaatggaatgtggatgcggtggcagaagactttgacatatgtaggggcaaaccgcaaattcagaacctgtttctgaagcacaaacttcattttcaatgtaagtttttatcgcctcgtcttctgtcattcttgcactgctagcattgacaacacatccttctgtatttcagttgatattgtaaagaggaaactacgaaagttcttccctccagatgattattattcttctccaatacttgggagtaggaagtgcagccttgaggaacctaagttgtctaaccaaccactgcaatgtgacttgacaacagagaagtgtaggctagttgatgagcatgatttatgtaatttttctcagaaaaagagaaggaagcgaggttcattttgtagtcctgaaactccacgaagatcaccaagactggcacgccagaataattctcatgacagtgcagagaatacattgaaagaaagatccgaagagcgacaaccatcaccagacagcatgatagatcaggcagagagcagatcagagcaagcatgtttatgccacgataaaacagacagtggtattcttaggctcctcttgttagaagtattgtgtaatgattgatattgtagtttgtagttaaatctgtttgtttcatttcaggttcattatttcaagactctaagaaagttaaaccagcacatggtgaggtggatttatgtgaagagcctcaacataatcaaggagaaaatgaagggaatttagatcaagtcaataataaagaaactgatgaagagcaaatagaaagaaatgcggtggagacctctgagtcattcacaaggagaggttgcatcaagtcatcgccagccagttgtgaggtgccagcatgtttgagaataaacgagttatctttgacatggaagcccgctgaacatgtcaaccctcttgagaaagttttacttgatatccaacgagacaatttcatgaagaccatctcacatgttcagggaatcatccgaaatcatccttcagacctactgactgctgatgtaattacagttgttgtgcagaaagaaatttttaaatggaattgttgtcttaaggatagggatgctcaaaggatagtgaatgcgttactggaacatgctagaaaaatcaaggagatgcacaattttaactcggagatgcggaaggaagagttttctgcaaagctgaaggttcatttgaagtggcagctcaaagaagtagaaactatatatacctcattggagttagattacaagaaagcaacgagtgatgataatattgctttctcaatgctgcatgataagaagaagaaattgcacaatcttcaggatgagataactggcttgcagcagtcgttggagatgaagaaggatgaaatgcagaaattggctcatcaagttgctgagcatgagagtgtatttcagaagtctttaatggaaagattaaggattaaggaagttatgaagggttatgagcaaactcttgctgaagttaaagttcagctaacttccactgaagttggatcaattgatatagaggcattggtgaaggtagagatggataacatgaccaaggaaattgaactgtctaaggaaagcctcctaaacatcactttccattaatgaccggaatggtgatgtcatgatcatgttcggttgcaagtagttcttctattgacggcattctacattatggtaatcctttttgttatcttgaaagttttaacccataatatgtaaagtaacatagcagaagcagaaatacaatagggccattaatggacatattggtttgttttgcagaaactatgctatctgataggtgagtccagttatgtactagtttgcatttattcatatcttagacctcttgaaagacaagttctaggtaagatacatcttctgatgacagaagaagaagaaattaccccaaaacttgttaagtggcactgatattatgctatattaagttgtcatgtcacttatggcagtactttacattatacaagcagtttatttctgaagagccgctaggttgtagaatgctcctttcttactcatgaggtgtggataagtaccacgttccactaccttaccctctcctaagaaggcaatcgaatctacattcttgattgtgttcagtcgatgtgccaccacaattgtagtccttcctgacatgattctatcaagggcttcctgcacaacttgctctgactgtgcatcgagagcacttgttgcttcgtcaagtagaagtattgctggattccggattattgccctcgcaattgcaattcgttgcttttgccctcctgatagttgtaatccatgctcaccacagtcagtatgatatccgtcctttagagatctgaaaaagaatatactttagtacattcataactggaattcatttaacaggaacattgctgcactgtatatttggaaaggaaaacttgaagaacttacgatatgaattcatgtgcatttgcagctttagcagcttccacgatctcgtcttcatcagcttctggtttaccaaaagcaatgttgtccctgacactaccagaaaatattgcaggctcctggctaacaagggctgtaaatcctcgataccaaaggatatccatctccctcacatccataccatcaacctttacagcccctctgtcaacatcatagaacctctggatcaaaccaatgatggtagattttccacagccgcttctcccaacaagaccaatacttgttcctgctttcacatccaagctaaaatcctgcaggataaggcattgtggtcttgtcggatatgcaaaatctacccttttgaactctatccttccttgtattttgttcttctgattgtccttttccacctgcaatttagctgtgttattttattcttatacaatctagcacaacaaggtcattatttagctaggctgccgatctcttttctaatattttatacaatgctcatgaaagtggtcatgaatatatgatacctgtgaattttgtggagagatagatttcctgtctagcacctcaaacactgaagcaactgcatttgctcccttagccaggtcggatgtcatgctgccagcatcagcaatcaactttcctgtactcaccaagacaaaaaatgttttgaagacatcacctgcggagatctccccagattgtgccaatttcccaccataccagaagtcaagagcccatgacaagaatgaaaggcaaggtgacagtccagtggtgatcccggccacccatgatttcttccttgctctcttcagtggttcctcttgtgtatgctcaaagagctga More
CDS seq		atggaggaggtgaggaggcatcatcacttcatcaaggtcatggtcggcgagttcgcccgccgcctcgagatacctcaaggcttccttattcacattccagaggtggaccacagtacttttgatgcttcattaccatcatctgccaaaggcacgcttcagaattcagaagggaagacttggcctgttgagctagagaaacttgatggccatgtatttctgaccactggatgggcgaagtttgtggaggacaattctttgagggaatatgagttccttctcttcagatatgatgataacatgcatttcatggttttgccatttggtctgaatgcttgtgagaaagtaattcggtcttcaggaagtccacaaggaaaacttccatgtgatatattctgctgtactaagaggggtcgggatggtgatagactaacagaggcagccaacagtctcacgcctagtcattcacaggtattgcaaaggacaactcaaggccatgagcttatttcaccacaaagtttccctgatcaacatgaagtatgcggctcgaaagatgggttagatgaacacttatcactgaacgggccaatggaggatgataaagctaatgcgatagctgaagtaatgagcatattggatgttgacaaagtgacagttgaattattctgtgcaatgcttgttttctataaatggaatgtggatgcggtggcagaagactttgacatatgtaggggcaaaccgcaaattcagaacctgtttctgaagcacaaacttcattttcaatttgatattgtaaagaggaaactacgaaagttcttccctccagatgattattattcttctccaatacttgggagtaggaagtgcagccttgaggaacctaagttgtctaaccaaccactgcaatgtgacttgacaacagagaagtgtaggctagttgatgagcatgatttatgtaatttttctcagaaaaagagaaggaagcgaggttcattttgtagtcctgaaactccacgaagatcaccaagactggcacgccagaataattctcatgacagtgcagagaatacattgaaagaaagatccgaagagcgacaaccatcaccagacagcatgatagatcaggcagagagcagatcagagcaagcatgtttatgccacgataaaacagacagtggtattcttaggctcctcttttgtgaggtgccagcatgtttgagaataaacgagttatctttgacatggaagcccgctgaacatgtcaaccctcttgagaaagttttacttgatatccaacgagacaatttcatgaagaccatctcacatgttcagggaatcatccgaaatcatccttcagacctactgactgctgatgtaattacagttgttgtgcagaaagaaatttttaaatggaattgttgtcttaaggatagggatgctcaaaggatagtgaatgcgttactggaacatgctagaaaaatcaaggagatgcacaattttaactcggagatgcggaaggaagagttttctgcaaagctgaaggttcatttgaagtggcagctcaaagaagtagaaactatatatacctcattggagttagattacaagaaagcaacgagtgatgataatattgctttctcaatgctgcatgataagaagaagaaattgcacaatcttcaggatgagataactggcttgcagcagtcgttggagatgaagaaggatgaaatgcagaaattggctcatcaagttgctgagcatgagagtgtatttcagaagtctttaatggaaagattaaggattaaggaagttatgaagggttatgagcaaactcttgctgaagttaaagttcagctaacttccactgaagttggatcaattgatatagaggcattggtgaaggtagagatggataacatgaccaaggaaattgaactgtctaaggaaagcctcctaaacatcactttccattaa More
Protein seq		MEEVRRHHHFIKVMVGEFARRLEIPQGFLIHIPEVDHSTFDASLPSSAKGTLQNSEGKTWPVELEKLDGHVFLTTGWAKFVEDNSLREYEFLLFRYDDNMHFMVLPFGLNACEKVIRSSGSPQGKLPCDIFCCTKRGRDGDRLTEAANSLTPSHSQVLQRTTQGHELISPQSFPDQHEVCGSKDGLDEHLSLNGPMEDDKANAIAEVMSILDVDKVTVELFCAMLVFYKWNVDAVAEDFDICRGKPQIQNLFLKHKLHFQFDIVKRKLRKFFPPDDYYSSPILGSRKCSLEEPKLSNQPLQCDLTTEKCRLVDEHDLCNFSQKKRRKRGSFCSPETPRRSPRLARQNNSHDSAENTLKERSEERQPSPDSMIDQAESRSEQACLCHDKTDSGILRLLFCEVPACLRINELSLTWKPAEHVNPLEKVLLDIQRDNFMKTISHVQGIIRNHPSDLLTADVITVVVQKEIFKWNCCLKDRDAQRIVNALLEHARKIKEMHNFNSEMRKEEFSAKLKVHLKWQLKEVETIYTSLELDYKKATSDDNIAFSMLHDKKKKLHNLQDEITGLQQSLEMKKDEMQKLAHQVAEHESVFQKSLMERLRIKEVMKGYEQTLAEVKVQLTSTEVGSIDIEALVKVEMDNMTKEIELSKESLLNITFH
Function		B3 domain-containing protein Os03g0120900 [UniProtKB/Swiss-Prot:Q5JNA1]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLiXu_01g0031310	OsLiXu_01g0031310.01	Chr01	31830224	31834243	+	NAM
CDS seq	atggaggaggtgaggaggcatcatcacttcatcaaggtcatggtcggcgagttcgcccgccgcctcgagatacctcaaggcttccttattcacattccagaggtggaccacagtacttttgatgcttcattaccatcatctgccaaaggcacgcttcagaattcagaagggaagacttggcctgttgagctagagaaacttgatggccatgtatttctgaccactggatgggcgaagtttgtggaggacaattctttgagggaatatgagttccttctcttcagatatgatgataacatgcatttcatggttttgccatttggtctgaatgcttgtgagaaagtaattcggtcttcaggaagtccacaaggaaaacttccatgtgatatattctgctgtactaagaggggtcgggatggtgatagactaacagaggcagccaacagtctcacgcctagtcattcacaggtattgcaaaggacaactcaaggccatgagcttatttcaccacaaagtttccctgatcaacatgaagtatgcggctcgaaagatgggttagatgaacacttatcactgaacgggccaatggaggatgataaagctaatgcgatagctgaagtaatgagcatattggatgttgacaaagtgacagttgaattattctgtgcaatgcttgttttctataaatggaatgtggatgcggtggcagaagactttgacatatgtaggggcaaaccgcaaattcagaacctgtttctgaagcacaaacttcattttcaatttgatattgtaaagaggaaactacgaaagttcttccctccagatgattattattcttctccaatacttgggagtaggaagtgcagccttgaggaacctaagttgtctaaccaaccactgcaatgtgacttgacaacagagaagtgtaggctagttgatgagcatgatttatgtaatttttctcagaaaaagagaaggaagcgaggttcattttgtagtcctgaaactccacgaagatcaccaagactggcacgccagaataattctcatgacagtgcagagaatacattgaaagaaagatccgaagagcgacaaccatcaccagacagcatgatagatcaggcagagagcagatcagagcaagcatgtttatgccacgataaaacagacagtggtattcttaggctcctcttttgtgaggtgccagcatgtttgagaataaacgagttatctttgacatggaagcccgctgaacatgtcaaccctcttgagaaagttttacttgatatccaacgagacaatttcatgaagaccatctcacatgttcagggaatcatccgaaatcatccttcagacctactgactgctgatgtaattacagttgttgtgcagaaagaaatttttaaatggaattgttgtcttaaggatagggatgctcaaaggatagtgaatgcgttactggaacatgctagaaaaatcaaggagatgcacaattttaactcggagatgcggaaggaagagttttctgcaaagctgaaggttcatttgaagtggcagctcaaagaagtagaaactatatatacctcattggagttagattacaagaaagcaacgagtgatgataatattgctttctcaatgctgcatgataagaagaagaaattgcacaatcttcaggatgagataactggcttgcagcagtcgttggagatgaagaaggatgaaatgcagaaattggctcatcaagttgctgagcatgagagtgtatttcagaagtctttaatggaaagattaaggattaaggaagttatgaagggttatgagcaaactcttgctgaagttaaagttcagctaacttccactgaagttggatcaattgatatagaggcattggtgaaggtagagatggataacatgaccaaggaaattgaactgtctaaggaaagcctcctaaacatcactttccattaa More
Protein seq	MEEVRRHHHFIKVMVGEFARRLEIPQGFLIHIPEVDHSTFDASLPSSAKGTLQNSEGKTWPVELEKLDGHVFLTTGWAKFVEDNSLREYEFLLFRYDDNMHFMVLPFGLNACEKVIRSSGSPQGKLPCDIFCCTKRGRDGDRLTEAANSLTPSHSQVLQRTTQGHELISPQSFPDQHEVCGSKDGLDEHLSLNGPMEDDKANAIAEVMSILDVDKVTVELFCAMLVFYKWNVDAVAEDFDICRGKPQIQNLFLKHKLHFQFDIVKRKLRKFFPPDDYYSSPILGSRKCSLEEPKLSNQPLQCDLTTEKCRLVDEHDLCNFSQKKRRKRGSFCSPETPRRSPRLARQNNSHDSAENTLKERSEERQPSPDSMIDQAESRSEQACLCHDKTDSGILRLLFCEVPACLRINELSLTWKPAEHVNPLEKVLLDIQRDNFMKTISHVQGIIRNHPSDLLTADVITVVVQKEIFKWNCCLKDRDAQRIVNALLEHARKIKEMHNFNSEMRKEEFSAKLKVHLKWQLKEVETIYTSLELDYKKATSDDNIAFSMLHDKKKKLHNLQDEITGLQQSLEMKKDEMQKLAHQVAEHESVFQKSLMERLRIKEVMKGYEQTLAEVKVQLTSTEVGSIDIEALVKVEMDNMTKEIELSKESLLNITFH More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLiXu_01g0031310	OsLiXu_01g0031310.02	Chr01	31833895	31835581	+	NAM
CDS seq	atggtgattcgatgtgccaccacaattgtagtccttcctgacatgattctatcaagggcttcctgcacaacttgctctgactgtgcatcgagagcacttgttgcttcgtcaagtagaagtattgctggattccggattattgccctcgcaattgcaattcgttgcttttgccctcctgatagttgtaatccatgctcaccacagtcaatagatttcctgtctagcacctcaaacactgaagcaactgcatttgctcccttagccaggtcggatgtcatgctgccagcatcagcaatcaactttcctgtactcaccaagacaaaaaatgttttgaagacatcacctgcggagatctccccagattgtgccaatttcccaccataccagaagtcaagagcccatgacaagaatgaaaggcaaggtgacagtccagtggtgatcccggccacccatgatttcttccttgctctcttcagtggttcctcttgtgtatgctcaaagagctga More
Protein seq	MVIRCATTIVVLPDMILSRASCTTCSDCASRALVASSSRSIAGFRIIALAIAIRCFCPPDSCNPCSPQSIDFLSSTSNTEATAFAPLARSDVMLPASAINFPVLTKTKNVLKTSPAEISPDCANFPPYQKSRAHDKNERQGDSPVVIPATHDFFLALFSGSSCVCSKS

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.073227	0.000000	0.033386

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0723700	RBH	0.087538	0.253824	1.711629
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os01g52540	RBH	0.051984	0.149915	0.386918
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0723700	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0032060	RBH	0.000000	0.000000	0.418554
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_01g0031580	RBH	0.057867	0.000000	0.716664
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0032030	RBH	0.189705	1.000940	3.324739
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0031240	RBH	0.000000	0.026570	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0030920	RBH	1.053169	0.000000	4.121243
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0500900	SBH	0.615732	1.605217	0.1001585
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0030650	RBH	0.000000	0.000000	0.454874
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0493500	RBH	2.3495675	0.682979	5.7284615
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_01g0030890	RBH	0.000000	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0030920	RBH	0.000000	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0031120	RBH	0.0	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0031290	RBH	0.0	0.0	0.0
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0031070	RBH	0.000000	0.437801	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G031520	RBH	0.000000	0.291894	0.173041
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0031170	RBH	0.0	0.000000	1.623791

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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