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_11g0016010		OGI:11058510 \| 16/16			LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)			Chr11:22783540-22788669		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		ctggctattggttaggaggatcgagctggacatacatatatgattttgttgcatgagtccggccgagtgccaagtgccaaccccaaactttggaaatatacaacttgagccatgagtgtcgaggagacggccagcggtagctgggtggtagagatcgagagttacatcagtggcgacacatctggagagatggcgcgaggatcgaagccgaggcactccatctaccgggtgccggagtacatcaagaacatgacgaaccccagagcctaccagccacaggtagtatcgctgggacctttccaccacggcgatcctgccctgctgccgatggagaagcacaagtgccgtgcggtggcgagcttggtcaagcggagcgggaagcctctgcaggagttcatcgctgccgttgaggagataaaggtgcagcttcaggacgcgtacgaaaagctagaagacgaatggtaccaaggtacacgcttcgtggagctgatgctcatggacggctgcttcttgctagagatggcgagggtttttcagctagatgggagagccgaggactatgaacccgatgaccctgtcttcagcgagcacggatgcttatacttgtccgatggtatcagatccgacgtggtcttgatggagaaccagctgcctcttcttctccgcaaacttgtcaatgttgcatatggccacgattttttggtacgttttcatgagcttgagtaactgtcgtgcacacattttttatgtcatttgatatattttgtaagtcaaaaccattaaaattttaatcctcttgattagtaacgagtggcttaaattagaaccatatcaaacacaatattagaaaatagattaaccaaatatacaatataattaaagactctctccttacctacttattggtttattagctatataaccaaaatttaaatttatacatacatacatatacatatacatatacatatatatatatatatatatgtatgtatgtatgtatgtatatgtatatatatatatgtatatatatatatatatatgtatgtatgtatgtatatgtatatatatatatgtatatacatatatatatatatatatattttaaatttgtttggtgcccggacaccattgttgaaattgagtatatacccaattcaaatgagtatgaaactttttcaaatattttttattaacatcaactactttactaactagttcaaagcaagttgaactatatactcaatttgaatatatatatatatatatatatatataattgttttacatatatattatttttggttgatccgctcatttttttcccggtttatcaactgtagcttagctaattggagccaaaaattttcatcaaaaaatataaaacaaaaatcacatagagatttcgctataaaaaacctagctaaaagtttgtatgtaaaaatcaatcttttttgcaatttttttgtgtgtaaggtatataggttttaaactcagtatctctctccacacgttgtcctcttaacacatgacaaccagggattgctgtatagacggaagatgctatcttttaggcaaaatttgctataggaaatccaaaaatagtgtaattagctaggagacaccgcaagaccgcgtttttctatagagcaccgtaaaaaactggtaattaattagctgctggacacccgcgggattattttattatatctgaaaaaattggagagagaaacagctgtgtaagtacggttctaccctttgattttttttctttttctttttttcttccttatccttttctccctctctcattttttttctctctttctctctctgttctcaaccgctgctttcaaccttgctcgccgccgcttcgcctgtcgtcgtggcgctcgcccgccgctcctgctcttcctaagctcgcccgccgtcgccgctccgcccgccacgctcgcctgtcgccgccgctccttcgctcgcctgccgtcaccggtgctactgccccatggcttcatgtcatgcgagcgaaggaggagcggcaaccactggtgttattgtttcacgaggaccaccggcgtgaacgtggcgccaaacgagcagtcggtggcagcctacgagtgcagcgtgctcatggccgtcgcgccctcgaggaggtcttggaccgccttggtgtagtacgcgcgcagccgccgcagcgagcggcagtacagcgccactagccaccacacccgcagccgccggaacgcaccgaacaaccgcctccgcccaccggcgccgacgccacgcctcgcacggtcacatggcggcacagcggcaacttgcggagggagggagcggtggtggcggaacagctgctgcacgcggagaaaggaagcggcagcggcggcggttgcttctttcggaaaatgggagctgcgacgacggttcctatgcgcagagaaagggagcagcgacgacggcgtagagggtgcgcgtggtccggtgcgcggtaacggcagtgcgaagggagcggcgacggctgcgctcgagaaagcggcagtggcgtggccagccgtgtgcagtgtgctgctgccctcggaggaaacgacacgactctgctgctgcgctcgagagaacgacggtggcgtggccagccgtgtgcagtgtgcttcacatccaccatcgtgtcttctcctaccacatactatttagtagttgactaaatctcggcaggacacatcacatatcatgtcttatacggaaacaatctgtggatatggagagagttccggataaggaaagacaactagagttctacatggaaacgacaaggactactcggattgtatccatattggtttccctagttctacttggataaggggacacctatggatataaatacaagcccccctaggaagacaggggacagacactcaccaggaagagacaatcaacacccaacgggatcagcgcccaacgggagaacgatcatggaagacacccatgacaatcaacacacgcccaccagaagccacaacatacaagccaacatacgccaagacatgccaccggatatcgacttcagggataggcatggctattcccctacggtgtctctagataccgtcaggagatacgaaagcgctatctctgatctcgccggacacgaattcgaggaggaatgctaccctgttgtcgactacgagtcagaccttcagaccgctatatcgataacagttagataggctaccccacgtattgtactggtgtgattatggtgaataaagaacaacaccggctccggccaataggatgtagggttattacctgaccactcagtgcccgaacctgtataaaaatcatcgtctccatctcttttacctcagtctcgcgtatatcctagcaccaacgatccccatactgtccaaataccgtagtcgtggcatcaaacgttgacagccccgtttaaatccctccccaaaatttttcatcctgtcacatcaaacgtttgaacacctgcatggaatattaaatataggctaaaaaagtaactaaatacaacgattgtgactaatttacgagacgaatcttttaagcctaattgctccatgatttgataatttggtgctacagtaaatatttactaataatggattaattaagtttaataaattcgtctcgcagtttataggcggattatgtaatttgttttgttattagactacgattaatactttaaatgtgtatccatatatctgatttgacacgccaaaactttaccccctgatctaaacaccccatacaattccgaacttacgaacacatttcaaaaagtacatgaaaagaaatctaagatatgagaatcacctcacatttgctaacaaaggagggtgcagtcctagttcgtggcagtggcggagaatgctgcaacacagtcgtctagaaatagtggcaacatagatacactgtatttaattagttccaccggcaaaacaaatttaccaggtcacatcacatatacgaacacacatttaaaatattaaacatatactaataataaaacaaattacataatccgcatataaactgtgagacgaatttattaagcctaattaatccgtcattagcaaatatttaatgtagcattatattgttagatcttggcgcaattaggcttaaaagatttgtctcataatttacaaacaaactgtgtaattgtttttttttaatatttaatactcaatacatatatttaaacgtttggcagaggagtgcacgagcctcaccagttcctggcgagtgacgactgtcgacacttgcacccctctcatgtttcctatctgggtgactctccggtacggtgctatctaattggagtattctactacgactataagtagaattaatctcaaccgtatattttaacgagtatattagtaatctcttaatacatattaggggtaattttggtatgggatgtttctctatctcggtcgcttgtttgcatcaggttgcgtcgccccgagcccccgacgccgcatcagctatcgctactccccgtaaaaaaaaaggttatcgctatgagttgagctcgcgtatcagcttgttgttgtgagttgagctgtttagacgcgtaatccgcatgagcaatcctgtctcgatttcatgctggtgatatttaatctgccctgcgtggctgctcgttacgttgggtgttcttaaactcggtaagtaaagtggtgccatgtcgggtgtgaggtttttggcatgcccaatggggcgaggtcatggctcgccgacttgcgtgtgcggttcggcggcggtgacggcgccagggaggagacggggctcaggatcctggtgttcgaggtggcgacagccatgtcgcggctcgtgtcgctctactgctcgctgtctgacgtggacgtcaggaggctccgcgcggacgggctgcgcgccgagggcgttgcgcacgtcacatccacgcatcagtcgctcctgctttggctcgcgtgtggcgagctcgtggcggacctcgaccatgcagctggcaccgccacgcggttcgggacgcggcgcgctgttcctgcacgattttcgaccgcatctacgcggaggctaagcgggggaacggactcgtgcggctag More
CDS seq		atgagtgtcgaggagacggccagcggtagctgggtggtagagatcgagagttacatcagtggcgacacatctggagagatggcgcgaggatcgaagccgaggcactccatctaccgggtgccggagtacatcaagaacatgacgaaccccagagcctaccagccacaggtagtatcgctgggacctttccaccacggcgatcctgccctgctgccgatggagaagcacaagtgccgtgcggtggcgagcttggtcaagcggagcgggaagcctctgcaggagttcatcgctgccgttgaggagataaaggtgcagcttcaggacgcgtacgaaaagctagaagacgaatggtaccaaggtacacgcttcgtggagctgatgctcatggacggctgcttcttgctagagatggcgagggtttttcagctagatgggagagccgaggactatgaacccgatgaccctgtcttcagcgagcacggatgcttatacttgtccgatggtatcagatccgacgtggtcttgatggagaaccagctgcctcttcttctccgcaaacttgtcaatgttgcatatggccacgattttttggtttttggcatgcccaatggggcgaggtcatggctcgccgacttgcgtgtgcggttcggcggcggtgacggcgccagggaggagacggggctcaggatcctggtgttcgaggtggcgacagccatgtcgcggctcgtgtcgctctactgctcgctgtctgacgtggacgtcaggaggctccgcgcggacgggctgcgcgccgagggcgttgcgcacgtcacatccacgcatcagtcgctcctgctttggctcgcgtgtggcgagctcgtggcggacctcgaccatgcagctggcaccgccacgcggttcgggacgcggcgcgctgttcctgcacgattttcgaccgcatctacgcggaggctaagcgggggaacggactcgtgcggctag More
Protein seq		MSVEETASGSWVVEIESYISGDTSGEMARGSKPRHSIYRVPEYIKNMTNPRAYQPQVVSLGPFHHGDPALLPMEKHKCRAVASLVKRSGKPLQEFIAAVEEIKVQLQDAYEKLEDEWYQGTRFVELMLMDGCFLLEMARVFQLDGRAEDYEPDDPVFSEHGCLYLSDGIRSDVVLMENQLPLLLRKLVNVAYGHDFLVFGMPNGARSWLADLRVRFGGGDGAREETGLRILVFEVATAMSRLVSLYCSLSDVDVRRLRADGLRAEGVAHVTSTHQSLLLWLACGELVADLDHAAGTATRFGTRRAVPARFSTASTRRLSGGTDSCG
Function		UPF0481 protein At3g47200 [UniProtKB/Swiss-Prot:Q9SD53]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLiXu_11g0016010	OsLiXu_11g0016010.01	Chr11	22783540	22788669	+	NAM
CDS seq	atgagtgtcgaggagacggccagcggtagctgggtggtagagatcgagagttacatcagtggcgacacatctggagagatggcgcgaggatcgaagccgaggcactccatctaccgggtgccggagtacatcaagaacatgacgaaccccagagcctaccagccacaggtagtatcgctgggacctttccaccacggcgatcctgccctgctgccgatggagaagcacaagtgccgtgcggtggcgagcttggtcaagcggagcgggaagcctctgcaggagttcatcgctgccgttgaggagataaaggtgcagcttcaggacgcgtacgaaaagctagaagacgaatggtaccaaggtacacgcttcgtggagctgatgctcatggacggctgcttcttgctagagatggcgagggtttttcagctagatgggagagccgaggactatgaacccgatgaccctgtcttcagcgagcacggatgcttatacttgtccgatggtatcagatccgacgtggtcttgatggagaaccagctgcctcttcttctccgcaaacttgtcaatgttgcatatggccacgattttttggtttttggcatgcccaatggggcgaggtcatggctcgccgacttgcgtgtgcggttcggcggcggtgacggcgccagggaggagacggggctcaggatcctggtgttcgaggtggcgacagccatgtcgcggctcgtgtcgctctactgctcgctgtctgacgtggacgtcaggaggctccgcgcggacgggctgcgcgccgagggcgttgcgcacgtcacatccacgcatcagtcgctcctgctttggctcgcgtgtggcgagctcgtggcggacctcgaccatgcagctggcaccgccacgcggttcgggacgcggcgcgctgttcctgcacgattttcgaccgcatctacgcggaggctaagcgggggaacggactcgtgcggctag More
Protein seq	MSVEETASGSWVVEIESYISGDTSGEMARGSKPRHSIYRVPEYIKNMTNPRAYQPQVVSLGPFHHGDPALLPMEKHKCRAVASLVKRSGKPLQEFIAAVEEIKVQLQDAYEKLEDEWYQGTRFVELMLMDGCFLLEMARVFQLDGRAEDYEPDDPVFSEHGCLYLSDGIRSDVVLMENQLPLLLRKLVNVAYGHDFLVFGMPNGARSWLADLRVRFGGGDGAREETGLRILVFEVATAMSRLVSLYCSLSDVDVRRLRADGLRAEGVAHVTSTHQSLLLWLACGELVADLDHAAGTATRFGTRRAVPARFSTASTRRLSGGTDSCG More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	1.197444	0.0	0.080057

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_11g0541200	SBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os11g33942	SBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os11g0541200	SBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_11g0016440	RBH	1.924836	0.0	4.441315
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_11g0017800	SBH	0.0	0.0	0.0
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_11g0016360	RBH	1.705922	0.0	7.307921
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_11g0015940	SBH	0.373016	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_11g0017580	SBH	0.0	0.0	0.0
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_11G0329500	SBH	0	0	0
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_11g0016690	RBH	0.0	0.0	0.0
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_11G0341800	SBH	0	0	0
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_11g0016670	SBH	0.0	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_11g0017970	SBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_11g0016230	RBH	22.133106	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_11g0016050	SBH	0.0	0.0	0.0
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_11g0016290	SBH	0.0	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_11G016170	SBH	0.0	0.0	0.0
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_11g0016500	RBH	0.0	0.0	0.0

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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