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_03g0005810		OGI:03011140 \| 16/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr03:4189276-4195361		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		RLCK103, GUDK, OsRLCK103
DNA seq		acacacccccaaaccaaaattaaccaaacccccgcgccgttaaccctctgagcttgtgatgaattaacgatcgtgaccgatcaagtgagcgattaataataacccagcggcacacaattaagcaatgcaagaagccgtcgtcgttaacaccggcggccggtgggcaccaacccgtatatatatacacttctatccggccaaagcagcgggcgcggccgggtaacccaaccacacacgcacgacacgaagaacgccatggcgaagcaggcgtggagctcgctgttcgggtgcttcacctcgcaccacgacggcggcggcaagaggaagaaaggcggcggcggcgggaagaaggcgaagaagaaggtggcggcggcggcgagccagaagcagcggaagctgcagagccggctgtcgttctccgacctgtcgttcggagggatggtgtcgccggaggacctgtcgctgtcgctggccgggtcgaacctccacgtcttcaccatcgccgagctccgcgccgtcaccagggacttctccatgaccaacttcatcggcgagggcggcttcggccccgtctacaagggctacgtcgacgacaagctcaagcccggcctccgcgcgcagcccgtcgccgtcaagctcctcgacctcgagggcacacagggacacaacgagtggctggtaagtacgacacttaatcactagtagctgcttaattacgcctcgctaaaatttaattataaactactccactgcttgctagctccatcggctcagttcattacttgcacggttgcacctgtacgtgacctcacattattactagctgacatgccttgacactccaattaggcggttattgttggtaactaaattaatacagaacaccactttgcaaaaagtacgaaactgatcataatgatcagtttgatgaatagtgtggttctttacctgctatacgcatgacggcatgagattattgctgctatctagtacctctagttgatgagacttgcttacttgttcaaagttagttgagctgttctagtaataaggtttgagttaattagctgggaatttaaaccatgataggacttcagataaaattaattaattaacctatatgtacatgttacataagttcaggaaagtatatacccagcgtaattagcattattaacttggccttgctacggtgggtacaaattaaagtatatattctgaaatgtcaggggaaagaattcagaaaatgattacatattttctataagaaaagaaaacttggttttctgttgaaatataaaataaattgcttgtatttcctcactagcttaagtttcaaaatggaaatagagccaaaggtctcgaattcaaatcttgccagctggtgcgtaattaaattaaaattgcatccacttttattctatcctataggcttgatgaggcccgcatgagaggatattagaatatgtaattacttgtttttctttattagcttaattaaacttttgggttaaattgatcggtgtatgcaaccgagctgaactttattttgcagtatctattgcttttttttgtttaaaatggttaattagtattccttaaaaaaggttaattagtattgtgatactgtatttgtttatgagtacgtacctgctctattctttctactatattttttctcaatattccaaaccactagtcttttcttatattaaaatggttaattggtattgtaatactgtattagtttatgaatacgtacctgctcgattatttttactattctttttctcaatattccaaatcactagtcttttcttagaagtagaagttttcttggttgacgtgttacacatactgaactccattcgagaaagtttcagaagtttgctgctagatagtagataccatggaacaataattcaatagaacagtgctgcttgcttagctgaaatgcttccttattttatttttctcccagttaaaagcaatcaaatgagaaaaaaaaatgtctggacttgactgacaagtctgcaaatgcatacatggcccgatgattatgcagactgaagtcatctttctggggcaactgaggcatcctcacctcgtcaaactgatcggctactgctacgaggatgaacacagacttctcgtttacgagttcatgacgaggggcagcttggagaagcatctcttcaaaagtaagcttgaaaaaaaatactaatattttgttattgtttcctatattatgctagctttctgctactctgaatatacaagaaatttggtgcaagcctcagttgttttctgacaaattagcagaagtaattaagaataaaagcgtaactgagattagagagaattgaaacgatttacatatatatcaacggtataagtatatattatagcagagtgacaatcttgcaggcaacaagaaagagatattcgtaaaacattgctatcactctgctttttcctcgctgcatcattaagctaaaaaggattcgacagaatctctaggctgaacatcggttgaaatggacggcgcgattttaccaactcgctggcataaacttttctgcaaattggtggcgcggctaagctcgattgatcgagtagcttttcttgctctacacccttcaatatgtttctccagtttttcctgatggttcaaactgcctttttagacctttgttgtgacgtccatttttgcgttacatcatatctcactctctgtatggagtcattttctcttaaccactttgatataattcacacctgcaacttgcttttgttctcctctttgtctgtctcttgtacagtcctactgtcatgtcttcattgtcaatttgcctctgcatagtgaagaggaaacagcgcagatttgatgtataatcatgagtatggtaggggtaggacaccttcaccactcgttgtctactatggttttttcacattagtacttgcgtcaaagtagtagacaacccctaatatgtgatttggatcaacctcacaagtcaaaattcgtggcttgtgttatcggtaaccacatgatctagtcacctcgatctatcaattactactggtttaagagacatagtagcacaatatgcttcatgttttattaatgaagcaaggtagccctgaaaactgaaaaatcacgtgtgagggagtacagtgattaaactgttgcaaattaattaagagatagcaacgtttcagcaaagttttttttaagtaaatccgatgtcattagtttcatgtagtcagtctactgtcatggacatgcagatgcatgctgaccaaaatgtacatttctcttcttaattcaagctccatatgtgcatactattattagttcaacttaatcgtcttatctgattacaaatcgtacttacacaccaaatgtgcagagtacgcagcgtcgttgccatggtcaacacggttgaagatcgccataggtgccgcgaaagggttggcctttctccatgaagccgagaagccggtcatctaccgagacttcaagacctccaacatcttgctagactcggtacgtccttgaccttaattacgttaccatcgtggcatcgtatatgtgttcttcacctacttccccaaaagattgacctggttgtcatttgatctctaataaggttattagtagtcagaaaagttatattcttttagataatagtcagaatagatgcatcatgcatgcatggtttggttgcttgtacgttcttaattagtttccatatgaaactgtcgtgatgccaaatgccaagtactaaacaacaaatcttgactactactcgatcgcctatgtatactgaactaagaattggtcaggtttcagactttcagtttcaactatagcagcgctcccgttttgtcatcaatgcgttaacgtgacaaaggccgcgaatttagttctaaactttttctttaaacttccaattttttattacatcaaaagtttcctacacacacaaatttttaacttttctgtcacatcgtttcaatttcaaccaaaggccgtgtttagttcctgaaaaaagttgaaaattttaggaaagttgggagtttgaaaaaaaagttgaaaatttatgtgtgtaggaaaatttttgatgtaatgtgatgtgatggaaagttgaaagtttagggtagttgggggtaaactaaacacggccaaacttccaattttagcgtgaactaaacacacccaaagaaagagcagggtggtatgactatttctccgtggagaaaaaaaactgaaaaaaaaggtaaaacatggagtgattcatcagtttaaactaaattattacgcgcgtgataaacagagttgttgggggtgcagttgttggagttgggtgcagtggtgatatttccctctgaacaataatccctagcaggctagcactactgctagtgcatttgctttggttacgctattatttctccatcaactgaatcctgcagttgcagcagaaaggttttcttacacaagtacaattctgtagcaatcttaattttgttttcgttgctgaattgtccgtaggacttcaaagccaagctctcagatttcgggctagcgaaggacgggccagaggatgacgagacgcatgtctcgacacgtgtgatgggcacacagggatacgctgcaccagagtacatcatgacaggtttgacagcagaaaaaactgcaaccttttaccccatcctaaataaacaatataatataaaatgtgatatatcctatttagatttgtaatactaaatctatcacatttctctttttctaaatttttttttgaaatatatggagtaagggtgagtttgaggagagggggatagaaaagattgggaagatacgtaaaacgaggtgagccattagcgtatgattaattgattattaactattttaaattttaaaaatggattaatatgattttttaaagcaactttcctatagaaaatttttacaaaaaatataccgtttagtagtttgagaagcgtgcgcacggaacccgatgtccctttctcacccaatccctcagaacgaacgcaccctaagttttactccgacaatctgatcgatggtttgtcagtagattagaagcaatataattatggtcttgttatcaaattatttttagggcatctgacggcgaagagcgacgtgtacggcttcggcgtggtgctgctggagctgctgacggggaggaagtcggtggacaagagccggccggcgcgggagcagaacctggtggagtgggcccggccgtacctgaccgacgcgcggcggctgggccgcgtcatggaccgcaacctcgccggccagtacccggccaaggcggcgcagaaggccgccgcgctggcgcaccgctgcgtcagcctcaaccccaagtcccgcccccacatgtccgccgtcgtcgaggcgctcgagccgctcctcgccctcgacgacgactgcctcgtcggcaccttcgtctacgtcgcgccgcccgacgacgtcgccgccaacggcgacggcagcagcaagaggcgagccggccggaggaggtctgacggcgccgcggcggcggcggcggcggcggccgatggtgtgcagcgggaatgactcggttttgcttgcgtttgtctgtactcgtcgagctacgtgctgatcaagcgatgccggtaaattaatccggatcagtgagttggctcgtgggtaaaaaatgattgtggatttgaagcatgttattatttgtcttaggcttgaatagcagaataggattagagcgtgtaaatacgagcatgtcagacgtacatgagcaaattgagcatgtaaacagtttgacaaaatatggatggttcatcacttctcatgttgggaggtttctctagtatcttcccagcgccgtgaaatatctctgttgatagacactgtatgctgtacgcgagtatgtttttactgtttgctgaaagactgtaggttttctccgtgtgcactgtatttaaattttgagaagctgcaaggatttagtaatggtaatgttggtggtgtacggtgtgggaatgcaatacaactgtaacaattggac More
CDS seq		atggcgaagcaggcgtggagctcgctgttcgggtgcttcacctcgcaccacgacggcggcggcaagaggaagaaaggcggcggcggcgggaagaaggcgaagaagaaggtggcggcggcggcgagccagaagcagcggaagctgcagagccggctgtcgttctccgacctgtcgttcggagggatggtgtcgccggaggacctgtcgctgtcgctggccgggtcgaacctccacgtcttcaccatcgccgagctccgcgccgtcaccagggacttctccatgaccaacttcatcggcgagggcggcttcggccccgtctacaagggctacgtcgacgacaagctcaagcccggcctccgcgcgcagcccgtcgccgtcaagctcctcgacctcgagggcacacagggacacaacgagtggctgactgaagtcatctttctggggcaactgaggcatcctcacctcgtcaaactgatcggctactgctacgaggatgaacacagacttctcgtttacgagttcatgacgaggggcagcttggagaagcatctcttcaaaaagtacgcagcgtcgttgccatggtcaacacggttgaagatcgccataggtgccgcgaaagggttggcctttctccatgaagccgagaagccggtcatctaccgagacttcaagacctccaacatcttgctagactcggacttcaaagccaagctctcagatttcgggctagcgaaggacgggccagaggatgacgagacgcatgtctcgacacggcatctgacggcgaagagcgacgtgtacggcttcggcgtggtgctgctggagctgctgacggggaggaagtcggtggacaagagccggccggcgcgggagcagaacctggtggagtgggcccggccgtacctgaccgacgcgcggcggctgggccgcgtcatggaccgcaacctcgccggccagtacccggccaaggcggcgcagaaggccgccgcgctggcgcaccgctgcgtcagcctcaaccccaagtcccgcccccacatgtccgccgtcgtcgaggcgctcgagccgctcctcgccctcgacgacgactgcctcgtcggcaccttcgtctacgtcgcgccgcccgacgacgtcgccgccaacggcgacggcagcagcaagaggcgagccggccggaggaggtctgacggcgccgcggcggcggcggcggcggcggccgatggtgtgcagcgggaatga More
Protein seq		MAKQAWSSLFGCFTSHHDGGGKRKKGGGGGKKAKKKVAAAASQKQRKLQSRLSFSDLSFGGMVSPEDLSLSLAGSNLHVFTIAELRAVTRDFSMTNFIGEGGFGPVYKGYVDDKLKPGLRAQPVAVKLLDLEGTQGHNEWLTEVIFLGQLRHPHLVKLIGYCYEDEHRLLVYEFMTRGSLEKHLFKKYAASLPWSTRLKIAIGAAKGLAFLHEAEKPVIYRDFKTSNILLDSDFKAKLSDFGLAKDGPEDDETHVSTRHLTAKSDVYGFGVVLLELLTGRKSVDKSRPAREQNLVEWARPYLTDARRLGRVMDRNLAGQYPAKAAQKAAALAHRCVSLNPKSRPHMSAVVEALEPLLALDDDCLVGTFVYVAPPDDVAANGDGSSKRRAGRRRSDGAAAAAAAAADGVQRE
Function		Serine/threonine-protein kinase RIPK [UniProtKB/Swiss-Prot:Q9ZUF4]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0005810	OsLima_03g0005810.01	Chr03	4189276	4195361	+	NAM
CDS seq	atggcgaagcaggcgtggagctcgctgttcgggtgcttcacctcgcaccacgacggcggcggcaagaggaagaaaggcggcggcggcgggaagaaggcgaagaagaaggtggcggcggcggcgagccagaagcagcggaagctgcagagccggctgtcgttctccgacctgtcgttcggagggatggtgtcgccggaggacctgtcgctgtcgctggccgggtcgaacctccacgtcttcaccatcgccgagctccgcgccgtcaccagggacttctccatgaccaacttcatcggcgagggcggcttcggccccgtctacaagggctacgtcgacgacaagctcaagcccggcctccgcgcgcagcccgtcgccgtcaagctcctcgacctcgagggcacacagggacacaacgagtggctgactgaagtcatctttctggggcaactgaggcatcctcacctcgtcaaactgatcggctactgctacgaggatgaacacagacttctcgtttacgagttcatgacgaggggcagcttggagaagcatctcttcaaaaagtacgcagcgtcgttgccatggtcaacacggttgaagatcgccataggtgccgcgaaagggttggcctttctccatgaagccgagaagccggtcatctaccgagacttcaagacctccaacatcttgctagactcggacttcaaagccaagctctcagatttcgggctagcgaaggacgggccagaggatgacgagacgcatgtctcgacacggcatctgacggcgaagagcgacgtgtacggcttcggcgtggtgctgctggagctgctgacggggaggaagtcggtggacaagagccggccggcgcgggagcagaacctggtggagtgggcccggccgtacctgaccgacgcgcggcggctgggccgcgtcatggaccgcaacctcgccggccagtacccggccaaggcggcgcagaaggccgccgcgctggcgcaccgctgcgtcagcctcaaccccaagtcccgcccccacatgtccgccgtcgtcgaggcgctcgagccgctcctcgccctcgacgacgactgcctcgtcggcaccttcgtctacgtcgcgccgcccgacgacgtcgccgccaacggcgacggcagcagcaagaggcgagccggccggaggaggtctgacggcgccgcggcggcggcggcggcggcggccgatggtgtgcagcgggaatga More
Protein seq	MAKQAWSSLFGCFTSHHDGGGKRKKGGGGGKKAKKKVAAAASQKQRKLQSRLSFSDLSFGGMVSPEDLSLSLAGSNLHVFTIAELRAVTRDFSMTNFIGEGGFGPVYKGYVDDKLKPGLRAQPVAVKLLDLEGTQGHNEWLTEVIFLGQLRHPHLVKLIGYCYEDEHRLLVYEFMTRGSLEKHLFKKYAASLPWSTRLKIAIGAAKGLAFLHEAEKPVIYRDFKTSNILLDSDFKAKLSDFGLAKDGPEDDETHVSTRHLTAKSDVYGFGVVLLELLTGRKSVDKSRPAREQNLVEWARPYLTDARRLGRVMDRNLAGQYPAKAAQKAAALAHRCVSLNPKSRPHMSAVVEALEPLLALDDDCLVGTFVYVAPPDDVAANGDGSSKRRAGRRRSDGAAAAAAAAADGVQRE More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0005810	OsLima_03g0005810.02	Chr03	4189483	4195162	+	IsoSeq
CDS seq	atgactcggttttgcttgcgtttgtctgtactcgtcgagctacgtgctgatcaagcgatgccggta
Protein seq	MTRFCLRLSVLVELRADQAMPV

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
A5	Chr03	4193909	4194432	+	OsLima_03g0005810.02	OsLima_03g0005810.02,OsLima_03g0005810.01	All

Expression

	Leaf	Root	Panicle
FPKM	0.084665	0.471470	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_03g0179400	RBH	0.267846	0.0	0.475514
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os03g08170	RBH	0.164254	0.0	0.111002
Nipponbare \| IRGSP 1.0 \| RAP-db	Os03g0179400	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_03g0005920	RBH	0.097051	24.293850	2.197371
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_03g0005880	RBH	0.000000	4.101585	1.040725
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_03g0005900	RBH	0.0	9.105957	5.023776
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_03g0005870	RBH	0.0	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_03g0005850	RBH	0.000000	3.528973	8.989991
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_03G0067800	RBH	0.9095405	5.5907675	0.137409
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_03g0005750	RBH	0.000000	0.254836	0.413344
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_03G0068100	RBH	1.378079	1.948176	0.1075115
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_10g0009370	RBH	0.0	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_03g0005830	RBH	0.000000	3.082309	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_03g0005790	RBH	0.0	18.813341	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_03g0005830	RBH	0.094188	0.801154	0.890983
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_03g0005830	RBH	0.0	3.186210	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_03G005830	RBH	0.0	0.0	0.652831
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_03g0005670	RBH	0.238632	14.594507	5.596814

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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