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_03g0021170		OGI:03045280 \| 16/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr03:17987882-17991843		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		ELS2, OsELS2
DNA seq		gcctcccccccacttcaagtctccattcctccatcgccgcctcgatctactcgccgatggcgctctcccctcccgcggccgcgcgctcttagcatccgccgtcgccgccgccgccgtccacgccttcgatccactcccatgtcggagccgccggcctcatcctgcctgcttcagtaggctaaccgacaggggggaattccggccgggagccaggctgggcgcccatgtccccctccgccacctcgccgccgaatcgcccacaccgcaagcgccgcgccggtgccggtggcggtggcgctgacgacggctcgacccgccgccgcggccgcagcgctgtcctcctcggccccacccacttccccgccgttcgctccttcggcctccgcctcgccctcgtcgtcgccccagccccacgtcaccgccgcaagcagcgcccgctccactacgcctgccgccccacctcccttccctgtcgccgccgccgtcgcctccgcagtatcatctccctcctccacctccccatcctccgcccgttctacctccgctacatcctcgcggcagccgcatcaggcccctgccgctgccgccggaaggaatccctggtaggcatgggaaactacatctcgcgggtgctccggaagagctctagtgaccgtggtaaggcgccgccagccgacgatacagccaagcaggtacccaatttttaatctaattgagtacatctggcatgtaatttgcttgaaccgtcagtttgcacagtaaaattgacaatgcaacatagtttcaaaagatggtaatacgtttgtgtcaatccaaattgcttttagtgaaataagtggataagtaggaatttatattagctatattgtatcaagtattttaatccacaagtgagagtaaaaagttaagtgcttgcatttccagcctgttcatttttttttcttttgaagtcaaatactgttaactaaattaatttgagcactgcaaattgacctttgttgtcatattttatccttgactattccaggatctatgtgaagtttttacacctctgacaaatgaagaagaaagtgaagtaaacaacattttgtatggcagtgatcaaaggtattgtaggcaaccatgaatttaattggctgattacttctcctatatctttagcacaatcaggaattgattttccctttctttttttgcagtaagaaaataatagtgatgcatggaccttccaatattgatattactaaagagaaaatctggtgcttgagaacttgtaattggttaaatgatgaggtgaatacggcctgtccatggaaggaatcctgaagaatatgttaaacaaatgtcccattctttctgatcttgacattagtggttccattttccatgcttcacagaaccaagactgcatcagcattctacttttgttccttgcaggtcattaatttgtaccttgaattgttaaaggagagggcgcaaagagaaccaaaaagatttttgaaatgccacttcttcaatacattcttttataagaaggttagataatttgcatatttttctttccggtgctgtacgatggaatgttcttttcaatatttctgtagttctgttacacacaccattttatgatcttcagcttatcagttgtctctttgaagcactatcaagtgatatttatgcaattattacttgactcttttccctttttttgaggggaatttattattttccttccatagtaggaattatctgccagttagcaggaaaacctgtgattcttttccttcgatagtggaaattgttggctagtttgcacaaaaaacctgtgtttcaacactcaagcatacggtaccatacatttgtttgagaacacgcaattcctaccttatccttaatatatgttgatgtgtgccttgtatttacttaattgatgacccttttcttgagttacaaattttgtgtggttgttattctcttactttttttttttgctaattttccttgtaggttgtaacatcccttactatttattaataaccttgcttacatatcaaatgaattctagcagtagtttgcaccttcatgattttctgaattctcttcagcttgcttatggaaaaactggttatgactatcaatctgtaagaagatggacaaccctcaatagattgggctatgggcttgttgagtgtgagaaagtaatgttactgttattatttttttaatgtttttcatgtctgtttgtctttcaaacaaatcatgagatttattgtgcagatctttattccaatacatagaaatgtgcattggtgccttgcgataataaacatgaaggataaaacttttcaataccttgattcttttggcggcatggaccatgctgtgctgagaatactggtaagcttagctgattacaagtatattactggattagagagccagttacttccaattagttcagttacaagtccgacttatgagacgttagtttggtaagatggcacattgatgacttaacagttgattcagtcatagcatttggacttaattgctccaaattaattttgctaagtatgttatggtgctctctatttggatgccataaatctccagctcccacaatagttaaagggtggacaaaattttacccctgatgcattcatggacttattttttggtgctatagaaatgagaaaggtcttacgttatcacaaatatttgtgatatcttaaaatctgacatgattcagagttattctttgaaatttaaattgtgacttacgaagcactaatccatgttaattagaatttacccatcaggtgctatttcaagctttcagttattttcaagtgaagttctgttttctattcctctcaggctagatatatcagggatgaattgaatgacaagagtaacatacaggtagacaccagttcatggctgaaaatatcatcagattcttgtcctttgcagcagaatgggtacgttctctttacatgctacatatgacctaccagaattacgtatggaatgaataatggtttaccttcggttctgcaatgaacacagatgaaggtctaaattttatcactcagtgcattaatacattatcgacatttgtgttgtgcatatcaatgaccaagcatggtccgcatggatatgtcttacactgaatttctcttttaataggtgggattgtggtatgtttatgcttaagttcattgatttccacagtagaggtattggcctatgctttactcaggtgagtatagtacaaaatactggattcaagttattatatatgcttaatctgttcactcattgatttgctgtttgcactattaagtcaatctcaaatgaagagtcttaacctgctaagatgaagcacaatctctctttcatacatctaaagtggagtaacatgtaccttgtacttaattgtgtttggtgtcatctaaatcaatcactatttgcaggaacatatggattactttaggaaacgaacagcgaaggagatactgagattgagagctgactgaaaagatgtcctttcttgttcacacattcttgggcattttgtcaaggtaggtattcttgcgacctattggaaaagacataatgatgtatttattttctactagggtgttttgttgattacaagtggctggaacgattttgcataattctttaccccttcattttctaggatcttattttgatagaatagggagagattgaaatgagaccccaagggaacaagacagagctaacagaagtcggaatgtaagagcttagatgattagaacaagaatgcttaacccataccatgtatagccgccaattagaactataaagagataaaagggggtatgaatccacattttgttattctttaaaatattctaagtgaactgttatgaaatagatatgaggtgatttacatcaattatattttgtgaaaa More
CDS seq		atgtccccctccgccacctcgccgccgaatcgcccacaccgcaagcgccgcgccggtgccggtggcggtggcgctgacgacggctcgacccgccgccgcggccgcagcgctgtcctcctcggccccacccacttccccgccgttcgctccttcggcctccgcctcgccctcgtcgtcgccccagccccacgtcaccgccgcaagcagcgcccgctccactacgcctgccgccccacctcccttccctgtcgccgccgccgtcgcctccgcagtatcatctccctcctccacctccccatcctccgcccgttctacctccgctacatcctcgcggcagccgcatcaggcccctgccgctgccgccggaaggaatccctggtaggcatgggaaactacatctcgcgggtgctccggaagagctctagtgaccgtggtaaggcgccgccagccgacgatacagccaagcaggatctatgtgaagtttttacacctctgacaaatgaagaagaaagtgaagtaaacaacattttgtatggcagtgatcaaagtaagaaaataatagtgatgcatggaccttccaatattgatattactaaagagaaaatctggtgcttgagaacttgtaattggttaaatgatgaggtcattaatttgtaccttgaattgttaaaggagagggcgcaaagagaaccaaaaagatttttgaaatgccacttcttcaatacattcttttataagaagcttgcttatggaaaaactggttatgactatcaatctgtaagaagatggacaaccctcaatagattgggctatgggcttgttgagtgtgagaaaatctttattccaatacatagaaatgtgcattggtgccttgcgataataaacatgaaggataaaacttttcaataccttgattcttttggcggcatggaccatgctgtgctgagaatactggctagatatatcagggatgaattgaatgacaagagtaacatacaggtagacaccagttcatggctgaaaatatcatcagattcttgtcctttgcagcagaatgggtgggattgtggtatgtttatgcttaagttcattgatttccacagtagaggtattggcctatgctttactcaggaacatatggattactttaggaaacgaacagcgaaggagatactgagattgagagctgactga More
Protein seq		MSPSATSPPNRPHRKRRAGAGGGGADDGSTRRRGRSAVLLGPTHFPAVRSFGLRLALVVAPAPRHRRKQRPLHYACRPTSLPCRRRRRLRSIISLLHLPILRPFYLRYILAAAASGPCRCRRKESLVGMGNYISRVLRKSSSDRGKAPPADDTAKQDLCEVFTPLTNEEESEVNNILYGSDQSKKIIVMHGPSNIDITKEKIWCLRTCNWLNDEVINLYLELLKERAQREPKRFLKCHFFNTFFYKKLAYGKTGYDYQSVRRWTTLNRLGYGLVECEKIFIPIHRNVHWCLAIINMKDKTFQYLDSFGGMDHAVLRILARYIRDELNDKSNIQVDTSSWLKISSDSCPLQQNGWDCGMFMLKFIDFHSRGIGLCFTQEHMDYFRKRTAKEILRLRAD
Function		Ubiquitin-like-specific protease 1A [UniProtKB/Swiss-Prot:Q8GYL3]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0021170	OsLima_03g0021170.01	Chr03	17987882	17991843	+	NAM
CDS seq	atgtccccctccgccacctcgccgccgaatcgcccacaccgcaagcgccgcgccggtgccggtggcggtggcgctgacgacggctcgacccgccgccgcggccgcagcgctgtcctcctcggccccacccacttccccgccgttcgctccttcggcctccgcctcgccctcgtcgtcgccccagccccacgtcaccgccgcaagcagcgcccgctccactacgcctgccgccccacctcccttccctgtcgccgccgccgtcgcctccgcagtatcatctccctcctccacctccccatcctccgcccgttctacctccgctacatcctcgcggcagccgcatcaggcccctgccgctgccgccggaaggaatccctggtaggcatgggaaactacatctcgcgggtgctccggaagagctctagtgaccgtggtaaggcgccgccagccgacgatacagccaagcaggatctatgtgaagtttttacacctctgacaaatgaagaagaaagtgaagtaaacaacattttgtatggcagtgatcaaagtaagaaaataatagtgatgcatggaccttccaatattgatattactaaagagaaaatctggtgcttgagaacttgtaattggttaaatgatgaggtcattaatttgtaccttgaattgttaaaggagagggcgcaaagagaaccaaaaagatttttgaaatgccacttcttcaatacattcttttataagaagcttgcttatggaaaaactggttatgactatcaatctgtaagaagatggacaaccctcaatagattgggctatgggcttgttgagtgtgagaaaatctttattccaatacatagaaatgtgcattggtgccttgcgataataaacatgaaggataaaacttttcaataccttgattcttttggcggcatggaccatgctgtgctgagaatactggctagatatatcagggatgaattgaatgacaagagtaacatacaggtagacaccagttcatggctgaaaatatcatcagattcttgtcctttgcagcagaatgggtgggattgtggtatgtttatgcttaagttcattgatttccacagtagaggtattggcctatgctttactcaggaacatatggattactttaggaaacgaacagcgaaggagatactgagattgagagctgactga More
Protein seq	MSPSATSPPNRPHRKRRAGAGGGGADDGSTRRRGRSAVLLGPTHFPAVRSFGLRLALVVAPAPRHRRKQRPLHYACRPTSLPCRRRRRLRSIISLLHLPILRPFYLRYILAAAASGPCRCRRKESLVGMGNYISRVLRKSSSDRGKAPPADDTAKQDLCEVFTPLTNEEESEVNNILYGSDQSKKIIVMHGPSNIDITKEKIWCLRTCNWLNDEVINLYLELLKERAQREPKRFLKCHFFNTFFYKKLAYGKTGYDYQSVRRWTTLNRLGYGLVECEKIFIPIHRNVHWCLAIINMKDKTFQYLDSFGGMDHAVLRILARYIRDELNDKSNIQVDTSSWLKISSDSCPLQQNGWDCGMFMLKFIDFHSRGIGLCFTQEHMDYFRKRTAKEILRLRAD More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0021170	OsLima_03g0021170.03	Chr03	17987882	17991826	+	NAM
CDS seq	atgtccccctccgccacctcgccgccgaatcgcccacaccgcaagcgccgcgccggtgccggtggcggtggcgctgacgacggctcgacccgccgccgcggccgcagcgctgtcctcctcggccccacccacttccccgccgttcgctccttcggcctccgcctcgccctcgtcgtcgccccagccccacgtcaccgccgcaagcagcgcccgctccactacgcctgccgccccacctcccttccctgtcgccgccgccgtcgcctccgcagtatcatctccctcctccacctccccatcctccgcccgttctacctccgctacatcctcgcggcagccgcatcaggcccctgccgctgccgccggaaggaatccctggtaggcatgggaaactacatctcgcgggtgctccggaagagctctagtgaccgtggtaaggcgccgccagccgacgatacagccaagcaggatctatgtgaagtttttacacctctgacaaatgaagaagaaagtgaagtaaacaacattttgtatggcagtgatcaaagtaagaaaataatagtgatgcatggaccttccaatattgatattactaaagagaaaatctggtgcttgagaacttgtaattggttaaatgatgaggtcattaatttgtaccttgaattgttaaaggagagggcgcaaagagaaccaaaaagatttttgaaatgccacttcttcaatacattcttttataagaagcttgcttatggaaaaactggttatgactatcaatctgtaagaagatggacaaccctcaatagattgggctatgggcttgttgagtgtgagaaagtaatgttactgttattatttttttaa More
Protein seq	MSPSATSPPNRPHRKRRAGAGGGGADDGSTRRRGRSAVLLGPTHFPAVRSFGLRLALVVAPAPRHRRKQRPLHYACRPTSLPCRRRRRLRSIISLLHLPILRPFYLRYILAAAASGPCRCRRKESLVGMGNYISRVLRKSSSDRGKAPPADDTAKQDLCEVFTPLTNEEESEVNNILYGSDQSKKIIVMHGPSNIDITKEKIWCLRTCNWLNDEVINLYLELLKERAQREPKRFLKCHFFNTFFYKKLAYGKTGYDYQSVRRWTTLNRLGYGLVECEKVMLLLLFF More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0021170	OsLima_03g0021170.02	Chr03	17987882	17991826	+	NAM
CDS seq	atgagatttattgtgcagatctttattccaatacatagaaatgtgcattggtgccttgcgataataaacatgaaggataaaacttttcaataccttgattcttttggcggcatggaccatgctgtgctgagaatactggctagatatatcagggatgaattgaatgacaagagtaacatacaggtagacaccagttcatggctgaaaatatcatcagattcttgtcctttgcagcagaatgggtgggattgtggtatgtttatgcttaagttcattgatttccacagtagaggtattggcctatgctttactcaggaacatatggattactttaggaaacgaacagcgaaggagatactgagattgagagctgactga More
Protein seq	MRFIVQIFIPIHRNVHWCLAIINMKDKTFQYLDSFGGMDHAVLRILARYIRDELNDKSNIQVDTSSWLKISSDSCPLQQNGWDCGMFMLKFIDFHSRGIGLCFTQEHMDYFRKRTAKEILRLRAD

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
RI	Chr03	17989987	17990278	+	OsLima_03g0021170.02,OsLima_03g0021170.03	OsLima_03g0021170.01,OsLima_03g0021170.03,OsLima_03g0021170.02	All
A5	Chr03	17989174	17989319	+	OsLima_03g0021170.02	OsLima_03g0021170.01,OsLima_03g0021170.03,OsLima_03g0021170.02	All

Expression

	Leaf	Root	Panicle
FPKM	0.0	0.066326	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_03g0410100	RBH	1.135063	0.718530	0.000000
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os03g29630	RBH	0.865292	0.433060	0.000000
Nipponbare \| IRGSP 1.0 \| RAP-db	Os03g0410100	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_03g0021460	RBH	0.255854	0.0	0.394851
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_03g0021280	RBH	0.000000	0.0	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_03g0021340	RBH	0.378515	0.000000	1.103502
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_03g0021340	RBH	0.000000	0.032215	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_03g0021180	RBH	1.472447	0.000000	1.715243
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_03G0278700	RBH	0.4006	0.77058	0.534492
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_03g0020910	RBH	0.106736	0.061434	0.133506
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_03G0283000	RBH	0.427924	1.1235085	1.776112
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_03g0021200	RBH	0.0	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_03g0021280	RBH	0.0	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_03g0021140	RBH	0.000000	0.262777	0.000000
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_03g0021020	RBH	0.000000	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_03G020980	RBH	0.000000	0.0	0.193797
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_03g0020860	RBH	0.227023	0.0	0.909672

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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