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_02g0004360		OGI:02001240 \| 16/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr02:3086824-3091694		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		ttagccataatatctggacaagactagctggtcatacaacactccaattccaaagaacacaccaaaggcaattgcggagattgttttgctgctgcattgttgatcttcagagatagttgggatggtgtgagctacctctactgaaccacaaggagccaacatagatccacatagctttggattcccggcaaaactggagcttgagaacgtgttcatctggcctcctgtcggaataggtccttccagatcattgtcagaaatgttgaactttgagagaaagttgagcttgtttagtgcttcaggtattgggccagtgaggtagtttctggacaagtccagcacctgcaagtttgtgagattgcagatagatggtgggatctctccttgtaattggttagagctgaaatcaagatgagtaagagctttcagctcaccaatcttgggtggaatcacactggtaaagctgttagcactaagattcaagagtgcagggaaagatgtgactgcacggtattgtcgcgatagagtggttacatacacaggtagatcaaatagtattgttcgatgagctttgtaatcatctgattttagcatgggtatctctatcaaggtggctggtatttgtcctgtaaggctgttgtttgatacatccaaatagaagaggttgttgaaggagttgagccaactcggcattggcccagtaagttgattgttggataaatctagtacctccaaattttttagctttgatagccaaagaggtatgtttccgatcaatgagcaacgataaattgagagatgtcgaatactctctaaactttcaattgtctcatcttgtggtataacctcaccccagaaattctccccaataaacagggtagtgaggttccgggagctcttgaaagcatggagtgtctttgcaatatcactgaaagagttttcagtaattgacaggaaagaaaggtacttgagatcacctatttttgatgagatctcaccatgaatttggttggacgatagccgcagcgcagtcaaattgttgcatgagtatatgctttctggtattacaccactgaagtcattatgcaggagatccagggctctcagattgtgtagggaagagaagtcaacactaccaaggtctccactgaagctgttcatcttcagatcaatggttgtgagacgtgtgcagtttccaagactcgatggtagattccctgacatgttgttgttgctcaacctaatcacttccagcttcttgagctgaccaatggactccggaatctcaccatgtaaattgttggtcgagacgttgagcacctgcagctgcagaggatgcttcaagccagtgatcaacattggcagtggcggtagcactccgtcgaggctgttgaagctgacgtcaaggacaaggaggctcgcagtgtacatgagctccggtggaaggtcgccggagagagcattgtgagagaggttgagacgtgtcaggccggtcagaccggcgagggacgacggtgagatgtggccatggatccctcgagacggcagggaaacctcggtgaccgtgccttcgccgtcacagacgacgccctcccaggcgtggcagcagtcgacgtccggtcgccacgacgcagcgaggccgccgtcgtgtgacagcccggcaaggaagcggaggagggagctcctgtcctcctccgtgcaggagatggccggagaggcgaagagtatcatcatcagcagtatctgaattaaactgctggatgatctgttgctgtaggaagaattaggtattgttggattgttcatggtcagtatctgaattgaactggtttggaaactgatgggctagtagtagtgagcctgatatatgccgaaccacacggctcctgagcattatattatattgtcgaagcatcaaagagttaaatatattataagctgatggagtgttgacatatgagttcactttgctgctgctaccctacctaagctcactactagctgcttggtgccatgcttaggtttggaagttcagtccaactattgccgttttctcttaccaatcttgtgttttggctcatgatgctttgacaggagagcttccacttaaattggatttttcctcgtacagctcgctggccacttgactagaatttgttaacttctccattcgtttactcagagtcatagtccaggtctccggccactactgatctagagggagatatggcgtacactatgtgcttgtgatcttttatcacttcaagcagctgcattttgaattcgtccccaataactcacttgtgacttttgactgctcttggcttgtgataatcttttgcagcaatcggaacatcaacctacattggttacatacttcttttaaaaaaaacttgaaatggtttggctacactgctaaaagtctaactgatttaaagtttaacatactccatctattttcatctgtttcaggttataagatgttttgactttagttaaagtcaaactgctttaagtttgattaagtttataaacaaatataataatatttatattaccaaattagtttttattaaattaataattaaatatatttttataataaatttatcttgggtcgaaaatattattattttttctataaacttagttaaacttgaagcggtttgattttgaccaaaatcaaaaacatcttataatctgaaattataaacggaaggagtagctgcttgctattccgagggtttttcctctctcatttcctttttgccgacatgatgtgagtctcagattgtttgacattataccctaattaaaagaaagtttgtttgacattgacaatagagcttgctcttgaattggaccaagtaaatttcttcaccatacacctggcctctggaaacacgcttttatattagggtaatttggaacatgatggtgacgcttcaccataaattataacacggcttgttaaattctggttcttttaccatgatggtgacgtacactgccggcccgctgctaataatctcattactctctctatcatctgcattttcataatccatccctagcaatcaatttgctctaattgcattactttttttttctccagagagagatggttggtttggttatgaaagagtaaactgatgcaggtatataacatgtttgcgtgcatggttgggctactgaaattcgtttgcgtttgcatggttgaacaaactttgtgccttcaatgtcaatttggaagactacaagagttctttgggagaactcaattccagcacaagccaatttggaagtctttcaccctcctcaatgtcgttacttcctctggctggtcactctcaaccgatgctagacggcagaccgccttcgaagccgcggcctatcgcacccggatcgctgccccctctatgatcaatgcgacgaaacgattgatcatctcttggtcgcatgcccggagtaccgacaactttggtggattgctcttagtgctattggtcatcccgaatgtctaccactcaacgagcagtccttccatgcctagttgtgtgacagtcgcaaaaggatgattaaggatcatcgccgagggttcgacacaattgcgacactggtagcgtggataatctggaaggaaagaaacaattgggtcttcaaccagaagagcagaccttggatggaggtagctagagctatgttgggggaagcggacctttggcagatggctagatcaaccataccggtcatgacagctcgttcgtttgttcttgggtcgccgaatcattcgggagattaggcttttgcttttctccccccccccctctcctgtaccctgtcccattctttttatttttccggcccgccctgtacatatatttattcatcttaatacaaaaatgcgtgtctcgcgtattcccaaaactttatgccttcaagtttttatatatcccttcgttgttgttttctgcgaaatttcaacaaaagttgatgtgaaaattctatgctaattacagtcttgcatacgcatattccaaaattactctgtctaaagcatgtcagattccgcgctttgttccggacctatatatttatacccttctttcagtctttgaggccactactaaagaaagtacttatataagcaggcttgataaattgtcacataaaacttatatttagatggtgaagagaatagagtgaataattaagggcacaaaatttatagctagctataggggaagacactatataaatgagagatgaattggatattaatgatgtaagagtagtatatatttataagtaactattctagagtaaactattagactatttggaggaatataagattttgataagcaacctgttaatatccagcttctgagaatttagatagctgaaaaactcagtttttaacttttaattcattttctagattttacaattataaattcttaggatctggcttagattctacaactattagagcaaggttaatagtgtcacccgttgcttactcttgtagccttccccctcagttatagacgtcaatggaatagtttcttcataagctattgcacgacacattctccaatacaaagcatactttattcccctttctctctaagttgttcacatttctctttcttctttcacttgctagtgttttcaccatgagcttagctcctagcaacaaattaaaacattgcaatagaactcttgcataccgagcgtggtatagctaagcgggagatgacacggctgagctcgacagcctccttcggcgctgtcattgagctcgacagcgagtaggctgagccggttgtttctatgctcaagagcacctcctccgatgctattgccat More
CDS seq		atggcaatagcatcggaggaggtgctcttgagcatagaaacaaccggctcagcctactcgctgtcgagctcaatgacagcgccgaaggaggctgtcgagctcagccgtgtcatctcccgcttagctataccacgctcggttgatgttccgattgctgcaaaagattatcacaagccaagagcagtcaaaagtcacaacaacagatcatccagcagtttaattcagatactgctgatgatgatactcttcgcctctccggccatctcctgcacggaggaggacaggagctccctcctccgcttccttgccgggctgtcacacgacggcggcctcgctgcgtcgtggcgaccggacgtcgactgctgccacgcctgggagggcgtcgtctgtgacggcgaaggcacggtcaccgaggtttccctgccgtctcgagggatccatggccacatctcaccgtcgtccctcgccggtctgaccggcctgacacgtctcaacctctctcacaatgctctctccggcgaccttccaccggagctcatgtacactgcgagcctccttgtccttgacgtcagcttcaacagcctcgacggagtgctaccgccactgccaatgttgatcactggcttgaagcatcctctgcagctgcaggtgctcaacgtctcgaccaacaatttacatggtgagattccggagtccattggtcagctcaagaagctggaagtgattaggttgagcaacaacaacatgtcagggaatctaccatcgagtcttggaaactgcacacgtctcacaaccattgatctgaagatgaacagcttcagtggagaccttggtagtgttgacttctcttccctacacaatctgagagccctggatctcctgcataatgacttcagtggtgtaataccagaaagcatatactcatgcaacaatttgactgcgctgcggctatcgtccaaccaaattcatggtgagatctcatcaaaaataggtgatctcaagtacctttctttcctgtcaattactgaaaactctttcagtgatattgcaaagacactccatgctttcaagagctcccggaacctcactaccctgtttattggggagaatttctggggtgaggttataccacaagatgagacaattgaaagtttagagagtattcgacatctctcaatttatcgttgctcattgatcggaaacatacctctttggctatcaaagctaaaaaatttggaggtactagatttatccaacaatcaacttactgggccaatgccgagttggctcaactccttcaacaacctcttctatttggatgtatcaaacaacagccttacaggacaaataccagccaccttgatagagatacccatgctaaaatcagatgattacaaagctcatcgaacaatactatttgatctacctgtgtatgtaaccactctatcgcgacaataccgtgcagtcacatctttccctgcactcttgaatcttagtgctaacagctttaccagtgtgattccacccaagattggtgagctgaaagctcttactcatcttgatttcagctctaaccaattacaaggagagatcccaccatctatctgcaatctcacaaacttgcaggtgctggacttgtccagaaactacctcactggcccaatacctgaagcactaaacaagctcaactttctctcaaagttcaacatttctgacaatgatctggaaggacctattccgacaggaggccagatgaacacgttctcaagctccagttttgccgggaatccaaagctatgtggatctatgttggctccttgtggttcagtagaggtagctcacaccatcccaactatctctgaagatcaacaatgcagcagcaaaacaatctccgcaattgcctttggtgtgttctttggaattggagtgttgtatgaccagctagtcttgtccagatattatggctaa More
Protein seq		MAIASEEVLLSIETTGSAYSLSSSMTAPKEAVELSRVISRLAIPRSVDVPIAAKDYHKPRAVKSHNNRSSSSLIQILLMMILFASPAISCTEEDRSSLLRFLAGLSHDGGLAASWRPDVDCCHAWEGVVCDGEGTVTEVSLPSRGIHGHISPSSLAGLTGLTRLNLSHNALSGDLPPELMYTASLLVLDVSFNSLDGVLPPLPMLITGLKHPLQLQVLNVSTNNLHGEIPESIGQLKKLEVIRLSNNNMSGNLPSSLGNCTRLTTIDLKMNSFSGDLGSVDFSSLHNLRALDLLHNDFSGVIPESIYSCNNLTALRLSSNQIHGEISSKIGDLKYLSFLSITENSFSDIAKTLHAFKSSRNLTTLFIGENFWGEVIPQDETIESLESIRHLSIYRCSLIGNIPLWLSKLKNLEVLDLSNNQLTGPMPSWLNSFNNLFYLDVSNNSLTGQIPATLIEIPMLKSDDYKAHRTILFDLPVYVTTLSRQYRAVTSFPALLNLSANSFTSVIPPKIGELKALTHLDFSSNQLQGEIPPSICNLTNLQVLDLSRNYLTGPIPEALNKLNFLSKFNISDNDLEGPIPTGGQMNTFSSSSFAGNPKLCGSMLAPCGSVEVAHTIPTISEDQQCSSKTISAIAFGVFFGIGVLYDQLVLSRYYG
Function		Tyrosine-sulfated glycopeptide receptor 1 [UniProtKB/Swiss-Prot:Q9C7S5]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_02g0004360	OsLima_02g0004360.01	Chr02	3086824	3091694	-	NAM
CDS seq	atggcaatagcatcggaggaggtgctcttgagcatagaaacaaccggctcagcctactcgctgtcgagctcaatgacagcgccgaaggaggctgtcgagctcagccgtgtcatctcccgcttagctataccacgctcggttgatgttccgattgctgcaaaagattatcacaagccaagagcagtcaaaagtcacaacaacagatcatccagcagtttaattcagatactgctgatgatgatactcttcgcctctccggccatctcctgcacggaggaggacaggagctccctcctccgcttccttgccgggctgtcacacgacggcggcctcgctgcgtcgtggcgaccggacgtcgactgctgccacgcctgggagggcgtcgtctgtgacggcgaaggcacggtcaccgaggtttccctgccgtctcgagggatccatggccacatctcaccgtcgtccctcgccggtctgaccggcctgacacgtctcaacctctctcacaatgctctctccggcgaccttccaccggagctcatgtacactgcgagcctccttgtccttgacgtcagcttcaacagcctcgacggagtgctaccgccactgccaatgttgatcactggcttgaagcatcctctgcagctgcaggtgctcaacgtctcgaccaacaatttacatggtgagattccggagtccattggtcagctcaagaagctggaagtgattaggttgagcaacaacaacatgtcagggaatctaccatcgagtcttggaaactgcacacgtctcacaaccattgatctgaagatgaacagcttcagtggagaccttggtagtgttgacttctcttccctacacaatctgagagccctggatctcctgcataatgacttcagtggtgtaataccagaaagcatatactcatgcaacaatttgactgcgctgcggctatcgtccaaccaaattcatggtgagatctcatcaaaaataggtgatctcaagtacctttctttcctgtcaattactgaaaactctttcagtgatattgcaaagacactccatgctttcaagagctcccggaacctcactaccctgtttattggggagaatttctggggtgaggttataccacaagatgagacaattgaaagtttagagagtattcgacatctctcaatttatcgttgctcattgatcggaaacatacctctttggctatcaaagctaaaaaatttggaggtactagatttatccaacaatcaacttactgggccaatgccgagttggctcaactccttcaacaacctcttctatttggatgtatcaaacaacagccttacaggacaaataccagccaccttgatagagatacccatgctaaaatcagatgattacaaagctcatcgaacaatactatttgatctacctgtgtatgtaaccactctatcgcgacaataccgtgcagtcacatctttccctgcactcttgaatcttagtgctaacagctttaccagtgtgattccacccaagattggtgagctgaaagctcttactcatcttgatttcagctctaaccaattacaaggagagatcccaccatctatctgcaatctcacaaacttgcaggtgctggacttgtccagaaactacctcactggcccaatacctgaagcactaaacaagctcaactttctctcaaagttcaacatttctgacaatgatctggaaggacctattccgacaggaggccagatgaacacgttctcaagctccagttttgccgggaatccaaagctatgtggatctatgttggctccttgtggttcagtagaggtagctcacaccatcccaactatctctgaagatcaacaatgcagcagcaaaacaatctccgcaattgcctttggtgtgttctttggaattggagtgttgtatgaccagctagtcttgtccagatattatggctaa More
Protein seq	MAIASEEVLLSIETTGSAYSLSSSMTAPKEAVELSRVISRLAIPRSVDVPIAAKDYHKPRAVKSHNNRSSSSLIQILLMMILFASPAISCTEEDRSSLLRFLAGLSHDGGLAASWRPDVDCCHAWEGVVCDGEGTVTEVSLPSRGIHGHISPSSLAGLTGLTRLNLSHNALSGDLPPELMYTASLLVLDVSFNSLDGVLPPLPMLITGLKHPLQLQVLNVSTNNLHGEIPESIGQLKKLEVIRLSNNNMSGNLPSSLGNCTRLTTIDLKMNSFSGDLGSVDFSSLHNLRALDLLHNDFSGVIPESIYSCNNLTALRLSSNQIHGEISSKIGDLKYLSFLSITENSFSDIAKTLHAFKSSRNLTTLFIGENFWGEVIPQDETIESLESIRHLSIYRCSLIGNIPLWLSKLKNLEVLDLSNNQLTGPMPSWLNSFNNLFYLDVSNNSLTGQIPATLIEIPMLKSDDYKAHRTILFDLPVYVTTLSRQYRAVTSFPALLNLSANSFTSVIPPKIGELKALTHLDFSSNQLQGEIPPSICNLTNLQVLDLSRNYLTGPIPEALNKLNFLSKFNISDNDLEGPIPTGGQMNTFSSSSFAGNPKLCGSMLAPCGSVEVAHTIPTISEDQQCSSKTISAIAFGVFFGIGVLYDQLVLSRYYG More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.0	0.0	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_02g0155700	SBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os02g06130	SBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os02g0155700	SBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_02g0004270	SBH	0.000000	0.000000	0.509504
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_02g0004510	SBH	0.087645	0.000000	0.391188
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_02g0004360	SBH	0.038443	0.407024	0.900679
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_02g0004020	SBH	0.031011	0.040793	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_02g0004230	SBH	1.051280	0.000000	0.000000
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_02G0051700	SBH	0.0241275	0.069187	0.0711565
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_02g0004230	SBH	0.101042	0.0	0.119829
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_02G0054000	SBH	0.3132295	0.1186905	0.2864165
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_02g0004550	SBH	0.022579	0.127643	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_02g0004140	RBH	0.000000	0.691538	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_02g0004420	SBH	0.000000	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_02g0004370	RBH	0.114374	0.000000	0.000000
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_02g0004290	SBH	0.032945	0.534010	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_02G004060	RBH	0.292437	2.052631	0.572981
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_02g0004010	SBH	0.630622	3.130005	0.941510

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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