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_07g0025490		OGI:07075170 \| 16/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr07:28207497-28210812		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		gagatgagaatacacttgccttttgttatttacagttttgactgatcaattgaatagattatttctgaatttacaattagattcatcgcatatcccaacatacaaccaatcacaggcatttaccattttcagtctgtcctgtggtcatttgttaactgtcttgcagagcctgcatgatctccatggcatcatctacaagtgaggccagagttgagctgtgcctgctcagcccaatgctgccagagaacatgttgaagctctcgagctcggacgtcgacctgacgacgctcctgagctccttctccagctccatgctcctgaagaaggggacgagctcggcgtcgcctctcatcatggcgatggcgagctcgatgacgaaccttctcatcctcggaaccttcaccctgggtgtcctgtgctctttcagaatctccactagcctccttgcaatgtctgtatctggtacacctgcctttccaaagatttccttgtgaaattcaggtgttgcaagccttgtaatctgtattgccaatcctatagacacctcaagcaagctgctcttctcaaccataattgctttgaacacctgtgaaatcatgtagcagacatcattcatcaaatcatagcaacgatgtctactgaagaatgaaataagtgatcttgttctagagaatctattctatgtccatgagtttactctagttaaatgttttttttattggtttctttgatttgtttcaaacgaacatcaacacaagaattctctcatggttgcagtgacatgagtagcactttatggtcctgagttcaagtctctaaaggagcgaatttcagtttgggttatttgagggctaaattccttgtttgatgggttaagttcccaattaaaaaggctatatatatccggttggatgtagaggctacggccttgtttagttccaaactttttcttcaaactttcaactttttcatcatattaaaacttttctacacacataaactttcaacttttccatcacattgttccaatttcaaccaaacttccaattttaacgtgaactaaacacagcctaggtaaaaattacccttctctaaaaaaaaagaattctcatccttttttggttggtttttgagaactttctattgggacagctaagttccctattaaaaaggctatatatatccggttagatgtagaggctaggtaaaaattacccttgtaaaaaaagaattctctcatattttttggttggtttttgagaacttactattgggacagctgcagtgaggctgctgagctgcaagaagtggtcgctcctgctgtacctgcacaggttcagtaggattctcgatgacgtgatctgcagcccggggtggtgcagcgtcatcaccagcctctcgacgacggcggcttcccggagtatccggtcgcagttggcggcgctctcgagggcgagcagcgccaccacctcgccggcctgcagcctgatgtgcgccgccccctgcgccgcgtaggcgaccgccggagccgactccggcgagccggcgaacatgtccagcagatgcgcgatcatgtcgcccgtgcagccgatcttctccttggcatcgccgtcgatggcgaggtcggcgaggacgccgatcgccgtcagctgcatcttgccgtggcgctcgccgccgtgctggagcaccttgcggatgttgccgaggacgaacacgttgtcggagatctccctcctgatcgcctcgccggtgtgccccggcgtgctcgagaggttcttcaccacctgcagcgaccggagcaccgtcttcgccggcaggctcccctcgccgccggcgccgatctgcagcgccgccctgctcgtccgggtgaagtgtatgatcctggagaggacgccccttgtgctcgagatcttcgccgcgttaccgtgctcgcgcgccagcttcttcatgatgtggagccccatctcgttcatggcgaggtcgccggcggcggcgtcggtggtgggggtctcgagtaaggtggagatggactcgatggcgccggggatggtggcgacgcggatgaggttgcggcgcttgccagcgaggcggaggacgacctcggcggcgagcgacctgacgcggcgcttgctggggctcttccagctcaccatctccaccagccgctcgacggtggccgccgacgtgccgatcttgcgcaccgcccgcctcgccgagtcgcggttggcgatggagccccggaggatgtgcgcgccgatgagctgctcgtcgccggagtccgatgagaggagctcgacggcgaaggagacgaggtccatccgcgtggcgtcgaggatgccgccctcgaccgacctcgagaaggcacggtagaagaaccgcttgatcggcaccacgccggcgtcgccgaggtcgcactcgccgctcaccgcctcgaccaggcgccgatagctgagcacccactcccagtacgcgcgctccaccaggaagatcaccgcctccgacagcgcgagcacgtagaacagcatcagcgcgtagtacgcgttcttgttgccgccgccgccattgtcgccggcgaagcggagcgtggcgaggcgcagcagcgacagcgcgacgcacgccgacgccgagaggagctggagccagtagaggacgtagctcacgttcctcgcctcgacgagccagccgccgaggggcaggaggtggatgggcgaggccgccgccgccgccttgtgcggcggcggcgggtcgtcgtcgtcgtctccggcggcggcggcggcggcgtccgggaggtgcatcggctgctcctgcagatcgagctcgttgctccggctgaacaccctcgtcccctcgacgaggaggatggcggtgacgagccagaagtcccgggcgtcgaggtcggcggcgaacccgccgaggatgaccaccgtcgcccacacgaagcagacggcgccgacgtgcgacgcggccttctcgagcaccgcgacgtggagcgcgaacgccgtcaccttgcgctccggcaccacgtcgtcgacgccgccgccgtcgtcggaggcggtggcggcgtgcatggacgagacctggtgctccaccggccgccgctgcggctcgtacgacgacgccgtcgagtcgccggtgtgcgttctccggtgcctcgccgtcgccgtcgccgtcggcggcggcaacggcggcggctgcactagtatttgcatgggaatgtccacgccgccggcgccggcgccgccgccatgatcagccgtagtgtcgatggccattagccttgtattcccgagtgcgtgcacaagtgcacttggggttt More
CDS seq		atggccatcgacactacggctgatcatggcggcggcgccggcgccggcggcgtggacattcccatgcaaatactagtgcagccgccgccgttgccgccgccgacggcgacggcgacggcgaggcaccggagaacgcacaccggcgactcgacggcgtcgtcgtacgagccgcagcggcggccggtggagcaccaggtctcgtccatgcacgccgccaccgcctccgacgacggcggcggcgtcgacgacgtggtgccggagcgcaaggtgacggcgttcgcgctccacgtcgcggtgctcgagaaggccgcgtcgcacgtcggcgccgtctgcttcgtgtgggcgacggtggtcatcctcggcgggttcgccgccgacctcgacgcccgggacttctggctcgtcaccgccatcctcctcgtcgaggggacgagggtgttcagccggagcaacgagctcgatctgcaggagcagccgatgcacctcccggacgccgccgccgccgccgccggagacgacgacgacgacccgccgccgccgcacaaggcggcggcggcggcctcgcccatccacctcctgcccctcggcggctggctcgtcgaggcgaggaacgtgagctacgtcctctactggctccagctcctctcggcgtcggcgtgcgtcgcgctgtcgctgctgcgcctcgccacgctccgcttcgccggcgacaatggcggcggcggcaacaagaacgcgtactacgcgctgatgctgttctacgtgctcgcgctgtcggaggcggtgatcttcctggtggagcgcgcgtactgggagtgggtgctcagctatcggcgcctggtcgaggcggtgagcggcgagtgcgacctcggcgacgccggcgtggtgccgatcaagcggttcttctaccgtgccttctcgaggtcggtcgagggcggcatcctcgacgccacgcggatggacctcgtctccttcgccgtcgagctcctctcatcggactccggcgacgagcagctcatcggcgcgcacatcctccggggctccatcgccaaccgcgactcggcgaggcgggcggtgcgcaagatcggcacgtcggcggccaccgtcgagcggctggtggagatggtgagctggaagagccccagcaagcgccgcgtcaggtcgctcgccgccgaggtcgtcctccgcctcgctggcaagcgccgcaacctcatccgcgtcgccaccatccccggcgccatcgagtccatctccaccttactcgagacccccaccaccgacgccgccgccggcgacctcgccatgaacgagatggggctccacatcatgaagaagctggcgcgcgagcacggtaacgcggcgaagatctcgagcacaaggggcgtcctctccaggatcatacacttcacccggacgagcagggcggcgctgcagatcggcgccggcggcgaggggagcctgccggcgaagacggtgctccggtcgctgcaggtggtgaagaacctctcgagcacgccggggcacaccggcgaggcgatcaggagggagatctccgacaacgtgttcgtcctcggcaacatccgcaaggtgctccagcacggcggcgagcgccacggcaagatgcagctgacggcgatcggcgtcctcgccgacctcgccatcgacggcgatgccaaggagaagatcggctgcacgggcgacatgatcgcgcatctgctggacatgttcgccggctcgccggagtcggctccggcggtcgcctacgcggcgcagggggcggcgcacatcaggctgcaggccggcgaggtggtggcgctgctcgccctcgagagcgccgccaactgcgaccggatactccgggaagccgccgtcgtcgagaggctggtgatgacgctgcaccaccccgggctgcagatcacgtcatcgagaatcctactgaacctgtgcaggtacagcaggagcgaccacttcttgcagctcagcagcctcactgcagctgtcccaatagtgttcaaagcaattatggttgagaagagcagcttgcttgaggtgtctataggattggcaatacagattacaaggcttgcaacacctgaatttcacaaggaaatctttggaaaggcaggtgtaccagatacagacattgcaaggaggctagtggagattctgaaagagcacaggacacccagggtgaaggttccgaggatgagaaggttcgtcatcgagctcgccatcgccatgatgagaggcgacgccgagctcgtccccttcttcaggagcatggagctggagaaggagctcaggagcgtcgtcaggtcgacgtccgagctcgagagcttcaacatgttctctggcagcattgggctgagcaggcacagctcaactctggcctcacttgtagatgatgccatggagatcatgcaggctctgcaagacagttaa More
Protein seq		MAIDTTADHGGGAGAGGVDIPMQILVQPPPLPPPTATATARHRRTHTGDSTASSYEPQRRPVEHQVSSMHAATASDDGGGVDDVVPERKVTAFALHVAVLEKAASHVGAVCFVWATVVILGGFAADLDARDFWLVTAILLVEGTRVFSRSNELDLQEQPMHLPDAAAAAAGDDDDDPPPPHKAAAAASPIHLLPLGGWLVEARNVSYVLYWLQLLSASACVALSLLRLATLRFAGDNGGGGNKNAYYALMLFYVLALSEAVIFLVERAYWEWVLSYRRLVEAVSGECDLGDAGVVPIKRFFYRAFSRSVEGGILDATRMDLVSFAVELLSSDSGDEQLIGAHILRGSIANRDSARRAVRKIGTSAATVERLVEMVSWKSPSKRRVRSLAAEVVLRLAGKRRNLIRVATIPGAIESISTLLETPTTDAAAGDLAMNEMGLHIMKKLAREHGNAAKISSTRGVLSRIIHFTRTSRAALQIGAGGEGSLPAKTVLRSLQVVKNLSSTPGHTGEAIRREISDNVFVLGNIRKVLQHGGERHGKMQLTAIGVLADLAIDGDAKEKIGCTGDMIAHLLDMFAGSPESAPAVAYAAQGAAHIRLQAGEVVALLALESAANCDRILREAAVVERLVMTLHHPGLQITSSRILLNLCRYSRSDHFLQLSSLTAAVPIVFKAIMVEKSSLLEVSIGLAIQITRLATPEFHKEIFGKAGVPDTDIARRLVEILKEHRTPRVKVPRMRRFVIELAIAMMRGDAELVPFFRSMELEKELRSVVRSTSELESFNMFSGSIGLSRHSSTLASLVDDAMEIMQALQDS
Function		-

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_07g0025490	OsLima_07g0025490.01	Chr07	28207497	28210812	-	NAM
CDS seq	atggccatcgacactacggctgatcatggcggcggcgccggcgccggcggcgtggacattcccatgcaaatactagtgcagccgccgccgttgccgccgccgacggcgacggcgacggcgaggcaccggagaacgcacaccggcgactcgacggcgtcgtcgtacgagccgcagcggcggccggtggagcaccaggtctcgtccatgcacgccgccaccgcctccgacgacggcggcggcgtcgacgacgtggtgccggagcgcaaggtgacggcgttcgcgctccacgtcgcggtgctcgagaaggccgcgtcgcacgtcggcgccgtctgcttcgtgtgggcgacggtggtcatcctcggcgggttcgccgccgacctcgacgcccgggacttctggctcgtcaccgccatcctcctcgtcgaggggacgagggtgttcagccggagcaacgagctcgatctgcaggagcagccgatgcacctcccggacgccgccgccgccgccgccggagacgacgacgacgacccgccgccgccgcacaaggcggcggcggcggcctcgcccatccacctcctgcccctcggcggctggctcgtcgaggcgaggaacgtgagctacgtcctctactggctccagctcctctcggcgtcggcgtgcgtcgcgctgtcgctgctgcgcctcgccacgctccgcttcgccggcgacaatggcggcggcggcaacaagaacgcgtactacgcgctgatgctgttctacgtgctcgcgctgtcggaggcggtgatcttcctggtggagcgcgcgtactgggagtgggtgctcagctatcggcgcctggtcgaggcggtgagcggcgagtgcgacctcggcgacgccggcgtggtgccgatcaagcggttcttctaccgtgccttctcgaggtcggtcgagggcggcatcctcgacgccacgcggatggacctcgtctccttcgccgtcgagctcctctcatcggactccggcgacgagcagctcatcggcgcgcacatcctccggggctccatcgccaaccgcgactcggcgaggcgggcggtgcgcaagatcggcacgtcggcggccaccgtcgagcggctggtggagatggtgagctggaagagccccagcaagcgccgcgtcaggtcgctcgccgccgaggtcgtcctccgcctcgctggcaagcgccgcaacctcatccgcgtcgccaccatccccggcgccatcgagtccatctccaccttactcgagacccccaccaccgacgccgccgccggcgacctcgccatgaacgagatggggctccacatcatgaagaagctggcgcgcgagcacggtaacgcggcgaagatctcgagcacaaggggcgtcctctccaggatcatacacttcacccggacgagcagggcggcgctgcagatcggcgccggcggcgaggggagcctgccggcgaagacggtgctccggtcgctgcaggtggtgaagaacctctcgagcacgccggggcacaccggcgaggcgatcaggagggagatctccgacaacgtgttcgtcctcggcaacatccgcaaggtgctccagcacggcggcgagcgccacggcaagatgcagctgacggcgatcggcgtcctcgccgacctcgccatcgacggcgatgccaaggagaagatcggctgcacgggcgacatgatcgcgcatctgctggacatgttcgccggctcgccggagtcggctccggcggtcgcctacgcggcgcagggggcggcgcacatcaggctgcaggccggcgaggtggtggcgctgctcgccctcgagagcgccgccaactgcgaccggatactccgggaagccgccgtcgtcgagaggctggtgatgacgctgcaccaccccgggctgcagatcacgtcatcgagaatcctactgaacctgtgcaggtacagcaggagcgaccacttcttgcagctcagcagcctcactgcagctgtcccaatagtgttcaaagcaattatggttgagaagagcagcttgcttgaggtgtctataggattggcaatacagattacaaggcttgcaacacctgaatttcacaaggaaatctttggaaaggcaggtgtaccagatacagacattgcaaggaggctagtggagattctgaaagagcacaggacacccagggtgaaggttccgaggatgagaaggttcgtcatcgagctcgccatcgccatgatgagaggcgacgccgagctcgtccccttcttcaggagcatggagctggagaaggagctcaggagcgtcgtcaggtcgacgtccgagctcgagagcttcaacatgttctctggcagcattgggctgagcaggcacagctcaactctggcctcacttgtagatgatgccatggagatcatgcaggctctgcaagacagttaa More
Protein seq	MAIDTTADHGGGAGAGGVDIPMQILVQPPPLPPPTATATARHRRTHTGDSTASSYEPQRRPVEHQVSSMHAATASDDGGGVDDVVPERKVTAFALHVAVLEKAASHVGAVCFVWATVVILGGFAADLDARDFWLVTAILLVEGTRVFSRSNELDLQEQPMHLPDAAAAAAGDDDDDPPPPHKAAAAASPIHLLPLGGWLVEARNVSYVLYWLQLLSASACVALSLLRLATLRFAGDNGGGGNKNAYYALMLFYVLALSEAVIFLVERAYWEWVLSYRRLVEAVSGECDLGDAGVVPIKRFFYRAFSRSVEGGILDATRMDLVSFAVELLSSDSGDEQLIGAHILRGSIANRDSARRAVRKIGTSAATVERLVEMVSWKSPSKRRVRSLAAEVVLRLAGKRRNLIRVATIPGAIESISTLLETPTTDAAAGDLAMNEMGLHIMKKLAREHGNAAKISSTRGVLSRIIHFTRTSRAALQIGAGGEGSLPAKTVLRSLQVVKNLSSTPGHTGEAIRREISDNVFVLGNIRKVLQHGGERHGKMQLTAIGVLADLAIDGDAKEKIGCTGDMIAHLLDMFAGSPESAPAVAYAAQGAAHIRLQAGEVVALLALESAANCDRILREAAVVERLVMTLHHPGLQITSSRILLNLCRYSRSDHFLQLSSLTAAVPIVFKAIMVEKSSLLEVSIGLAIQITRLATPEFHKEIFGKAGVPDTDIARRLVEILKEHRTPRVKVPRMRRFVIELAIAMMRGDAELVPFFRSMELEKELRSVVRSTSELESFNMFSGSIGLSRHSSTLASLVDDAMEIMQALQDS More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.000000	0.000000	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_07g0648000	RBH	0.025167	0.000000	0.000000
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os07g45370	RBH	0.000000	0.000000	0.000000
Nipponbare \| IRGSP 1.0 \| RAP-db	Os07g0648000	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_07g0025580	RBH	0.000000	0.000000	0.000000
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_07g0025620	RBH	0.000000	0.000000	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_07g0025480	RBH	0.000000	0.843615	0.000000
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_07g0025490	RBH	0.000000	0.022394	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_07g0025710	RBH	0.000000	1.276777	0.000000
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_07G0445700	RBH	0	0.1976625	0.0060015
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_07g0026160	RBH	0.000000	0.121588	0.000000
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_07G0457600	RBH	0.028455	0.0761225	0.0424185
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_03g0018390	RBH	0.107891	0.094829	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_07g0025670	RBH	0.000000	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_07g0025490	RBH	0.000000	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_07g0025720	RBH	0.000000	0.000000	0.000000
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_07g0025390	RBH	0.000000	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_07G025360	RBH	0.000000	0.000000	0.000000
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_07g0025420	RBH	0.000000	3.001557	0.000000

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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