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
OsLaMu_11g0022580		OGI:11076840 \| 15/16			LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)			Chr11:28677396-28682359		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		LR21, Lr21, OsLr21
DNA seq		ttagccactcaaatacaaaacgggaatgctgctgttgctgctaccatggggagaatgagtagattccaaagcaattgttactctaggaatatgctggatcttgtgccagtttggatgcccatttgttttgcaagacctcatgaactcgtcatcgcaggcccccaatccaaactcctcaagagattggggcagctctggaagcgactgaatgttcaagcaaaaatacatcttcagttcatggagtgacatgagttgcttcagattatctggcaagaaggtccagctacttttccaaagccagagtgaacgaagatgaacgaaaaactcaaagagttcaggggcaggtctcagacggctgcatccactgagctcaaggtcgcgcaggtactttgggcctttgtgacctccgatcatccaatctgggtagcttgaaccgtgataatctgttatttctagtctttcaagctccaatggtgggcaaaggccctcaagcacctctgcctcaacctctggactgcagctctcatcatcccagacaagtaccagttctttcaggcgttccttgccatctaatttggcttcaagagcttcctccttgctcccaacgtttccaagaccgtggatatgtagcttgccacgaagcttgtttaggtgtctcagctgctgtaattcataccctggttccttctttactgggaacaatggtaatgtttgcagtgacattagcatgccgatgtttggacaattcagatcagccgtggcgattatatgctgcaagttgatgagattactcatgtcttcgccagagggaaacactaaatctccacatacaccaaaatctagcacatgcatatagcgaagcttggcaattgtgtttggtaaaacttgtctgatcaaggttgtccgaaaacaaagatggcgtagatgcctcagttgaccaatagattctgggaatgagaacacatgcgatcctgtgatgattttaatgctcagtacccgcaacttcctcagcctcatgaacattctttcaaatatcttttcttcagttggtatttctgtattgccactataaataatcagagtgcgtaaatttcccattttcaaaaccttttcagtaatcatcgttttattataactctcgatataaaggtggcgaacatctccaggaagatctcctgtccagccattctcaactttgaagcaatcatttctagcaaccttctctgctaaatcgtgaagcagatcatgaaccgtgaagtattcggaggcaccaaacctttctgcttgtttttctcctagttgcagaaatgaggctgataccaattcctcaaagtactttctaccaacagcctccatttctaatcctacttcagtagtcgttataaacccttctgccacccacaagttaattaactcatggcgttccagccgatgtcttctggggaaaatactgcagtaagcaaagcaccgtcttacctgctgatcaaggtgctggtagctccaccatagagctcccattgtctcattcaagaggttctgatttcgagcatcttgccaaaagtcaattgttggtctcatgtgtagttgccctccaactgttctggctgccagaggtgatctcttcagcttttttgcaatgtcagatcctatagctctgaatatcatccgatcgcgttcatctatgcctgcactgtcgagagcatagtgcatgaaaagttcaaggaacacagtgtcatccaattcagatatcggaatacattttgcagcacccaaagctaataatgcatctctagttcgactagttagtaggatcttacttcctaaagccccaaccttaagtggaaaaagaatcttttgtagctcctcctgactgtcatccttgttgtaccatacatcatctagtaccaaaaggaaccgttttcgactcaatgcctgttccagcttctgctctagggtgttaagactattgaactgagggcaagagttccctgtagcctcttcaagcatcttactgaaaatcttatccacattaaaattcctagaaacatgaacccacatgattaggtcgaaatggccagcctctttctcttgcctgccccttttctcatgggcacaaacatactgtgcaagggtagatttcccggacccaggaatgccatggatgccaatgatggaatgggataatgcacgactgggtttatgttgaccatcattttctgtctcatgaagcaatactaagatcttatcacgatcttcatctcggccaattactacaaatggaggagatgcagtagtgactgcaatacgtgaatcgtcagaaacagtttgtctcttgttgatattactgtggcctggcaaattcagaagctgcaaaattttgtgtccatcgttgataatattttctatcaggaggaggagcatctgaaggctgtaaaacaaaattagcaggtcaggtttttatggtattttacagaaactcatcaatcattcatcaccacccccctcacataaaaggactgacataacttgcgtaaatttatataaaaagataaggattcgttgaagaaaatagaacttccgcagttccctccaagaacgactgctaaaatgcattgtgcattaggtctttggtaccctatctccttcaagttgagtctccagtgatggattgttacagatagcttgaatttgtacatatttttttcctaggaagttggtatctccggtggcggtggttgcagggaacaagaacacagtgaggcgacgtgcactagtagcaagctactctgcagcagccacagatattgatacaagcatgcatagatgtactgaagaggaatattgttttgctgcaccaattgtatgttttagtttgacagaaaggaaacctgcactggaaaagaatatcctgttttgtatatttaatgttatgattcagttcaacaaaattcttttttctttctgattaccctgtgtgaaagaaaaaaaaaagactcattccagtgaatactacaaagggaatctataagttcagttatactaagaatgttgtgtgttctaggagtcaccctttggagttatagcacataggttcagagttcttataggcgcagtacaattatggatgaatttgtcatatcaacaaaatactgtagcccttgcaaggaaatctttatcgaacagaatatgaaaagatttctggtgttgagtaaattacaaagagattttttactgtccttgagactgtacagtactaaatcgtgaccgttgatctggcatcatccaacggtaaaaaaaacgtcggtacctcatggtaccgcaccttcccaatggagtggtaccgtgggtggggggtagttttgtactttcgcgttgtatcggcatctcttccttctctgttcgcgggagaaaacgaatcgctgggcaggagcagaaagagaaacgacgatggtccagttcaggccgtcaggagcagcaagagaaacgacgatggctggtctgcgccagagacgtaggaagaacggagtccacagcagcagcggggtggaagcgacgccggagtcttcgaggtggatgcgacgacgggatgcgctggtcttgatgcgacggcggccgcggcggcctcgatgcaacgtcagctgcggcggcctcgatgtgacatcagccgcggcggactagctgcgatgcgacggcggccgcggcggattcgatgcggcacggagatgctattggctgagaggctgagatgggtggtgtttagcgccgccctaaatttgtttagtccgatcatacccttcctaaatcaacggttcaacggttagattagatcggtatctcatagtacctcgtaccttataatacctcatggtacctcctcaaggatgagaaaaatgctcaattataaaagggtttcctttccagggtgtaaaagattacaaagctttagtattatgatacaaccaacagttagataagaaatagaagagcaataatagcaggcaaaacatattggcttattatgacacaacaaagttcaccttcagacttcagagggtctcaagcaggacagtaatacctggttttttatgcggacgctcttcggtagggcagactggagcatcttcaccaaattcctcctacgaggaggcctgccgtttgactccaaattgtcatcaggctgagatgagatctgcctttcaagacggtgatactcaatatcatccaagatgtcttcagcttcatagacagccgacctaagctgctgcaaccattcctccaaacggcctctgtgaggactctcctcaactgcttccagcactagttccagctgtagaactttagtctgaagttgtttcagcttctctgatccatgaaagccgaggtaggagaagcctttgttgaggatcttggtgatgatcggtgagacgacccaacctacagcagatatgccccagccaactgcggccacctccgccatccgacgctcacagcaagaggagaggggggaattggggatgggctgcaagttcttgatttctcttgatgtacatcctggatataaggacagaattccattacttccatcgctatctcggtttacttttgcaaccagtcattgtattccctattcagtcatcaacttgcaattggcatgttgtcacgagactaagatatgtttgcaacttttttttttaagtcaaatgcaatttttaatttccatatgctacttattttcctatccagctattctttcagaagaccatatccagtctgtccatcaccatggtgagaggtgaggacctaacacaattacactgagtataattgtcctttcatttcctgaaagacttcattcccattgtatgttcatgtatgattagtttgaccaattaagagctaaccatgaatgaaagacttcatttctatcgttttcatactccagaagtcctcaactgtttttttcc More
CDS seq		atggcggaggtggccgcagttggctggggcatatctgctgtaggttgggtcgtctcaccgatcatcaccaagatcctcaacaaaggcttctcctacctcggctttcatggatcagagaagctgaaacaacttcagactaaagttctacagctggaactagtgctggaagcagttgaggagagtcctcacagaggccgtttggaggaatggttgcagcagcttaggtcggctgtctatgaagctgaagacatcttggatgatattgagtatcaccgtcttgaaaggcagatctcatctcagcctgatgacaatttggagtcaaacggcaggcctcctcgtaggaggaatttggtgaagatgctccagtctgccctaccgaagagcgtccgcataaaaaaccagcttctgaatttgccaggccacagtaatatcaacaagagacaaactgtttctgacgattcacgtattgcagtcactactgcatctcctccatttgtagtaattggccgagatgaagatcgtgataagatcttagtattgcttcatgagacagaaaatgatggtcaacataaacccagtcgtgcattatcccattccatcattggcatccatggcattcctgggtccgggaaatctacccttgcacagtatgtttgtgcccatgagaaaaggggcaggcaagagaaagaggctggccatttcgacctaatcatgtgggttcatgtttctaggaattttaatgtggataagattttcagtaagatgcttgaagaggctacagggaactcttgccctcagttcaatagtcttaacaccctagagcagaagctggaacaggcattgagtcgaaaacggttccttttggtactagatgatgtatggtacaacaaggatgacagtcaggaggagctacaaaagattctttttccacttaaggttggggctttaggaagtaagatcctactaactagtcgaactagagatgcattattagctttgggtgctgcaaaatgtattccgatatctgaattggatgacactgtgttccttgaacttttcatgcactatgctctcgacagtgcaggcatagatgaacgcgatcggatgatattcagagctataggatctgacattgcaaaaaagctgaagagatcacctctggcagccagaacagttggagggcaactacacatgagaccaacaattgacttttggcaagatgctcgaaatcagaacctcttgaatgagacaatgggagctctatggtggagctaccagcaccttgatcagcaggtaagacggtgctttgcttactgcagtattttccccagaagacatcggctggaacgccatgagttaattaacttgtgggtggcagaagggtttataacgactactgaagtaggattagaaatggaggctgttggtagaaagtactttgaggaattggtatcagcctcatttctgcaactaggagaaaaacaagcagaaaggtttggtgcctccgaatacttcacggttcatgatctgcttcacgatttagcagagaaggttgctagaaatgattgcttcaaagttgagaatggctggacaggagatcttcctggagatgttcgccacctttatatcgagagttataataaaacgatgattactgaaaaggttttgaaaatgggaaatttacgcactctgattatttatagtggcaatacagaaataccaactgaagaaaagatatttgaaagaatgttcatgaggctgaggaagttgcgggtactgagcattaaaatcatcacaggatcgcatgtgttctcattcccagaatctattggtcaactgaggcatctacgccatctttgttttcggacaaccttgatcagacaagttttaccaaacacaattgccaagcttcgctatatgcatgtgctagattttggtgtatgtggagatttagtgtttccctctggcgaagacatgagtaatctcatcaacttgcagcatataatcgccacggctgatctgaattgtccaaacatcggcatgctaatgtcactgcaaacattaccattgttcccagtaaagaaggaaccagggtatgaattacagcagctgagacacctaaacaagcttcgtggcaagctacatatccacggtcttggaaacgttgggagcaaggaggaagctcttgaagccaaattagatggcaaggaacgcctgaaagaactggtacttgtctgggatgatgagagctgcagtccagaggttgaggcagaggtgcttgagggcctttgcccaccattggagcttgaaagactagaaataacagattatcacggttcaagctacccagattggatgatcggaggtcacaaaggcccaaagtacctgcgcgaccttgagctcagtggatgcagccgtctgagacctgcccctgaactctttgagtttttcgttcatcttcgttcactctggctttggaaaagtagctggaccttcttgccagataatctgaagcaactcatgtcactccatgaactgaagatgtatttttgcttgaacattcagtcgcttccagagctgccccaatctcttgaggagtttggattgggggcctgcgatgacgagttcatgaggtcttgcaaaacaaatgggcatccaaactggcacaagatccagcatattcctagagtaacaattgctttggaatctactcattctccccatggtagcagcaacagcagcattcccgttttgtatttgagtggctaa More
Protein seq		MAEVAAVGWGISAVGWVVSPIITKILNKGFSYLGFHGSEKLKQLQTKVLQLELVLEAVEESPHRGRLEEWLQQLRSAVYEAEDILDDIEYHRLERQISSQPDDNLESNGRPPRRRNLVKMLQSALPKSVRIKNQLLNLPGHSNINKRQTVSDDSRIAVTTASPPFVVIGRDEDRDKILVLLHETENDGQHKPSRALSHSIIGIHGIPGSGKSTLAQYVCAHEKRGRQEKEAGHFDLIMWVHVSRNFNVDKIFSKMLEEATGNSCPQFNSLNTLEQKLEQALSRKRFLLVLDDVWYNKDDSQEELQKILFPLKVGALGSKILLTSRTRDALLALGAAKCIPISELDDTVFLELFMHYALDSAGIDERDRMIFRAIGSDIAKKLKRSPLAARTVGGQLHMRPTIDFWQDARNQNLLNETMGALWWSYQHLDQQVRRCFAYCSIFPRRHRLERHELINLWVAEGFITTTEVGLEMEAVGRKYFEELVSASFLQLGEKQAERFGASEYFTVHDLLHDLAEKVARNDCFKVENGWTGDLPGDVRHLYIESYNKTMITEKVLKMGNLRTLIIYSGNTEIPTEEKIFERMFMRLRKLRVLSIKIITGSHVFSFPESIGQLRHLRHLCFRTTLIRQVLPNTIAKLRYMHVLDFGVCGDLVFPSGEDMSNLINLQHIIATADLNCPNIGMLMSLQTLPLFPVKKEPGYELQQLRHLNKLRGKLHIHGLGNVGSKEEALEAKLDGKERLKELVLVWDDESCSPEVEAEVLEGLCPPLELERLEITDYHGSSYPDWMIGGHKGPKYLRDLELSGCSRLRPAPELFEFFVHLRSLWLWKSSWTFLPDNLKQLMSLHELKMYFCLNIQSLPELPQSLEEFGLGACDDEFMRSCKTNGHPNWHKIQHIPRVTIALESTHSPHGSSNSSIPVLYLSG
Function		Disease resistance protein RGA2 [UniProtKB/Swiss-Prot:Q7XBQ9]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLaMu_11g0022580	OsLaMu_11g0022580.01	Chr11	28677396	28682359	-	NAM
CDS seq	atggcggaggtggccgcagttggctggggcatatctgctgtaggttgggtcgtctcaccgatcatcaccaagatcctcaacaaaggcttctcctacctcggctttcatggatcagagaagctgaaacaacttcagactaaagttctacagctggaactagtgctggaagcagttgaggagagtcctcacagaggccgtttggaggaatggttgcagcagcttaggtcggctgtctatgaagctgaagacatcttggatgatattgagtatcaccgtcttgaaaggcagatctcatctcagcctgatgacaatttggagtcaaacggcaggcctcctcgtaggaggaatttggtgaagatgctccagtctgccctaccgaagagcgtccgcataaaaaaccagcttctgaatttgccaggccacagtaatatcaacaagagacaaactgtttctgacgattcacgtattgcagtcactactgcatctcctccatttgtagtaattggccgagatgaagatcgtgataagatcttagtattgcttcatgagacagaaaatgatggtcaacataaacccagtcgtgcattatcccattccatcattggcatccatggcattcctgggtccgggaaatctacccttgcacagtatgtttgtgcccatgagaaaaggggcaggcaagagaaagaggctggccatttcgacctaatcatgtgggttcatgtttctaggaattttaatgtggataagattttcagtaagatgcttgaagaggctacagggaactcttgccctcagttcaatagtcttaacaccctagagcagaagctggaacaggcattgagtcgaaaacggttccttttggtactagatgatgtatggtacaacaaggatgacagtcaggaggagctacaaaagattctttttccacttaaggttggggctttaggaagtaagatcctactaactagtcgaactagagatgcattattagctttgggtgctgcaaaatgtattccgatatctgaattggatgacactgtgttccttgaacttttcatgcactatgctctcgacagtgcaggcatagatgaacgcgatcggatgatattcagagctataggatctgacattgcaaaaaagctgaagagatcacctctggcagccagaacagttggagggcaactacacatgagaccaacaattgacttttggcaagatgctcgaaatcagaacctcttgaatgagacaatgggagctctatggtggagctaccagcaccttgatcagcaggtaagacggtgctttgcttactgcagtattttccccagaagacatcggctggaacgccatgagttaattaacttgtgggtggcagaagggtttataacgactactgaagtaggattagaaatggaggctgttggtagaaagtactttgaggaattggtatcagcctcatttctgcaactaggagaaaaacaagcagaaaggtttggtgcctccgaatacttcacggttcatgatctgcttcacgatttagcagagaaggttgctagaaatgattgcttcaaagttgagaatggctggacaggagatcttcctggagatgttcgccacctttatatcgagagttataataaaacgatgattactgaaaaggttttgaaaatgggaaatttacgcactctgattatttatagtggcaatacagaaataccaactgaagaaaagatatttgaaagaatgttcatgaggctgaggaagttgcgggtactgagcattaaaatcatcacaggatcgcatgtgttctcattcccagaatctattggtcaactgaggcatctacgccatctttgttttcggacaaccttgatcagacaagttttaccaaacacaattgccaagcttcgctatatgcatgtgctagattttggtgtatgtggagatttagtgtttccctctggcgaagacatgagtaatctcatcaacttgcagcatataatcgccacggctgatctgaattgtccaaacatcggcatgctaatgtcactgcaaacattaccattgttcccagtaaagaaggaaccagggtatgaattacagcagctgagacacctaaacaagcttcgtggcaagctacatatccacggtcttggaaacgttgggagcaaggaggaagctcttgaagccaaattagatggcaaggaacgcctgaaagaactggtacttgtctgggatgatgagagctgcagtccagaggttgaggcagaggtgcttgagggcctttgcccaccattggagcttgaaagactagaaataacagattatcacggttcaagctacccagattggatgatcggaggtcacaaaggcccaaagtacctgcgcgaccttgagctcagtggatgcagccgtctgagacctgcccctgaactctttgagtttttcgttcatcttcgttcactctggctttggaaaagtagctggaccttcttgccagataatctgaagcaactcatgtcactccatgaactgaagatgtatttttgcttgaacattcagtcgcttccagagctgccccaatctcttgaggagtttggattgggggcctgcgatgacgagttcatgaggtcttgcaaaacaaatgggcatccaaactggcacaagatccagcatattcctagagtaacaattgctttggaatctactcattctccccatggtagcagcaacagcagcattcccgttttgtatttgagtggctaa More
Protein seq	MAEVAAVGWGISAVGWVVSPIITKILNKGFSYLGFHGSEKLKQLQTKVLQLELVLEAVEESPHRGRLEEWLQQLRSAVYEAEDILDDIEYHRLERQISSQPDDNLESNGRPPRRRNLVKMLQSALPKSVRIKNQLLNLPGHSNINKRQTVSDDSRIAVTTASPPFVVIGRDEDRDKILVLLHETENDGQHKPSRALSHSIIGIHGIPGSGKSTLAQYVCAHEKRGRQEKEAGHFDLIMWVHVSRNFNVDKIFSKMLEEATGNSCPQFNSLNTLEQKLEQALSRKRFLLVLDDVWYNKDDSQEELQKILFPLKVGALGSKILLTSRTRDALLALGAAKCIPISELDDTVFLELFMHYALDSAGIDERDRMIFRAIGSDIAKKLKRSPLAARTVGGQLHMRPTIDFWQDARNQNLLNETMGALWWSYQHLDQQVRRCFAYCSIFPRRHRLERHELINLWVAEGFITTTEVGLEMEAVGRKYFEELVSASFLQLGEKQAERFGASEYFTVHDLLHDLAEKVARNDCFKVENGWTGDLPGDVRHLYIESYNKTMITEKVLKMGNLRTLIIYSGNTEIPTEEKIFERMFMRLRKLRVLSIKIITGSHVFSFPESIGQLRHLRHLCFRTTLIRQVLPNTIAKLRYMHVLDFGVCGDLVFPSGEDMSNLINLQHIIATADLNCPNIGMLMSLQTLPLFPVKKEPGYELQQLRHLNKLRGKLHIHGLGNVGSKEEALEAKLDGKERLKELVLVWDDESCSPEVEAEVLEGLCPPLELERLEITDYHGSSYPDWMIGGHKGPKYLRDLELSGCSRLRPAPELFEFFVHLRSLWLWKSSWTFLPDNLKQLMSLHELKMYFCLNIQSLPELPQSLEEFGLGACDDEFMRSCKTNGHPNWHKIQHIPRVTIALESTHSPHGSSNSSIPVLYLSG More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.015212	0.477175	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_11g0668100	RBH	0.545508	1.187026	0.660127
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os11g44580	RBH	0.270107	0.700377	0.157062
Nipponbare \| IRGSP 1.0 \| RAP-db	Os11g0668100	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_11g0023060	RBH	0.721716	4.629389	1.179042
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_11g0023140	RBH	0.000000	0.000000	1.017373
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_11g0022770	RBH	0.979597	4.284066	2.042390
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_11g0022460	RBH	0.124196	0.081978	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_11g0022720	RBH	2.844949	2.401514	2.983024
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_11G0405000	RBH	2.546412	9.46714	0.3946455
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_11g0023620	RBH	0.393959	0.167419	0.935478
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_11G0430200	SBH	14.200319	23.9624835	0.1261395
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_11g0023250	RBH	0.086567	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_11g0023370	RBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_11g0022960	RBH	0.000000	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_11g0022690	RBH	0.796213	0.0	0.076279
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_11g0021950	SBH	0.0	0.950097	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_11G022940	RBH	0.684989	0.867905	0.231093
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_11g0023370	RBH	1.251961	12.032497	1.134784

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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