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_03g0040470		OGI:03097220 \| 16/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr03:37894132-37898420		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		SDRLK-60
DNA seq		cgttcctgtactttttttttagaactcataaactttattccatatcagaaacagagtacatgattcatcatatattttcctgcactgaaatgctctattagacttctagcataacagcatctgctaggaccgttcctgtagttatgccatccatagcattctaccgatcaaaatgtaaaacttatagctgcataatgtaaaagacttggttgtcaattttcagggtgttccatgatgcaagctcatgtatttgaactggctgatagacggacgacccttgctgtactttgcagcgcttcaagcaaacttcatcaTttttctgcaaattaaacaaggatttctatcagcaaacgacctgacatttcaactaaaaaaagtctgaaatattataattgctaaaattagaaaaattagctaggttcttttgtgcctgttgacaaagagttgttctgtaatgggtatctgctatcaaatgctttttccctttacacaatcaatgaggtttcttctgatcgcaccttttgctaagtgccacttctcatatactctggatctattcagtagattcagattgcactctgcttatcaacagtttttttttaaaaaaaaaatgttactggtagacctcTTtttttttttgccttttacttactcagaattatgcttgcagctcatgttagtgactgcgaatatgatgcagggggtgggggctggtgaacttcgatggcaccttcaatcataagagcaACactcttcatcgctggtcgcatcacaggttcactctgtgtgcaccaaatgccgacgttcaccattctcaccagctcagcttcgtcgacaccatctgccaccttgccagcatcaccaaacatcacacactcatatgcccactcggaaatgttgtactcctccccagcccgcttcagatccatgcttttcttacagcttatgacctccagaagcatgatcccgtagctgtacacgtctgccttcacggtgattgctctgttcttgctccactccggtgctagatagccccgggttcctcggatgccggtgaatgtctttgtttggttcccaatcagtagctttgctagcccaaagtcagcaatcttagctatccccaaactgtcaatgagtatgttctCtggcttgatatcgcagtggattattgggccctctatctctgaatgcaggtattgcaaccctctggcaacatctagtgcaattgcaaccctcttgctccaggcaggggaggcatctgagtgaaagaggaggtttgccagggatccatttggcatgtactcatacacaagcaggcgatgaatgccctcattgcagaaaccaagcaatcgcagcaggttccggtggtgtgttcttgcaatcacacgcacttccctgttaaattcacgctgcccatcctcagccatcttttcgagcctcttcacagcgatgacctggttggtgtcggccacgacacctttgaataccgtcccgtatgcccccttgccaagctcttcgccgaaaccatttgttgccacatctagttcctggaaagaataggatctgaggccaacaatgttcccatcaatcctggagtcctcttgccgtggtgccgtcatcgtcatgtgcgccaatgatcgccgatgcctgcagataagtaatagagatgccactaatagcacaagcagagAaaagatggccaaggaaactcctgatatcaatgcagaatttgcatggatactcatagccctttggcgagtaccggatatggtctggtaagtgtagatcttcacaaagagtgtggtgttaccaggcatcctgccatatctaatcggaagcatctgttttgagcagtaggaatcactaaacatggcgatatcgcaaccacaatcggagaggcaaagtagtttgcaggcttcaatactagttgtggccggtagaacagcatacgggttctctaaccaagtagtgttcttcacttcgaccatcgtggttgtcactctcgtctcatcgttagagctgttcctcacgcagccaccggttggcaatgctctccagcaaccaagtgtgctctggttagtgctcaagaattcaaaaccaggaaggcaagagcagcttgtctctcctgtcacggtgagatggcagaagctattcggaccacaaacacctttcacaaggcagcgatcactgccaggctcaagccactcaacctctgttgtaggtgccctgccaagcttaaagaaaacatgtgagtagagtcgtaggatgccatcgggatcaaatgtcaaatgatagtaaatttccatatcaggggaggcattggaaggctggttggcatggaacagtatctttgtataggagtttttcctgtcaaacatccatatggtaccattaggatctaatgaaagcgtgaggaggaggcccatgttgaaagtccaggtagaccagtacgcactaccagaatcaatggtgccaacagggtacatcacaagattgccatcttgttggttctcaagcctatacttgccactggcaggattactctgagagacacttgaaagaagaaatctgccaggacgcaagttctgacctgccaacaatgtgtctgtcggaaaactgaaagtagaccatatgacctgtctgctcatatcatacagtacaaagttgccggtgttcaacatggcagcagaggcagcaggtgtagaaccgtcagatatggggttcagttggctacctggagttgatggagttcgtgaccattggagcgcaccaccatgCccaaatatgatagaaccaccagcaattGggggctcatcacggttggcagtccacacaattgtccttgacacaccaatcacaagccacaccccaatagaaaagccttcgccgttgggatagaagccgaacgcaaagcggcctgaagaggaggaccagtactgggtgctgcttgtgttgatagaggatCccaaagtaatgaatgactcattggctgaagctccagcggcaaaattggggtcttcaggaaccaagagcagcagggataggaagagaatatgtGggaacattgtccaggaggaagagtctactgcagttccttgagatgagatagtaattgtatgctgaagaaacctactggcaattctaagcagggaatggcttttgttagaccctgtgaagtgtaaactactgaatactactccctccgtccctaaatatttgacgccgttaactcttttaaacatgtttgaccgttCGTCttattaaaaaacttttgtgaatattattaaaaaacttgagtagtagtagtatatttaacaatgaatcaaatgataggaaaagaattaataattacttaaattttttgaataagacgaacagtccaacatgtttaaaaaagtcaacggcgtcaaatatttagggacggagggagtagtattttgacagtcaaggaaactgatagaaagaaattgtggacgaacttattagtcaagtctttagtggactagggagacttggacctgagtttaatctaaaaaattgatcatcatacagaaagaacgggaatgaacaacaccaagtgatctacagtaaggaaaatggtgaaaacaacaacctgagcagagatgaagggaagtgataaccaccttttcaaaaattggttccagttaaccgagattgaacaagttgatacagatacatgatacatgctgtacagctcaatgttttctgtataaagttagttatgatctagactcagcactgatgaggtaaTtttcagtcagTTtgttagtttgattcaatgaatcacactatgagtctgcaggaatggggatcgttccaattaccagatcctggttagtttgcacatgagagtgagtatgaattggaaaggcaaaattctataccttaatttacctccatttgccctctagattggccatactccagctccgcccgcgctcccgctgcacgtatccggcctacatctacacatcataccactgaagaatcaaacagggtaagcaatctcaactaaacgaggagagaggaggtagggggtggggggaggagcggagcgggactggtgagggggaggaggggtcgagaagttcgccggtgctgggcatagagggagtacttgggcgggcggtggaagtccggcggtgggcggtggcgccgccggagccgcgggtgaggaagtccggcggtgggcggtgccggtagcgtgggaaatggaggcggcggcgcgtgccgctggaacgattagaaattcgtgtgtgaatacgttt More
CDS seq		atgttccCacatattctcttcctatccctgctgctcttggttcctgaagaccccaattttgccgctggagcttcagccaatgagtcattcattactttggGatcctctatcaacacaagcagcacccagtactggtcctcctcttcaggccgctttgcgttcggcttctatcccaacggcgaaggcttttctattggggtgtggcttgtgattggtgtgtcaaggacaattgtgtggactgccaaccgtgatgagccccCaattgctggtggttctatcatatttggGcatggtggtgcgctccaatggtcacgaactccatcaactccaggtagccaactgaaccccatatctgacggttctacacctgctgcctctgctgccatgttgaacaccggcaactttgtactgtatgatatgagcagacaggtcatatggtctactttcagttttccgacagacacattgttggcaggtcagaacttgcgtcctggcagatttcttctttcaagtgtctctcagagtaatcctgccagtggcaagtataggcttgagaaccaacaagatggcaatcttgtgatgtaccctgttggcaccattgattctggtagtgcgtactggtctacctggactttcaacatgggcctcctcctcacgctttcattagatcctaatggtaccatatggatgtttgacaggaaaaactcctatacaaagatactgttccatgccaaccagccttccaatgcctcccctgatatggaaatttactatcatttgacatttgatcccgatggcatcctacgactctactcacatgttttctttaagcttggcagggcacctacaacagaggttgagtggcttgagcctggcagtgatcgctgccttgtgaaaggtgtttgtggtccgaatagcttctgccatctcaccgtgacaggagagacaagctgctcttgccttcctggttttgaattcttgagcactaaccagagcacacttggttgctggagagcattgccaaccggtggctgcgtgaggaacagctctaacgatgagacgagagtgacaaccacgatggtcgaagtgaagaacactacttggttagagaacccgtatgctgttctaccggccacaactagtattgaagcctgcaaactactttgcctctccgattgtggttgcgatatcgccatgtttagtgattcctactgctcaaaacagatgcttccgattagatatggcaggatgcctggtaacaccacactctttgtgaagatctacacttaccagaccatatccggtactcgccaaagggctatgagtatccatgcaaattctgcattgatatcaggagtttccttggccatctttTctctgcttgtgctattagtggcatctctattacttatctgcaggcatcggcgatcattggcgcacatgacgatgacggcaccacggcaagaggactccaggattgatgggaacattgttggcctcagatcctattctttccaggaactagatgtggcaacaaatggtttcggcgaagagcttggcaagggggcatacgggacggtattcaaaggtgtcgtggccgacaccaaccaggtcatcgctgtgaagaggctcgaaaagatggctgaggatgggcagcgtgaatttaacagggaagtgcgtgtgattgcaagaacacaccaccggaacctgctgcgattgcttggtttctgcaatgagggcattcatcgcctgcttgtgtatgagtacatgccaaatggatccctggcaaacctcctctttcactcagatgcctcccctgcctggagcaagagggttgcaattgcactagatgttgccagagggttgcaatacctgcattcagagatagagggcccaataatccactgcgatatcaagccaGagaacatactcattgacagtttggggatagctaagattgctgactttgggctagcaaagctactgattgggaaccaaacaaagacattcaccggcatccgaggaacccggggctatctagcaccggagtggagcaagaacagagcaatcaccgtgaaggcagacgtgtacagctacgggatcatgcttctggaggtcataagctgtaagaaaagcatggatctgaagcgggctggggaggagtacaacatttccgagtgggcatatgagtgtgtgatgtttggtgatgctggcaaggtggcagatggtgtcgacgaagctgagctggtgagaatggtgaacgtcggcatttggtgcacacagagtgaacctgtgatgcgaccagcgatgaagagtGTtgctcttatgattgaaggtgccatcgaaaaaaAtgatgaagtttgcttgaagcgctgcaaagtacagcaagggtcgtccgtctatcagccagttcaaatacatgagcttgcatcatggaacaccctgaaaattgacaaccaagtcttttacattatgcagctataa More
Protein seq		MFPHILFLSLLLLVPEDPNFAAGASANESFITLGSSINTSSTQYWSSSSGRFAFGFYPNGEGFSIGVWLVIGVSRTIVWTANRDEPPIAGGSIIFGHGGALQWSRTPSTPGSQLNPISDGSTPAASAAMLNTGNFVLYDMSRQVIWSTFSFPTDTLLAGQNLRPGRFLLSSVSQSNPASGKYRLENQQDGNLVMYPVGTIDSGSAYWSTWTFNMGLLLTLSLDPNGTIWMFDRKNSYTKILFHANQPSNASPDMEIYYHLTFDPDGILRLYSHVFFKLGRAPTTEVEWLEPGSDRCLVKGVCGPNSFCHLTVTGETSCSCLPGFEFLSTNQSTLGCWRALPTGGCVRNSSNDETRVTTTMVEVKNTTWLENPYAVLPATTSIEACKLLCLSDCGCDIAMFSDSYCSKQMLPIRYGRMPGNTTLFVKIYTYQTISGTRQRAMSIHANSALISGVSLAIFSLLVLLVASLLLICRHRRSLAHMTMTAPRQEDSRIDGNIVGLRSYSFQELDVATNGFGEELGKGAYGTVFKGVVADTNQVIAVKRLEKMAEDGQREFNREVRVIARTHHRNLLRLLGFCNEGIHRLLVYEYMPNGSLANLLFHSDASPAWSKRVAIALDVARGLQYLHSEIEGPIIHCDIKPENILIDSLGIAKIADFGLAKLLIGNQTKTFTGIRGTRGYLAPEWSKNRAITVKADVYSYGIMLLEVISCKKSMDLKRAGEEYNISEWAYECVMFGDAGKVADGVDEAELVRMVNVGIWCTQSEPVMRPAMKSVALMIEGAIEKNDEVCLKRCKVQQGSSVYQPVQIHELASWNTLKIDNQVFYIMQL
Function		G-type lectin S-receptor-like serine/threonine-protein kinase LECRK4 [UniProtKB/Swiss-Prot:Q7FAZ0]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0040470	OsLima_03g0040470.01	Chr03	37894249	37898405	-	NAM
CDS seq	cgaatttctaatcgttccagcggcacgcgccgccgcctccatttcccacgctaccggcaccgcccaccgccggacttcctcacccgcggctccggcggcgccaccgcccaccgccggacttccaccgcccgcccaagccggatacgtgcagcgggagcgcgggcggagctggagtatggccaatctagagggcaaatggagaaaaAtgatgaagtttgcttgaagcgctgcaaagtacagcaagggtcgtccgtctatcagccagttcaaatacatgagcttgcatcatggaacaccctgaaaattgacaaccaagtcttttacattatgcagctataa More
Protein seq	RISNRSSGTRRRLHFPRYRHRPPPDFLTRGSGGATAHRRTSTARPSRIRAAGARAELEYGQSRGQMEKNDEVCLKRCKVQQGSSVYQPVQIHELASWNTLKIDNQVFYIMQL

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0040470	OsLima_03g0040470.02	Chr03	37894249	37898405	-	NAM
CDS seq	atgttccCacatattctcttcctatccctgctgctcttggttcctgaagaccccaattttgccgctggagcttcagccaatgagtcattcattactttggGatcctctatcaacacaagcagcacccagtactggtcctcctcttcaggccgctttgcgttcggcttctatcccaacggcgaaggcttttctattggggtgtggcttgtgattggtgtgtcaaggacaattgtgtggactgccaaccgtgatgagccccCaattgctggtggttctatcatatttggGcatggtggtgcgctccaatggtcacgaactccatcaactccaggtagccaactgaaccccatatctgacggttctacacctgctgcctctgctgccatgttgaacaccggcaactttgtactgtatgatatgagcagacaggtcatatggtctactttcagttttccgacagacacattgttggcaggtcagaacttgcgtcctggcagatttcttctttcaagtgtctctcagagtaatcctgccagtggcaagtataggcttgagaaccaacaagatggcaatcttgtgatgtaccctgttggcaccattgattctggtagtgcgtactggtctacctggactttcaacatgggcctcctcctcacgctttcattagatcctaatggtaccatatggatgtttgacaggaaaaactcctatacaaagatactgttccatgccaaccagccttccaatgcctcccctgatatggaaatttactatcatttgacatttgatcccgatggcatcctacgactctactcacatgttttctttaagcttggcagggcacctacaacagaggttgagtggcttgagcctggcagtgatcgctgccttgtgaaaggtgtttgtggtccgaatagcttctgccatctcaccgtgacaggagagacaagctgctcttgccttcctggttttgaattcttgagcactaaccagagcacacttggttgctggagagcattgccaaccggtggctgcgtgaggaacagctctaacgatgagacgagagtgacaaccacgatggtcgaagtgaagaacactacttggttagagaacccgtatgctgttctaccggccacaactagtattgaagcctgcaaactactttgcctctccgattgtggttgcgatatcgccatgtttagtgattcctactgctcaaaacagatgcttccgattagatatggcaggatgcctggtaacaccacactctttgtgaagatctacacttaccagaccatatccggtactcgccaaagggctatgagtatccatgcaaattctgcattgatatcaggagtttccttggccatctttTctctgcttgtgctattagtggcatctctattacttatctgcaggcatcggcgatcattggcgcacatgacgatgacggcaccacggcaagaggactccaggattgatgggaacattgttggcctcagatcctattctttccaggaactagatgtggcaacaaatggtttcggcgaagagcttggcaagggggcatacgggacggtattcaaaggtgtcgtggccgacaccaaccaggtcatcgctgtgaagaggctcgaaaagatggctgaggatgggcagcgtgaatttaacagggaagtgcgtgtgattgcaagaacacaccaccggaacctgctgcgattgcttggtttctgcaatgagggcattcatcgcctgcttgtgtatgagtacatgccaaatggatccctggcaaacctcctctttcactcagatgcctcccctgcctggagcaagagggttgcaattgcactagatgttgccagagggttgcaatacctgcattcagagatagagggcccaataatccactgcgatatcaagccaGagaacatactcattgacagtttggggatagctaagattgctgactttgggctagcaaagctactgattgggaaccaaacaaagacattcaccggcatccgaggaacccggggctatctagcaccggagtggagcaagaacagagcaatcaccgtgaaggcagacgtgtacagctacgggatcatgcttctggaggtcataagctgtaagaaaagcatggatctgaagcgggctggggaggagtacaacatttccgagtgggcatatgagtgtgtgatgtttggtgatgctggcaaggtggcagatggtgtcgacgaagctgagctggtgagaatggtgaacgtcggcatttggtgcacacagagtgaacctgtgatgcgaccagcgatgaagagtGTtgctcttatgattgaaggtgccatcgaaaaaaAtgatgaagtttgcttgaagcgctgcaaagtacagcaagggtcgtccgtctatcagccagttcaaatacatgagcttgcatcatggaacaccctgaaaattgacaaccaagtcttttacattatgcagctataa More
Protein seq	MFPHILFLSLLLLVPEDPNFAAGASANESFITLGSSINTSSTQYWSSSSGRFAFGFYPNGEGFSIGVWLVIGVSRTIVWTANRDEPPIAGGSIIFGHGGALQWSRTPSTPGSQLNPISDGSTPAASAAMLNTGNFVLYDMSRQVIWSTFSFPTDTLLAGQNLRPGRFLLSSVSQSNPASGKYRLENQQDGNLVMYPVGTIDSGSAYWSTWTFNMGLLLTLSLDPNGTIWMFDRKNSYTKILFHANQPSNASPDMEIYYHLTFDPDGILRLYSHVFFKLGRAPTTEVEWLEPGSDRCLVKGVCGPNSFCHLTVTGETSCSCLPGFEFLSTNQSTLGCWRALPTGGCVRNSSNDETRVTTTMVEVKNTTWLENPYAVLPATTSIEACKLLCLSDCGCDIAMFSDSYCSKQMLPIRYGRMPGNTTLFVKIYTYQTISGTRQRAMSIHANSALISGVSLAIFSLLVLLVASLLLICRHRRSLAHMTMTAPRQEDSRIDGNIVGLRSYSFQELDVATNGFGEELGKGAYGTVFKGVVADTNQVIAVKRLEKMAEDGQREFNREVRVIARTHHRNLLRLLGFCNEGIHRLLVYEYMPNGSLANLLFHSDASPAWSKRVAIALDVARGLQYLHSEIEGPIIHCDIKPENILIDSLGIAKIADFGLAKLLIGNQTKTFTGIRGTRGYLAPEWSKNRAITVKADVYSYGIMLLEVISCKKSMDLKRAGEEYNISEWAYECVMFGDAGKVADGVDEAELVRMVNVGIWCTQSEPVMRPAMKSVALMIEGAIEKNDEVCLKRCKVQQGSSVYQPVQIHELASWNTLKIDNQVFYIMQL More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_03g0040470	OsLima_03g0040470.03	Chr03	37894132	37898420	-	IsoSeq
CDS seq	aacgtattcacacacgaatttctaatcgttccagcggcacgcgccgccgcctccatttcccacgctaccggcaccgcccaccgccggacttcctcacccgcggctccggcggcgccaccgcccaccgccggacttccaccgcccgcccaa
Protein seq	NVFTHEFLIVPAARAAASISHATGTAHRRTSSPAAPAAPPPTAGLPPPAQ

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
A3	Chr03	37898111	37898270	-	OsLima_03g0040470.03	OsLima_03g0040470.01,OsLima_03g0040470.03	All
A5	Chr03	37894450	37898047	-	OsLima_03g0040470.03	OsLima_03g0040470.01,OsLima_03g0040470.03	All
MX	Chr03	37894450	37898270	-	OsLima_03g0040470.02	OsLima_03g0040470.02,OsLima_03g0040470.03	All
MX	Chr03	37894450	37898270	-	OsLima_03g0040470.02	OsLima_03g0040470.02,OsLima_03g0040470.01	All

Expression

	Leaf	Root	Panicle
FPKM	0.271485	0.354828	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_03g0828800	RBH	0.172540	0.301019	0.210854
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os03g61310	RBH	0.116598	0.202317	0.054239
Nipponbare \| IRGSP 1.0 \| RAP-db	Os03g0828800	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_03g0040660	RBH	0.000000	0.0	0.247354
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_03g0040330	RBH	0.061437	0.0	0.152578
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_03g0040400	RBH	0.567751	0.0	0.0
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_03g0040620	RBH	0.041353	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_03g0040120	RBH	1.631896	6.705044	15.024420
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_03G0593700	RBH	0.5243275	0.4866635	0.470296
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_03g0039870	RBH	0.137256	0.0	0.107445
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_03G0596400	RBH	0.7260765	0.3968935	1.944333
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_03g0040230	RBH	0.0	0.229695	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_03g0040370	RBH	0.137516	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_03g0040060	RBH	1.386808	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_03g0040140	RBH	0.422968	0.176574	0.255410
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_03g0040190	RBH	0.130557	0.512819	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_03G039910	RBH	0.061556	0.255793	0.277252
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_03g0039660	RBH	0.559774	0.0	0.604041

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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