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
OsLiXu_04g0016910		OGI:04071640 \| 16/16			LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)			Chr04:25478506-25481728		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		atggcgaccaccgccgccgccgccaacctcctcctcttctcagccgtgttgctcctcgccacgccgtcgaacgccgcctcggcggcagcgccggcggtggcggcgatgccggtgcagccgcaggagctgctgctcagcttcaggtcctccctgaacgacccgtccggtgccctgtcgacgtggtcgcgctccacgccgtactgcaactggtcgcacgtcacctgcaccgccgccggcggcggcggcggcgtcgcggtcggcctgtcgctgcagggcctcggactctccggggacatcgccgccgagccgctgtgccgggtgccggggctggcggcgctcagcctcgcgtcgaacaccttcaaccagaccgtcccgctgcagctgtcgcggtgcgcgttgctcgtgtcgctcaacctcagctccgcggggctctggggtccgctccccgaccagctcgccatgctcgcctccctcgcgtcgctcgacctcagcggcaacgacatcgagggtcaggtgccgcccggcctcgccgcgctgcgggggctccaggtgctcgacctcggcggcaaccgcctctccggcgtgctccacccggcgctgttccgcaacctcacgaagctgcacttcctcgacctgtccaagaaccagttcctggagtccgagctgccgccggagctcggcgagatggccggactcaggtggctcttcttgcaggggtcagggttcggcggcgggatccccgagacacttctccagctggagcagcttgaggttcttgacctctccatgaacagcctcaccggagctctgccaccggcgttcggccacaacttccggaagctgctgtccctcgacctctcgcagaatggcttctccgggccgttccccaaggagatcggcaagtgcgtgatgctgcagaggttccaggtgcagggcaacgggttcaccggcgagctccccgccggcctctggtcgctgccggacttgcgggtggtccgcgccgagagcaaccgcttctccggccggctccccgagctgtccgcggcggcgtcccggctcgagcaggtgcaggtcgacaacaacagcatctccggcgagataccccggagcatcggcatggtccgcaccatgtaccggttcaccgcctccgcgaaccggctcgccggcggcctgccggacaccctctgcgactccccggcgatgagcatcatcaacgtctccggcaacgcgctctccggcgcgatcccggagctcacgaggtgcaggaggctggtgtcgctgtcgctgtcgggcaacgcgctcaccggcccgatacctgcgtccctcggcggcctgccggtgctgacgtacattgacgtgtccagcaacggcctcaccggcgccatcccggccgagctccagggcctcaagctcgcgctgctcaacgtctcctacaaccacctcaccggccgcgtcccgccgtcgctggtctccggcgccctccccgccgtgttcctccagggcaaccccggcctgtgcggcctgccggcggacggcggctgcgacgcgccggccgcgccgccgtcgagaaaccgcctcgcgctggccgcaaccgtggcgtccttcgtcaccggcgtgctgctgctgctggctctcggagcgttcgccgtctgcaggaggctgcacgccgccgccaagctggtgctcttctacccgatcaagatcaccgccgacgagctgctcgccgcactccgcgacaagaacgccattggcaggggagcattcggcaaggtctacctgatcgagctgcaagacgggcaaaacatcgcggtcaagaaattcatatgctcaagcaaccaaacattcggagcagtgaagaatcacatgaaaactttcgcaaaaatccggcacaagaacattgccagattgctgggcttctgctacgactcccatggcggcggcggcgaggtgagcgtcatctacgagcacctgaggatggggagcttgcaggatctgataggcgcgccgaagttcgcggtggggtggaacgacaggttgaggatcgcgatcggagtagcagaagggttggtgtaccttcaccgtgattacactcctcgcttgctgcatcgcgatctcaagtcgagcaatgtgttgctgggtgatgattttgagcccagagttaccggatttgggatcgatcgtgtcgttggcgagaaggcgtatcgatcttcgttggcttctgatctgaattacagctgctacatcgctccaggtaagcgtatcattcatacagttcagtccatgcaaccagttcaggacagtgtggatataatgcagttatgatcttcagaagtacgccatccgtttcagattataagtcaaagtcaaactcttcaaatttaatctaagttttatataaaaagtagtaacaaacttcaaacagtttgattttggccaaagttgaaacgacgacttataatcttaaatagagggagtgtatttttttgaacgaattcttcagaagtatttttggtacttaggcatcatcagctcgtttgtgttttcagttatacatttcacccagaagcagaatttcattaggatagctatttccacagcagaattacactcaagatttcataaaactctggctctctgcgcacttatcccactgaagttgtttgctcttttgctgaaaccagaggtaaactgcaccaagaaaccaacgcacctcatggacgtgtacagcttcggcgtcatcctcctggagctgatcaccgggaagccggcggggcagccggcgtcggacgactcggtggacatcgtccggtgggtgcggcggcgggtcaacgtggccggtggcgcggcgcagatactcgaccccgccgccgccgtctcccacgcggcgcagcaggggatgcaggcggcgctggagctcgccctgcgctgcacctcggtgatgcctgaccagagaccggccatggatgaggtcgtccggtcgctgcagctgctgcattcgccgcagactctgccgccaccgccgccgttcaccggagttgctgtggaaccttgagtggaacagctcgtcgagccaggttgcagattacttctgcctcaggacttcaggttgtgcttgagcagaaactaggacgggaattgagatgttcagagtttcagacttgcattgttgtacatagtttgggattctgattgacattggagaaggaatccacttagtataata More
CDS seq		atggcgaccaccgccgccgccgccaacctcctcctcttctcagccgtgttgctcctcgccacgccgtcgaacgccgcctcggcggcagcgccggcggtggcggcgatgccggtgcagccgcaggagctgctgctcagcttcaggtcctccctgaacgacccgtccggtgccctgtcgacgtggtcgcgctccacgccgtactgcaactggtcgcacgtcacctgcaccgccgccggcggcggcggcggcgtcgcggtcggcctgtcgctgcagggcctcggactctccggggacatcgccgccgagccgctgtgccgggtgccggggctggcggcgctcagcctcgcgtcgaacaccttcaaccagaccgtcccgctgcagctgtcgcggtgcgcgttgctcgtgtcgctcaacctcagctccgcggggctctggggtccgctccccgaccagctcgccatgctcgcctccctcgcgtcgctcgacctcagcggcaacgacatcgagggtcaggtgccgcccggcctcgccgcgctgcgggggctccaggtgctcgacctcggcggcaaccgcctctccggcgtgctccacccggcgctgttccgcaacctcacgaagctgcacttcctcgacctgtccaagaaccagttcctggagtccgagctgccgccggagctcggcgagatggccggactcaggtggctcttcttgcaggggtcagggttcggcggcgggatccccgagacacttctccagctggagcagcttgaggttcttgacctctccatgaacagcctcaccggagctctgccaccggcgttcggccacaacttccggaagctgctgtccctcgacctctcgcagaatggcttctccgggccgttccccaaggagatcggcaagtgcgtgatgctgcagaggttccaggtgcagggcaacgggttcaccggcgagctccccgccggcctctggtcgctgccggacttgcgggtggtccgcgccgagagcaaccgcttctccggccggctccccgagctgtccgcggcggcgtcccggctcgagcaggtgcaggtcgacaacaacagcatctccggcgagataccccggagcatcggcatggtccgcaccatgtaccggttcaccgcctccgcgaaccggctcgccggcggcctgccggacaccctctgcgactccccggcgatgagcatcatcaacgtctccggcaacgcgctctccggcgcgatcccggagctcacgaggtgcaggaggctggtgtcgctgtcgctgtcgggcaacgcgctcaccggcccgatacctgcgtccctcggcggcctgccggtgctgacgtacattgacgtgtccagcaacggcctcaccggcgccatcccggccgagctccagggcctcaagctcgcgctgctcaacgtctcctacaaccacctcaccggccgcgtcccgccgtcgctggtctccggcgccctccccgccgtgttcctccagggcaaccccggcctgtgcggcctgccggcggacggcggctgcgacgcgccggccgcgccgccgtcgagaaaccgcctcgcgctggccgcaaccgtggcgtccttcgtcaccggcgtgctgctgctgctggctctcggagcgttcgccgtctgcaggaggctgcacgccgccgccaagctggtgctcttctacccgatcaagatcaccgccgacgagctgctcgccgcactccgcgacaagaacgccattggcaggggagcattcggcaaggtctacctgatcgagctgcaagacgggcaaaacatcgcggtcaagaaattcatatgctcaagcaaccaaacattcggagcagtgaagaatcacatgaaaactttcgcaaaaatccggcacaagaacattgccagattgctgggcttctgctacgactcccatggcggcggcggcgaggtgagcgtcatctacgagcacctgaggatggggagcttgcaggatctgataggcgcgccgaagttcgcggtggggtggaacgacaggttgaggatcgcgatcggagtagcagaagggttggtgtaccttcaccgtgattacactcctcgcttgctgcatcgcgatctcaagtcgagcaatgtgttgctgggtgatgattttgagcccagagttaccggatttgggatcgatcgtgtcgttggcgagaaggcgatagctatttccacagcagaattacactcaagatttcataaaactctggctctctgcgcacttatcccactgaagttgtttgctcttttgctgaaaccagaggtaaactgcaccaagaaaccaacgcacctcatggacgtgtacagcttcggcgtcatcctcctggagctgatcaccgggaagccggcggggcagccggcgtcggacgactcggtggacatcgtccggtgggtgcggcggcgggtcaacgtggccggtggcgcggcgcagatactcgaccccgccgccgccgtctcccacgcggcgcagcaggggatgcaggcggcgctggagctcgccctgcgctgcacctcggtgatgcctgaccagagaccggccatggatgaggtcgtccggtcgctgcagctgctgcattcgccgcagactctgccgccaccgccgccgttcaccggagttgctgtggaaccttga More
Protein seq		MATTAAAANLLLFSAVLLLATPSNAASAAAPAVAAMPVQPQELLLSFRSSLNDPSGALSTWSRSTPYCNWSHVTCTAAGGGGGVAVGLSLQGLGLSGDIAAEPLCRVPGLAALSLASNTFNQTVPLQLSRCALLVSLNLSSAGLWGPLPDQLAMLASLASLDLSGNDIEGQVPPGLAALRGLQVLDLGGNRLSGVLHPALFRNLTKLHFLDLSKNQFLESELPPELGEMAGLRWLFLQGSGFGGGIPETLLQLEQLEVLDLSMNSLTGALPPAFGHNFRKLLSLDLSQNGFSGPFPKEIGKCVMLQRFQVQGNGFTGELPAGLWSLPDLRVVRAESNRFSGRLPELSAAASRLEQVQVDNNSISGEIPRSIGMVRTMYRFTASANRLAGGLPDTLCDSPAMSIINVSGNALSGAIPELTRCRRLVSLSLSGNALTGPIPASLGGLPVLTYIDVSSNGLTGAIPAELQGLKLALLNVSYNHLTGRVPPSLVSGALPAVFLQGNPGLCGLPADGGCDAPAAPPSRNRLALAATVASFVTGVLLLLALGAFAVCRRLHAAAKLVLFYPIKITADELLAALRDKNAIGRGAFGKVYLIELQDGQNIAVKKFICSSNQTFGAVKNHMKTFAKIRHKNIARLLGFCYDSHGGGGEVSVIYEHLRMGSLQDLIGAPKFAVGWNDRLRIAIGVAEGLVYLHRDYTPRLLHRDLKSSNVLLGDDFEPRVTGFGIDRVVGEKAIAISTAELHSRFHKTLALCALIPLKLFALLLKPEVNCTKKPTHLMDVYSFGVILLELITGKPAGQPASDDSVDIVRWVRRRVNVAGGAAQILDPAAAVSHAAQQGMQAALELALRCTSVMPDQRPAMDEVVRSLQLLHSPQTLPPPPPFTGVAVEP
Function		Probably inactive leucine-rich repeat receptor-like protein kinase At5g06940 [UniProtKB/Swiss-Prot:Q9FL51]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLiXu_04g0016910	OsLiXu_04g0016910.01	Chr04	25478506	25481728	+	NAM
CDS seq	atggcgaccaccgccgccgccgccaacctcctcctcttctcagccgtgttgctcctcgccacgccgtcgaacgccgcctcggcggcagcgccggcggtggcggcgatgccggtgcagccgcaggagctgctgctcagcttcaggtcctccctgaacgacccgtccggtgccctgtcgacgtggtcgcgctccacgccgtactgcaactggtcgcacgtcacctgcaccgccgccggcggcggcggcggcgtcgcggtcggcctgtcgctgcagggcctcggactctccggggacatcgccgccgagccgctgtgccgggtgccggggctggcggcgctcagcctcgcgtcgaacaccttcaaccagaccgtcccgctgcagctgtcgcggtgcgcgttgctcgtgtcgctcaacctcagctccgcggggctctggggtccgctccccgaccagctcgccatgctcgcctccctcgcgtcgctcgacctcagcggcaacgacatcgagggtcaggtgccgcccggcctcgccgcgctgcgggggctccaggtgctcgacctcggcggcaaccgcctctccggcgtgctccacccggcgctgttccgcaacctcacgaagctgcacttcctcgacctgtccaagaaccagttcctggagtccgagctgccgccggagctcggcgagatggccggactcaggtggctcttcttgcaggggtcagggttcggcggcgggatccccgagacacttctccagctggagcagcttgaggttcttgacctctccatgaacagcctcaccggagctctgccaccggcgttcggccacaacttccggaagctgctgtccctcgacctctcgcagaatggcttctccgggccgttccccaaggagatcggcaagtgcgtgatgctgcagaggttccaggtgcagggcaacgggttcaccggcgagctccccgccggcctctggtcgctgccggacttgcgggtggtccgcgccgagagcaaccgcttctccggccggctccccgagctgtccgcggcggcgtcccggctcgagcaggtgcaggtcgacaacaacagcatctccggcgagataccccggagcatcggcatggtccgcaccatgtaccggttcaccgcctccgcgaaccggctcgccggcggcctgccggacaccctctgcgactccccggcgatgagcatcatcaacgtctccggcaacgcgctctccggcgcgatcccggagctcacgaggtgcaggaggctggtgtcgctgtcgctgtcgggcaacgcgctcaccggcccgatacctgcgtccctcggcggcctgccggtgctgacgtacattgacgtgtccagcaacggcctcaccggcgccatcccggccgagctccagggcctcaagctcgcgctgctcaacgtctcctacaaccacctcaccggccgcgtcccgccgtcgctggtctccggcgccctccccgccgtgttcctccagggcaaccccggcctgtgcggcctgccggcggacggcggctgcgacgcgccggccgcgccgccgtcgagaaaccgcctcgcgctggccgcaaccgtggcgtccttcgtcaccggcgtgctgctgctgctggctctcggagcgttcgccgtctgcaggaggctgcacgccgccgccaagctggtgctcttctacccgatcaagatcaccgccgacgagctgctcgccgcactccgcgacaagaacgccattggcaggggagcattcggcaaggtctacctgatcgagctgcaagacgggcaaaacatcgcggtcaagaaattcatatgctcaagcaaccaaacattcggagcagtgaagaatcacatgaaaactttcgcaaaaatccggcacaagaacattgccagattgctgggcttctgctacgactcccatggcggcggcggcgaggtgagcgtcatctacgagcacctgaggatggggagcttgcaggatctgataggcgcgccgaagttcgcggtggggtggaacgacaggttgaggatcgcgatcggagtagcagaagggttggtgtaccttcaccgtgattacactcctcgcttgctgcatcgcgatctcaagtcgagcaatgtgttgctgggtgatgattttgagcccagagttaccggatttgggatcgatcgtgtcgttggcgagaaggcgatagctatttccacagcagaattacactcaagatttcataaaactctggctctctgcgcacttatcccactgaagttgtttgctcttttgctgaaaccagaggtaaactgcaccaagaaaccaacgcacctcatggacgtgtacagcttcggcgtcatcctcctggagctgatcaccgggaagccggcggggcagccggcgtcggacgactcggtggacatcgtccggtgggtgcggcggcgggtcaacgtggccggtggcgcggcgcagatactcgaccccgccgccgccgtctcccacgcggcgcagcaggggatgcaggcggcgctggagctcgccctgcgctgcacctcggtgatgcctgaccagagaccggccatggatgaggtcgtccggtcgctgcagctgctgcattcgccgcagactctgccgccaccgccgccgttcaccggagttgctgtggaaccttga More
Protein seq	MATTAAAANLLLFSAVLLLATPSNAASAAAPAVAAMPVQPQELLLSFRSSLNDPSGALSTWSRSTPYCNWSHVTCTAAGGGGGVAVGLSLQGLGLSGDIAAEPLCRVPGLAALSLASNTFNQTVPLQLSRCALLVSLNLSSAGLWGPLPDQLAMLASLASLDLSGNDIEGQVPPGLAALRGLQVLDLGGNRLSGVLHPALFRNLTKLHFLDLSKNQFLESELPPELGEMAGLRWLFLQGSGFGGGIPETLLQLEQLEVLDLSMNSLTGALPPAFGHNFRKLLSLDLSQNGFSGPFPKEIGKCVMLQRFQVQGNGFTGELPAGLWSLPDLRVVRAESNRFSGRLPELSAAASRLEQVQVDNNSISGEIPRSIGMVRTMYRFTASANRLAGGLPDTLCDSPAMSIINVSGNALSGAIPELTRCRRLVSLSLSGNALTGPIPASLGGLPVLTYIDVSSNGLTGAIPAELQGLKLALLNVSYNHLTGRVPPSLVSGALPAVFLQGNPGLCGLPADGGCDAPAAPPSRNRLALAATVASFVTGVLLLLALGAFAVCRRLHAAAKLVLFYPIKITADELLAALRDKNAIGRGAFGKVYLIELQDGQNIAVKKFICSSNQTFGAVKNHMKTFAKIRHKNIARLLGFCYDSHGGGGEVSVIYEHLRMGSLQDLIGAPKFAVGWNDRLRIAIGVAEGLVYLHRDYTPRLLHRDLKSSNVLLGDDFEPRVTGFGIDRVVGEKAIAISTAELHSRFHKTLALCALIPLKLFALLLKPEVNCTKKPTHLMDVYSFGVILLELITGKPAGQPASDDSVDIVRWVRRRVNVAGGAAQILDPAAAVSHAAQQGMQAALELALRCTSVMPDQRPAMDEVVRSLQLLHSPQTLPPPPPFTGVAVEP More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.000000	0.000000	0.000000

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_04g0472500	RBH	0.091201	0.000000	0.177881
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os04g39650	RBH	0.000000	0.000000	0.047302
Nipponbare \| IRGSP 1.0 \| RAP-db	Os04g0472500	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_04g0016740	RBH	0.000000	0.000000	0.728568
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_04g0017490	RBH	0.000000	0.273128	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_04g0017220	RBH	0.000000	0.000000	0.230616
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_04g0016940	RBH	0.000000	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_04g0017180	RBH	0.000000	2.430900	0.597021
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_04G0367400	RBH	7.4905005	24.330746	32.45985
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_04g0015970	RBH	0.000000	0.059676	0.000000
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_04G0366400	RBH	0.3957635	0.853745	8.953487
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_04g0016530	RBH	0.000000	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_04g0016400	RBH	0.000000	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_04g0016400	RBH	0.000000	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_02g0020740	SBH	0.000000	0.052192	0.000000
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_04g0017000	RBH	0.041030	0.671152	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_04G016210	RBH	0.000000	0.0	0.184575
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_04g0016260	RBH	0.000000	0.0	0.273681

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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