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
LOC_Os12g41710		OGI:12066610 \| 16/16			Nipponbare \| IRGSP 1.0 \| MSU			Chr12:25820749-25824699		Homologues MicroCollinearity RGI-JBrowse RGAP Ricevarmap2
Gene Symbol		RLCK373, OsRLCK373
DNA seq		GAGTCGTAGAATTCTTTTTCTTGTTTTCTGTATAATTGAATTGTTTATATGAAATCATTGCAAAATTATCGTGTTTCAAGTAGGGCCTAAATTTTGTAAACCTCAAGGACTAGTATAAACACCAAGGGTTTGTATAGCTGGTGATAATAAAACTCAGATGCTATGTATACAAACAACATTCCTACAATAGTATCTACCTAGCAAAACTACACAAACAAAAAAAAATGTATAAGATCCTCTTTGGCTCTTTCCATCTCCCTTTCAATTTACAACCATTGCTTTTCAGGCATCTTTTCATTCTTCTTTTATATCTTTCTAACCTGAAATCATCTTTTCCTTCAGATATCCAACCTTCCATCAGGGGCTCTCTTCTACCACAGTGCTACCAGCTACTGCAAGCATGGACACCTGGGAGTTGCTGTCTGAAGGAGATTTGGGTGGAGAGGCACTGAACTGAACCGGCTCAACTGTTCTGATTTTCAGGTCCATGACATCTGTGATCAGGCCTGGCCTCATGATCTTATCGCCAATTGCGCACTCGCCCTTGAGCATCTTGACGATCGTCGACATGGAGGGCCTGATCTTCGGAGTATCTTGAGTGCACAGGAGACCTATTTTCAGTAACCGTTGCGCTTCCTCGGTGTCGAAGACGCCTTTCAAGGTGCCGTCAACTAGGCTTTTGAGATCACCGGACTCGTAGAGCGCCCAAGCCTGTCAAAAAAAGCATGAGTTTATGATTTCAGATGCTTTGGACCAGTTCTAAGAGTAGATATCCATGCCATGAAAGTGGTGCTTCAAGTATTGCTGAGCTAATTATTCAATTCTTTTAAGAATCAATTCATCTCAAAGCAATCCATACAATAATTGGACCAACACGGAAACACCAATGGATGTGACTTCAGAATTAGAAAGCCTAGTGGTTGCAGTGACCTGAGTAGCACCCTAAGGTTCTGAGTTCAAATCTCCATAGGAGCGGATTTCAGATTGAGTTGTTTACGAAGCTAAGTTCCCAATTTAAATGGCTGCATATATTCGATTGGATGTAGAGGCCGGGTGAAAAAATAATCTTCTCTAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATCAAGAACCACAAAGCCAGCAAATGCATGTGGTATTGAAGACCATTTCTGACATAATTCAGAGCGGTGGCCCATACAAGAACACGAAGACCCGTCAAAGGGAGCTGATTCAGTTCTATGAATTGTTTACTTTAATAAGAGAGGAAACTTCCTTGTGCATATCATTGCAAAGCTCCCAGTCTCACAAGCATATCAACCATATTATCTGAATTGACCAGTCATTGTGACCAGAACAGGTATGTGCCTAGTGGTTTGTCATACAGGGAACATACGGAATCTATCATAGGTGTTTACTGGACTTATACATAAAAAAATGGTTCTTGCTCCAATTTGTTGTCTGAAATAGCTAAAGAATCAGACAGTAGTCTGGGAGAAGTCATATGCAATAATAATAATGCAGATTTAGAAAAGTTATATGCTATTGTCGGCATTGTTCTTTACCCTTTCGAGTAGGAACTGATCTTGAAGAGGCAATCTGGGGTCAGTGTGGCATCTTCCACTGACAATCTCCAGAAGTAGAACTCCAAAGCTGTAGACGTCGGCCTTCTTTGTCAGCTGCCCTCGGATCGCATACTCCGGTGCAAGATATCCTCTAGAAGGAGAAGAATGAAATGCCAAATTATTCATACACAACAATATGCATGAAAGATCAAAGCTGAAGAGCAACAAGAAAATGCCTCTGCTTACAGTGTTCCTGCAACCCTGGTGCTGATATGCGTCATGTTGCCCGGGAAAAGCTTTGCCAGCCCAAAATCTGATATCTTGGGGCTCAGATCCTTGTCAAGAAGAATGTTGCTTGCCTTGATATCACGGTGGACGATGACCGGCCGGACTTCTTCATGAAGATACTTGAGCCCACTCGCGACGCCGATGCATATTTTCACTCTTGTTTTCCAGTCTAATTGGATACTACTATGGGAATTGCCTGAAGGACATGATCATGATGCTTCAGAGATTCAGAGTTCTGAGAACAAAACGTATCACAAATTCACCATGATTTGAGAATCTAGTGGAAACTGATTTTTTTTTTTGTTCTTTACCAAAGAGGGACTGTGCAAGACTGTTGTTCTCCAGGTAATTGTAGACCAGCATTTTCTGATCTCCGTCGACGCAGCAGCCATGCAATTTCACAAGATTGTGATGGTTTATGTTGGATATGACACTCAGCTCATTTAAGAACTCCCTTGTTCCTTGCCTTGACTCGGAGGAGAGCACCTTGATGGCAACTTTCTGACCATTCCTGAGCTTTCCCTGAACAATTCATGTGAGGAAATGCGAAATCATGTTAATGACTGGTCCAAATGGTACAGCCATAGAAACTTCTAAGCATGAAGAGAATGGCAATATTGCTTCTACCACTGTTCACTAATTCATTGATAGAAACTGCATGAAGAGTATATGTATATATTCATCAGTTTATGATAATTCAGGCATTTGGAGGAACTAATTGGGTTATGGCACACAGGGCTTTGAGCTTTGGACTTTGAAATGTCAATGCTTGAAATGACTAGCAAGCTACCAGGTAGACGCAGCCAAAAGAACCCTGTCCTAGTTTGTGTCCTGAGCAGAAATTTTTTGTGGCTTTTCTGAGCTCCTTGGAGGAGTAGATCTTCACATTTCTGATGATCGGTGTATCTGGGAAAGAACAAGATCAATCAGAAGAAGGCATCTGGATGTTTCAGAAGAAGAAAATTTGATGAAATGTGAGGGTTTACCTTTGTCATGCTGCACAATTTGACTCCTGGATTTTTTGTTTCTCCAGAACGCAGGAAAGCAAGTCATTACTGTAATTCAGGGTTTTTCTTCTAGGACTCTTCAGCTATATCTTCAGAATATCATGTAGAGATCACCGTAAAAGTACTCTTGGTATAAAAGTATAAACCTGAGAGAAAATAATCGATCGATAAAAAGAGATTGAGATAATGTAGTACTTTGTTGAAAAATTCTACACAATGAACCTACTTTTCTCTTTCTAGAGTAATTTCAAGAAAAAAGGGCAAAACTCATGCCCTCAAGGAAGAAAAGACACACCGTCTCTTTTCTTGTGTTTCTCCTTGCTGTGAGCCCAGAGAGCAGAAACGAAGAACAAAATCTCTAGAAAACTCAGAAAAATTGTAACAAAGAAATAAAGACATGAAGTATGCAAATCTGACAGAGAAACACTCGTCCCAGTCAGAGTTAAGAATTGTATGTTGTCCAACAAAATCCATGAGAAAAAACACTTGTATTCACATTGAATTGTAGAGTAACCAAGTTTGCGGTGTGACCGTTGATCTTCAGAAGATGAACTGACGGTTACAAACAGAAATAGATGAACTGATGATAAGCACAAGAACCGAAAGGAAGAGCCCATTAAATACAGTCTAATCCAAAGAAAACTGAACTAATACCTTTCCTGAAAAAGGTTTCCATGAAAAACTTTCCCTAGATGAATTGAAATATTCAGTAGAGACAAGAGCAATGAAATTCTTGCAACAGACCTAGACACAGAATTTAGTAGATTCAGCAATGAAGAAAAAAAAATCCAATAAGCAAAACTCACCTGAAGATCAGTTAATTCACCAGCAGAAAGACTTGAGGCCTGTAATCTGTATGAATATCCAAGAACAGCCAGCACCCAGCAAAGAACTCTTGGAGAAGAGGAGAAAGAAGAGGAGAGAGTATGAATCTGCAATTTTAGAAGCAAAAGCATACTGCTCTCTGCCCTGAATCCCTGAATATATGGGAGTCCACCAGCAGATGTCCCACTGGGATTGACTTTAGCTGGTTGCAACTCTGGGAAGTAGCATGGAAAAGACATAG More
CDS seq		ATGACTTGCTTTCCTGCGTTCTGGAGAAACAAAAAATCCAGGAGTCAAATTGTGCAGCATGACAAAGATACACCGATCATCAGAAATGTGAAGATCTACTCCTCCAAGGAGCTCAGAAAAGCCACAAAAAATTTCTGCTCAGGACACAAACTAGGACAGGGTTCTTTTGGCTGCGTCTACCTGGGAAAGCTCAGGAATGGTCAGAAAGTTGCCATCAAGGTGCTCTCCTCCGAGTCAAGGCAAGGAACAAGGGAGTTCTTAAATGAGCTGAGTGTCATATCCAACATAAACCATCACAATCTTGTGAAATTGCATGGCTGCTGCGTCGACGGAGATCAGAAAATGCTGGTCTACAATTACCTGGAGAACAACAGTCTTGCACAGTCCCTCTTTGGCAATTCCCATAGTAGTATCCAATTAGACTGGAAAACAAGAGTGAAAATATGCATCGGCGTCGCGAGTGGGCTCAAGTATCTTCATGAAGAAGTCCGGCCGGTCATCGTCCACCGTGATATCAAGGCAAGCAACATTCTTCTTGACAAGGATCTGAGCCCCAAGATATCAGATTTTGGGCTGGCAAAGCTTTTCCCGGGCAACATGACGCATATCAGCACCAGGGTTGCAGGAACACTAGGATATCTTGCACCGGAGTATGCGATCCGAGGGCAGCTGACAAAGAAGGCCGACGTCTACAGCTTTGGAGTTCTACTTCTGGAGATTGTCAGTGGAAGATGCCACACTGACCCCAGATTGCCTCTTCAAGATCAGTTCCTACTCGAAAGGGCTTGGGCGCTCTACGAGTCCGGTGATCTCAAAAGCCTAGTTGACGGCACCTTGAAAGGCGTCTTCGACACCGAGGAAGCGCAACGGTTACTGAAAATAGGTCTCCTGTGCACTCAAGATACTCCGAAGATCAGGCCCTCCATGTCGACGATCGTCAAGATGCTCAAGGGCGAGTGCGCAATTGGCGATAAGATCATGAGGCCAGGCCTGATCACAGATGTCATGGACCTGAAAATCAGAACAGTTGAGCCGGTTCAGTTCAGTGCCTCTCCACCCAAATCTCCTTCAGACAGCAACTCCCAGGTGTCCATGCTTGCAGTAGCTGGTAGCACTGTGGTAGAAGAGAGCCCCTGA More
Protein seq		MTCFPAFWRNKKSRSQIVQHDKDTPIIRNVKIYSSKELRKATKNFCSGHKLGQGSFGCVYLGKLRNGQKVAIKVLSSESRQGTREFLNELSVISNINHHNLVKLHGCCVDGDQKMLVYNYLENNSLAQSLFGNSHSSIQLDWKTRVKICIGVASGLKYLHEEVRPVIVHRDIKASNILLDKDLSPKISDFGLAKLFPGNMTHISTRVAGTLGYLAPEYAIRGQLTKKADVYSFGVLLLEIVSGRCHTDPRLPLQDQFLLERAWALYESGDLKSLVDGTLKGVFDTEEAQRLLKIGLLCTQDTPKIRPSMSTIVKMLKGECAIGDKIMRPGLITDVMDLKIRTVEPVQFSASPPKSPSDSNSQVSMLAVAGSTVVEESP
Function		Cold-responsive protein kinase 1 [UniProtKB/Swiss-Prot:Q93YN1]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
LOC_Os12g41710	LOC_Os12g41710.1	Chr12	25820749	25824699	-	MSU_osa1r7
CDS seq	ATGACTTGCTTTCCTGCGTTCTGGAGAAACAAAAAATCCAGGAGTCAAATTGTGCAGCATGACAAAGATACACCGATCATCAGAAATGTGAAGATCTACTCCTCCAAGGAGCTCAGAAAAGCCACAAAAAATTTCTGCTCAGGACACAAACTAGGACAGGGTTCTTTTGGCTGCGTCTACCTGGGAAAGCTCAGGAATGGTCAGAAAGTTGCCATCAAGGTGCTCTCCTCCGAGTCAAGGCAAGGAACAAGGGAGTTCTTAAATGAGCTGAGTGTCATATCCAACATAAACCATCACAATCTTGTGAAATTGCATGGCTGCTGCGTCGACGGAGATCAGAAAATGCTGGTCTACAATTACCTGGAGAACAACAGTCTTGCACAGTCCCTCTTTGGCAATTCCCATAGTAGTATCCAATTAGACTGGAAAACAAGAGTGAAAATATGCATCGGCGTCGCGAGTGGGCTCAAGTATCTTCATGAAGAAGTCCGGCCGGTCATCGTCCACCGTGATATCAAGGCAAGCAACATTCTTCTTGACAAGGATCTGAGCCCCAAGATATCAGATTTTGGGCTGGCAAAGCTTTTCCCGGGCAACATGACGCATATCAGCACCAGGGTTGCAGGAACACTAGGATATCTTGCACCGGAGTATGCGATCCGAGGGCAGCTGACAAAGAAGGCCGACGTCTACAGCTTTGGAGTTCTACTTCTGGAGATTGTCAGTGGAAGATGCCACACTGACCCCAGATTGCCTCTTCAAGATCAGTTCCTACTCGAAAGGGCTTGGGCGCTCTACGAGTCCGGTGATCTCAAAAGCCTAGTTGACGGCACCTTGAAAGGCGTCTTCGACACCGAGGAAGCGCAACGGTTACTGAAAATAGGTCTCCTGTGCACTCAAGATACTCCGAAGATCAGGCCCTCCATGTCGACGATCGTCAAGATGCTCAAGGGCGAGTGCGCAATTGGCGATAAGATCATGAGGCCAGGCCTGATCACAGATGTCATGGACCTGAAAATCAGAACAGTTGAGCCGGTTCAGTTCAGTGCCTCTCCACCCAAATCTCCTTCAGACAGCAACTCCCAGGTGTCCATGCTTGCAGTAGCTGGTAGCACTGTGGTAGAAGAGAGCCCCTGA More
Protein seq	MTCFPAFWRNKKSRSQIVQHDKDTPIIRNVKIYSSKELRKATKNFCSGHKLGQGSFGCVYLGKLRNGQKVAIKVLSSESRQGTREFLNELSVISNINHHNLVKLHGCCVDGDQKMLVYNYLENNSLAQSLFGNSHSSIQLDWKTRVKICIGVASGLKYLHEEVRPVIVHRDIKASNILLDKDLSPKISDFGLAKLFPGNMTHISTRVAGTLGYLAPEYAIRGQLTKKADVYSFGVLLLEIVSGRCHTDPRLPLQDQFLLERAWALYESGDLKSLVDGTLKGVFDTEEAQRLLKIGLLCTQDTPKIRPSMSTIVKMLKGECAIGDKIMRPGLITDVMDLKIRTVEPVQFSASPPKSPSDSNSQVSMLAVAGSTVVEESP More

Gene	Transcript	Chromosome	Start	End	Strand	Source
LOC_Os12g41710	LOC_Os12g41710.2	Chr12	25820749	25824699	-	MSU_osa1r7
CDS seq	ATGACGCATATCAGCACCAGGGTTGCAGGAACACTAGGATATCTTGCACCGGAGTATGCGATCCGAGGGCAGCTGACAAAGAAGGCCGACGTCTACAGCTTTGGAGTTCTACTTCTGGAGATTGTCAGTGGAAGATGCCACACTGACCCCAGATTGCCTCTTCAAGATCAGTTCCTACTCGAAAGGGCTTGGGCGCTCTACGAGTCCGGTGATCTCAAAAGCCTAGTTGACGGCACCTTGAAAGGCGTCTTCGACACCGAGGAAGCGCAACGGTTACTGAAAATAGGTCTCCTGTGCACTCAAGATACTCCGAAGATCAGGCCCTCCATGTCGACGATCGTCAAGATGCTCAAGGGCGAGTGCGCAATTGGCGATAAGATCATGAGGCCAGGCCTGATCACAGATGTCATGGACCTGAAAATCAGAACAGTTGAGCCGGTTCAGTTCAGTGCCTCTCCACCCAAATCTCCTTCAGACAGCAACTCCCAGGTGTCCATGCTTGCAGTAGCTGGTAGCACTGTGGTAGAAGAGAGCCCCTGA More
Protein seq	MTHISTRVAGTLGYLAPEYAIRGQLTKKADVYSFGVLLLEIVSGRCHTDPRLPLQDQFLLERAWALYESGDLKSLVDGTLKGVFDTEEAQRLLKIGLLCTQDTPKIRPSMSTIVKMLKGECAIGDKIMRPGLITDVMDLKIRTVEPVQFSASPPKSPSDSNSQVSMLAVAGSTVVEESP

Gene	Transcript	Chromosome	Start	End	Strand	Source
LOC_Os12g41710	LOC_Os12g41710.3	Chr12	25820840	25824699	-	MSU_osa1r7
CDS seq	ATGACGCATATCAGCACCAGGGTTGCAGGAACACTAGGATATCTTGCACCGGAGTATGCGATCCGAGGGCAGCTGACAAAGAAGGCCGACGTCTACAGCTTTGGAGTTCTACTTCTGGAGATTGTCAGTGGAAGATGCCACACTGACCCCAGATTGCCTCTTCAAGATCAGTTCCTACTCGAAAGGGCTTGGGCGCTCTACGAGTCCGGTGATCTCAAAAGCCTAGTTGACGGCACCTTGAAAGGCGTCTTCGACACCGAGGAAGCGCAACGGTTACTGAAAATAGGTCTCCTGTGCACTCAAGATACTCCGAAGATCAGGCCCTCCATGTCGACGATCGTCAAGATGCTCAAGGGCGAGTGCGCAATTGGCGATAAGATCATGAGGCCAGGCCTGATCACAGATGTCATGGACCTGAAAATCAGAACAGTTGAGCCGGTTCAGTTCAGTGCCTCTCCACCCAAATCTCCTTCAGACAGCAACTCCCAGGTGTCCATGCTTGCAGTAGCTGGTAGCACTGTGGTAGAAGAGAGCCCCTGA More
Protein seq	MTHISTRVAGTLGYLAPEYAIRGQLTKKADVYSFGVLLLEIVSGRCHTDPRLPLQDQFLLERAWALYESGDLKSLVDGTLKGVFDTEEAQRLLKIGLLCTQDTPKIRPSMSTIVKMLKGECAIGDKIMRPGLITDVMDLKIRTVEPVQFSASPPKSPSDSNSQVSMLAVAGSTVVEESP

Gene	Transcript	Chromosome	Start	End	Strand	Source
LOC_Os12g41710	LOC_Os12g41710.4	Chr12	25820840	25824699	-	MSU_osa1r7
CDS seq	ATGACGCATATCAGCACCAGGGTTGCAGGAACACTAGGATATCTTGCACCGGAGTATGCGATCCGAGGGCAGCTGACAAAGAAGGCCGACGTCTACAGCTTTGGAGTTCTACTTCTGGAGATTGTCAGTGGAAGATGCCACACTGACCCCAGATTGCCTCTTCAAGATCAGTTCCTACTCGAAAGGGCTTGGGCGCTCTACGAGTCCGGTGATCTCAAAAGCCTAGTTGACGGCACCTTGAAAGGCGTCTTCGACACCGAGGAAGCGCAACGGTTACTGAAAATAGGTCTCCTGTGCACTCAAGATACTCCGAAGATCAGGCCCTCCATGTCGACGATCGTCAAGATGCTCAAGGGCGAGTGCGCAATTGGCGATAAGATCATGAGGCCAGGCCTGATCACAGATGTCATGGACCTGAAAATCAGAACAGTTGAGCCGGTTCAGTTCAGTGCCTCTCCACCCAAATCTCCTTCAGACAGCAACTCCCAGGTGTCCATGCTTGCAGTAGCTGGTAGCACTGTGGTAGAAGAGAGCCCCTGA More
Protein seq	MTHISTRVAGTLGYLAPEYAIRGQLTKKADVYSFGVLLLEIVSGRCHTDPRLPLQDQFLLERAWALYESGDLKSLVDGTLKGVFDTEEAQRLLKIGLLCTQDTPKIRPSMSTIVKMLKGECAIGDKIMRPGLITDVMDLKIRTVEPVQFSASPPKSPSDSNSQVSMLAVAGSTVVEESP

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.119130	0.388853	0.184350

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_12g0574700	SBH	0.085684	0.0	0.158709
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os03g44140	SBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os12g0574700	SBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_12g0020480	RBH	0.537014	1.109105	1.923650
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_12g0020580	RBH	0.0	0.808210	0.788525
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_12g0020920	RBH	1.030617	6.886726	2.053297
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_12g0020230	RBH	0.041983	0.000000	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_12g0019820	RBH	0.986022	3.047392	7.619263
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_12G0347400	RBH	2.7500945	32.6012325	0.819948
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_12g0019720	RBH	0.182210	0.159759	0.639804
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_12G0376900	RBH	3.1579	41.4187205	0.3747955
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_12g0019960	RBH	0.034753	0.230908	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_12g0020190	RBH	0.000000	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_12g0020140	RBH	1.258959	7.702566	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_12g0020170	RBH	0.893615	0.0	0.400186
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_12g0020360	RBH	0.483095	0.457500	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_12G019870	RBH	0.265773	0.0	0.449621
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_12g0019660	RBH	1.084110	16.445843	1.585951

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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