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
OsARC_02g0029780		OGI:02081330 \| 16/16			ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)			Chr02:28689722-28695552		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		CDKF;4, CDKF;4, Orysa;CDKF;4
DNA seq		GCCGGAGACGGGACGGGTTTGAGGTTGGGGAGTATGGTTATAAAAAGTAACGGGGCGCGACGCGGGTAGAAACCGTGGTGGAGGCAAAGGCGCCGCGGGCTTGGCTTGGCTGGCACCCTCTCCTTCTCGTCTTCGGCTTCGTCTTCCCCCGTCAAACCCACCCACGCCGGCCGCCGACGCCGCCGCCGTTGCGGCGGGTGCTTCCCCCGCTCGCGTCGGTGCCGGGGGGCTGAGGGGAAGAGGGGGAGGGGGAGGGAAGGCACGCGGCTGACCTCGTGGGGGAGGGGAGGGGGGGAACGGGGCGACACCACCCACCCACCGCCACCATGTGCTCGTTGCCCGCCTGGTAAGGTATGGTATCTGTTTCATTCCATTGCCCCCCATCTTTCTCGTGCTTGCGCCCCTGCCCCCGCCGCTGTACTTTCGCGTGCCCTGGATTAGCTGGTTGGTTCATCTGCTTGTTGCGGCGCGCGGCGGATCTGTGCCTCCAGCCGCCGGATCTGGGTGGTTCGCGGGCGTTCGGTGCAATGCGAGTCTGCGCGTAAGTTTTTTTTTGTGTGTTGTGGTGAACAGTGGTGATAATTATTGCAGGGTTTTTTTTTTATCTTGTGGGGGTCGTGTCCCTGTTGGGACCTCGGATCTGTTCTTGTTTCGTGGCTAATTTGGATTTTATGGCAGAAGGAAGACGTTTTGTCACAATAGATTGAGAACGCTCTCTTTTTCCTTCCCATGGATGGTCATAATCTGTGCCTTTTGGTGCTTAGCGTTGTAATTTGTGATTAGGGTAGCAATGCAGATTGTTTCACATCATGTTCCAACCCAAGGCAATGCTTCTGAGTTACGAAATGTTTGTAATATTTATGACCTTGCTGTCTTGCCATGCTTGATCGATCATTGTTGTTAAATTGGATACCCGCATTACTTCCAATTTTTTGCACTTCTTAGGTAGTTAGGGGTATAGGATGATCATTCCATGTCGACGCCTTATTGCAACTGATTGAATAGTAGCATCGGTGTCAATATTTTGTCAATGCAGCAGCAACACTCTACCTTATCAGGCAATGTTACCTATAGTGCATTTTTTTTTATTCTAGGAGGAAGTGTATTTGTTTGCTGCCAAGAAGGCAGTGCTTCATTTTGCACACATCAGTTTTGGTACTTGCATCATGTGGCCTGTACATCATTGTTTGCAAAGAAGAGAAAGCTGAAGCGCTATAAATCCTTCAAGCAGTTTTTTCGGTCTAAACCCAGCCATATCTGAGTATGTTAGAATGATTATTATGTGCAAGGTTTCTGTCGGTTTTGATTGTGATCCTCAGACATACCTTGTGACGCAGATATTCATGCTGAGTTGATTCCTTCTAGTCACTTTGCATGTACCTATAGTTTGAACATGTGCACGGAAGTAATGATCTTTGACTGTGTTATATGTTTCTGACTTAAATCTGTTATATTAGATTGGACCAGCTGTGATTTGGGGAGCTTAAAGTGTTGATCAGAGACATGGAAAAAGTGATCTTCTGGGCACATCTCCTTAAATGCAAGCTTTTTCTTTCAAAAGAAACTCTTGATTGGTGTGTTTTAGCTCGTGGGAACACCCACCACTTCTCTCTGGTGAACTACACATAGTGGTTTTATGCTCCTTTATGCTCAAGAACATTTGGCTGATTCAATCTTTTTCCTGAAGCCATATTTCAAGTCTGCCAAACATCTACATGTAATGCACCTACTTCATAGCTTGTTCTTCCTTCATTTTGTGTCATATGGACTAATTTAGCTAACCACCATCTTTTTATTCTACTAGCACGTCATCTCTAAAGAAGCTTCCTTTAAGTTGTAGATGCTGATCATATAAGCTGGGTATGCCTCTTTTTACTGTTCATTGATGCATTTATTGGCATTTAGAGAAATAAATTCTTGCAACTTGAAATATTCTAAACAACTTACTCCTTCCCTTATTTTGTAGGGTTAATACCTTTGCTCATTTGTTTGTCATCTGTTGCTCCCTAGTTAATTACCACTAGTGTTGCATTGAGGTCAGGGTTCATCCTTGCTATAGTATGCAACTATATACTATGGTTGCTGCTTGATCTTCTGAGTGAACCAAGATCCAAGAAAACATAAGGTGCTGGGGCTACTGTTCAATTGACTGGTTGCATATATTTGTTCGTGCTAATCGATAGACTAGTCAATTGGAAGTGGTGGCAAACACCTGTCTTTGTGACTTGGCTGTCCAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAGGTAACTTTCATATTGACTTACTATTTTTAGGTCACCTTTTTCTTATCAAGTATGTTGTCTTTGCAGATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTTGTATGTATCTGAAGATAAATCCATAGGAGGAAATATGCATTTCATACTTTTGCAAAATATTCCCAGTGAAATAAATAACTGATTGTAAGCAAAATGTGCACTGATCTATAGGTGGCAGTTAAGAAAATGAAGAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAAGTAAAGGTATTTTAACTGAAAGATGTACCCTCTTTCCTGCTATGAACCTTCAACTGATATTTCTCCTATATTGAAGTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATGGTACTTAAGGATGTCATATACCGCAAAAGTTTAATTAGCTCTGTATCGCTTTTGTTAAGTCTCCCATGTTCTTCCAGGAGTGCAATCTCTACCAGCTTATGAAGGATAGAGTCAAGCCTTTCTCAGAGGCAGAAGTCCGGAATTGGTGCTTTCAGATTTTTCAGGCTCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTGGTAGGTTCTCTTGTTTAGTCAACATCTTCACCTATATTTCTGTGGCAATCAAATTATGAAACTACGGATGAGTATCAGATGTAGGTATGCAGAATCAGGGTATTATTGTATTGAGAATATGAGACATTTAGCCTTTATTTTTACCACATCTACTTTGCAAACTGACCGAGATATACTTTCTAATAAATATATACTTTCATGTGGGATTGTATTGTGCTTATAGCTATGGCACTAATCACTGTACTAATGCAGAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCGCTGGTTAGTAGCACTCTACTCGCACACGTGGACACAAATCCCTTTTCTTTGTTAATGTTGATCCACATGTGTTTGAACATCTCAGGTACCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGGTAAAGTTTCTACTATCTACTTTGTATTTTGGCACATATAGTACATACTAAGTCATGATTGGATGATCCCCTTTTTGCCAACTTGCAGATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGGTATAATATGCATATATCATATGTATATGCATTGTTGTTATGATTTGTAGTCACGTATCTCTCTGTGTTTGCCATGTATTTTGGGCATCTGTTATTCTGTCTCTCTTATTATATTTCTTCTTTGTGGTGGTCATATTTGCTCATTGCTGTTCTCTTTATCCAACTGTTTAGTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGAACAATCATGGCCACAAGGATTGTCTCTTGCAGAGACCATGAAGTTTCAGTTCCCTCAGGTCAGTATTCATCTTCCCCTTTTCCCTTTGCCTATATATGTTTTCTTTTGGGGGTAAGCTCTTTGTTGTGATTATACTTGTTTCTGAATGTGTCATGAATCTTTGATATGTGTTGAGCCCATTCTGCAACTGTTTATTTTAATCCCTTGGTCATTCTCTGATGAATTTTGTCCTTGTGCCTCCCTATCTCTCTAGACAATGGTGGAATTATATCACTTCGCATGCCTTACAATCTTTCATCTCCATTAGTCCATTGCCTCCTTTTCCTCGCATATTATCATAGGTTTAAAAGCGTAGTGTCTTGTTCTAACTTGATTCATGAGTTTGACATAGATTGTCCATAAATAGTGGCTTAACACTTAACTAATCTCATGTGGATCTTATCAATGCAGGTCAGTGGCAATCAACTGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCAGTAAGTTCTACAATTCTGTTGCCCCAGATGGCGTACTTAAAATCTTTAGATTATTTTATTATATTTGTTTCTTTCTACATCTGCAGTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGGTAAAATTACTATTCGAACTCCGTTGCTGTTGTCTGTACCTCTGTTGCAGAAGATAAATCAAATTTATTTTTGCCATCCACTAGGGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCTAAAACGCCTCCATGTGGTTAGTTTCCACACTGTTTTGCCTCACAACCTTGGTGTTCCTGGTACTCTTGTTATATCTATGATCTATTTGTTTCAGTTGGAGTAAAAGGAGTTTCGGAGCACGGCATGCCTCGAAGATACTCTACAGGAACTCTATCAACAACCAAACCTCATAGTAATGCATCTCTGAAATCAAGTGGCTTATCTAAGACCGGTAATATGTTTAATCTTTTTTCTCAATTGCTTGTTAGCTTGCATTGTAGGCTATATTTTTATTTCTCTTTCCACCTTCCAGGTGTACAAAGAAAACTTCAAATGGATCGTCAGGCGCCACAGAAGATTAAAAAACCTACTGAGAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGGCAAGTTTCCATAGTTGCTTTATTTGAATTCTACATCAATTTGTGGTTGACTTTGAAGATTTACATTCCCTTTGTGGCAATTATAGGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAACAATGCACAAGGTTTCAACCCTTACCGAGAGATTAACTCATATGTCTGTTACCTCTCGAACGCGTACTACTCCCAAGCCTGCTGCCCCGTTACTGAAGGCTGGGCTCGGCAAGTCTGACTTACTGGGAAAAACAGACGAAATACCTCCTGCAAAGAGGTTGACAAGAAAATTAGTAAGCTAACGTAGCAGCATCCATACAGTGGAAGCTGGTTAGCTGGTGCAGAGAGGTGTTATAAGCTACAGAGCAAAATCCCGGTCTGCTGAAAATGATGGCACTGCCGGAGTGTTTGCCAAATTTGCTGCATCCAAGTGCCATAGTAGAATAAGTCGAGCCTGCCGATCCACGTGGATCTGCTTTTGCCCCAAGTTTGTTCCATGTTTGAATAGAACATGAGTGTGCTATATCGATTTGAATTGTTGTCGACCAGTGTTCACTCGCATATGCGGTCTGACAAATGATAGACCCGCGAGCAGGAGGATGTTTGGCTTTTGCTTGTACAGTTTATGAGCTTTTGGGTGGCGGTCAAGTCTTTGTCGGGTCCTTGGCAAATGATACAATGCATAGTCTGGTTTTGACTTCGTCTGTGGCTCTATTCAGGTCTTTGTTTGAAGATGATGTCTCATTTCTCATG More
CDS seq		ATGAAGAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAAGTAAAGTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATGGAGTGCAATCTCTACCAGCTTATGAAGGATAGAGTCAAGCCTTTCTCAGAGGCAGAAGTCCGGAATTGGTGCTTTCAGATTTTTCAGGCTCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTGAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCGCTGGTACCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGAACAATCATGGCCACAAGGATTGTCTCTTGCAGAGACCATGAAGTTTCAGTTCCCTCAGGTCAGTGGCAATCAACTGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCATCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGGGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCTAAAACGCCTCCATGTGTTGGAGTAAAAGGAGTTTCGGAGCACGGCATGCCTCGAAGATACTCTACAGGAACTCTATCAACAACCAAACCTCATAGTAATGCATCTCTGAAATCAAGTGGCTTATCTAAGACCGGTGTACAAAGAAAACTTCAAATGGATCGTCAGGCGCCACAGAAGATTAAAAAACCTACTGAGAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAACAATGCACAAGGTTTCAACCCTTACCGAGAGATTAACTCATATGTCTGTTACCTCTCGAACGCGTACTACTCCCAAGCCTGCTGCCCCGTTACTGAAGGCTGGGCTCGGCAAGTCTGACTTACTGGGAAAAACAGACGAAATACCTCCTGCAAAGAGGTTGACAAGAAAATTAGTAAGCTAA More
Protein seq		MKRKYYSFEECMSLREVKSLRRMNHPNIVKLKEVIRENDILYFIMEYMECNLYQLMKDRVKPFSEAEVRNWCFQIFQALAYMHQRGYFHRDLKPENLLVSKDVIKLADFGLAREVTSVPPYTEYVSTRWYRAPEVLLQSSIYDSAVDMWAMGAIMAELLTLHPLFPGTSEADEILKICNVIGSPDEQSWPQGLSLAETMKFQFPQVSGNQLAEVMTSVSSEAVDLISSLCSWDPCKRPKAAEVLQHTFFQGCTFVPPTVRSKAGVLPKTPPCVGVKGVSEHGMPRRYSTGTLSTTKPHSNASLKSSGLSKTGVQRKLQMDRQAPQKIKKPTESNNKLTTNRVPARNSPGHPVLRHSRSLPETGRATMHKVSTLTERLTHMSVTSRTRTTPKPAAPLLKAGLGKSDLLGKTDEIPPAKRLTRKLVS
Function		Cyclin-dependent kinase F-4 [UniProtKB/Swiss-Prot:Q6Z8C8]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_02g0029780	OsARC_02g0029780.01	Chr02	28692151	28695552	+	NAM
CDS seq	ATGAAGAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAAGTAAAGTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATGGAGTGCAATCTCTACCAGCTTATGAAGGATAGAGTCAAGCCTTTCTCAGAGGCAGAAGTCCGGAATTGGTGCTTTCAGATTTTTCAGGCTCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTGAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCGCTGGTACCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGAACAATCATGGCCACAAGGATTGTCTCTTGCAGAGACCATGAAGTTTCAGTTCCCTCAGGTCAGTGGCAATCAACTGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCATCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGGGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCTAAAACGCCTCCATGTGTTGGAGTAAAAGGAGTTTCGGAGCACGGCATGCCTCGAAGATACTCTACAGGAACTCTATCAACAACCAAACCTCATAGTAATGCATCTCTGAAATCAAGTGGCTTATCTAAGACCGGTGTACAAAGAAAACTTCAAATGGATCGTCAGGCGCCACAGAAGATTAAAAAACCTACTGAGAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAACAATGCACAAGGTTTCAACCCTTACCGAGAGATTAACTCATATGTCTGTTACCTCTCGAACGCGTACTACTCCCAAGCCTGCTGCCCCGTTACTGAAGGCTGGGCTCGGCAAGTCTGACTTACTGGGAAAAACAGACGAAATACCTCCTGCAAAGAGGTTGACAAGAAAATTAGTAAGCTAA More
Protein seq	MKRKYYSFEECMSLREVKSLRRMNHPNIVKLKEVIRENDILYFIMEYMECNLYQLMKDRVKPFSEAEVRNWCFQIFQALAYMHQRGYFHRDLKPENLLVSKDVIKLADFGLAREVTSVPPYTEYVSTRWYRAPEVLLQSSIYDSAVDMWAMGAIMAELLTLHPLFPGTSEADEILKICNVIGSPDEQSWPQGLSLAETMKFQFPQVSGNQLAEVMTSVSSEAVDLISSLCSWDPCKRPKAAEVLQHTFFQGCTFVPPTVRSKAGVLPKTPPCVGVKGVSEHGMPRRYSTGTLSTTKPHSNASLKSSGLSKTGVQRKLQMDRQAPQKIKKPTESNNKLTTNRVPARNSPGHPVLRHSRSLPETGRATMHKVSTLTERLTHMSVTSRTRTTPKPAAPLLKAGLGKSDLLGKTDEIPPAKRLTRKLVS More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsARC_02g0029780	OsARC_02g0029780.02	Chr02	28689722	28695501	+	IsoSeq
CDS seq	ATGCTCCTTTATGCTCAAGAACATTTGGCTGATTCAATCTTTTTCCTGAAGCCATATTTCAAGTCTGCCAAACATCTACATCACGTCATCTCTAAAGAAGCTTCCTTTAAG
Protein seq	MLLYAQEHLADSIFFLKPYFKSAKHLHHVISKEASFK

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.025781	1.978131	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_02g0700600	RBH	2.051837	3.009068	26.007885
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os02g47220	RBH	1.025902	1.121897	6.035221
Nipponbare \| IRGSP 1.0 \| RAP-db	Os02g0700600	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_02g0030240	RBH	0.384334	94.858284	37.680092
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_02g0030330	RBH	0.471104	13.926110	22.739553
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_02g0030190	RBH	0.842514	71.670586	80.974892
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_04g0018120	SBH	0.889525	0.518265	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_02g0030000	RBH	2.644928	80.128044	73.014198
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_02G0469300	RBH	19.5742855	42.136076	67.8799475
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_02g0029770	RBH	0.238268	3.808028	19.830395
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_02G0496400	RBH	24.7043145	16.1566445	95.9260255
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_02g0030090	RBH	0.124778	0.687250	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_02g0029820	RBH	0.437247	41.506050	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_02g0030150	RBH	0.848383	78.474091	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_02g0030000	RBH	0.556496	4.896557	7.662339
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_02g0029670	RBH	0.158756	37.534065	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_02G030240	RBH	0.546507	24.224600	15.405527
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_02g0030020	RBH	0.537813	70.923141	50.471336

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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