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
OsZS97_12G0181000		OGI:12031710 \| 15/16			Zhenshan 97 \| ZS97RS3 \| HZAU			Chr12:11179925-11184356		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		CYCA1;3, cycA1;3, CycA1;3, CYCA1-3
DNA seq		CTAGAAACATCAAGAACACTAGTAGCACTTATTCAGAATGAGCACTGTTGAAAATGTGGTGCTCTTATTGAGAATTTCACAAGAGCAACACGAACAGAGACTCTATCATACATCAACCTAGGAGACGCCCAGGTTGGCAGCTAATATCAAACAAGATGTTTAAAGCTTTGCTGCAGGACTCCGATGTACAAAGTACTGAAAACCATGGATCATCTAGGTACAGGGAAAAGAAGATAGAAGAAAGCACATCAGTACCATAAAAGTTACCACACACAGCAGAAGCATCGATCTATCTACACTCAGCCAAACCACCTGAAAGAACAGGGGGGGCAAGCAGCATGCCTTGCATCAAGCTTATCTGAACGGTCTACGGCACAACCTGGCATAGGTGCCTCTGGAGGAAGAATTCAGTCAGCAACTGTAACTAATCCTTGGTTTATTTTTCTAGTTCAGCATGTTGAGTCGCGAAAGAATTCGGTCGGTATTGAGGGTGGGCAGGGCTTCTTCGCCACAAATTTGTACTGCAGAAACAAAGGTACAGGAGGCAGCATTAGGAACAGTACAGATAACTGAAGAAATGGGGAGGATATGCAGTTTATACCTTATGTTGGGTATACTTCTCCCTGATTGCAGGAAGGTTACTCCCAGGACCAACACAGAAAAGGCGGTGCAATGCCTTAACGCAGTCGCTTAACTCTGACGACTTGTATTGTGTGTAGTGAGCAAGGGTGGAATTCTGCTTCCAATTTACAATGAGAAGCATATGTTAGCTCTTGTAATTTTTTTATTTGAATGTTGATATAAAAGATGTATGGAAAGTTCAATATGATGATGCCACCACGTACCCAAGGGTGCTTTGCTGGCTGCAGTATGAATTTGGCCAGGAAAATAGCTGATGCCGCTACTAGTGAAGGAGGGTAAGAAAGTAGATTGTACTCCAGCAGTGATAGCTCAGCAACATAATTGGCTAGGAACTCAAGATGCAATGCTGGATCCTGCACGATGAAAAGCTGTTAATGCAATGCAGCATATAAATAGTATGAAATTGCAGCAAGCAGGAGATGATTAAGAGAGCAGCACCTCATCAGATACTTGTGCAACACGGACAAATCTCCTGTTGTAGGCAAGAAGATAGTTATTAGAGTTCGATTCATTCCAGCATTATAGACATCGATGAGATGAAAGAGAATAGAACCTCAAAAAGCATTTTGCTGTAGGTGCAGTCATTTCAAACTTCAGGTAATTCAGGACAGAAGCTTCCATTTCCAAAACCTGACAATCTATGTGTTAGTCATGGAGATAAACATAGAAATGTTCACAGATATGCAAAACAAACCTCATCTCTGAAGTATGTGTTGTCAGTTATATAGCAGAATTCTTCTACTTGAGGTGCACATATCTCCTCGTATTTTCTGATATAGGAACAAGCCAAAATCAGTACACAAAACTCAGATGCAAACTGAGAAACACATTTAAAAAAATTGCTAATCAGATCTTACGCAGCAATAAGCATACAAGCAACTCCAAGTAATTGCAGTCTTTGACGATTGATCTCATTGCCAGAAAGATAACGGTCAATGTAGTTAACTGTCAGGTATAATGTATCAGGAACAAGACGATATTCTTCAGCGACCTGCACAAAGGAAAAGCACAAATAGAGTGGTAAGTAACGATTGTGGTCTTTAGGCTCCAATCAACTAAAAAAATTTGTTCGGTATAAAAGCTTACTTCCACAAGCCAGTCTATCAGGATCGCTCTCATGCTTGGGTTTACATCCTTTTGGAGTGTTTCCATAAAATCGGTTGATGGATGTTTCCTGGTCTGCTTCAAGTCAAATAGAAAATCACAATGTAAATATGAAATTCAACCTAGATTTGAAACCACTGTGCTCAGGTCAGATTAATTGTCATTTGATCAAACTGACTGCAGTAGTGCAGTCCATGTCACAGCAAAAATAATGAGCAATTGAAAAATACTTCAAGAGCATTGATTACAACAATTGAAATGTATCAATTCATCGGTTCAGTCAATGCTTTAAGAAGATAACTCCATTACAATTTCTCCATATTATACTGTGCTTCTACTGGTTCTATAAGGAATTTCAATATGATGGCCATTAAATGGAACCCACTATTCAGAAAAAAAAAAGTATTCAAGAATGTTTTATGTAAGGTGTTTACATAATATGCAGAACAAAACTACTGAAAATTGATGGTCACAAAGCATGTCTGGTAGATGATAAGGTGCACCAACAAAGCGAAAAGCAGAAAAGAACGGATTGTGGTGAAATGTGAAAAATATCCTGATAAATTACATTGGAATAATGCCTTATATCAGTGATGTGCACTTATTCTCTTCTTAATTTATGGTCTCATCAAAGTAAACTTTTTTTACTTGTGTTTCATATGGATGCAATCAAGTCTCAAATCATGAGGAAGCAAAACAAAGCCTTCCTATGAAAACATACTACAATAAGGTGCTCAAGGGAAATGTTTTCAGAGAAATAAGGTTTAGTCAAGAATGTATTACCTCGGCCTCGCGCAAGTGCATGTAGATATCAGAAGCAAGAGTAGCACACAACTGCGGATCCTCGTAGTTATTGTCAACATCACAAATTTGGTCGATTTCCATTGGGGAAGGAGCATCCTTCTTCCACTTAGTTTCTGCGAAACAAACAAGGGAAAAGATCAATCAACCATTCCAATAGAATGCACCATATAGCACAAATTTTTCTAGCTATAACTGTGCATTTCAGCAACCAAAACACACCTTCAACATCTCTATCCTCTGAGATACGCAGGTTCTCGTTTGCTCTTCGCTGCAAGGAACCTAGAACTGAGGAGGAATCCCCATTATCAATATACTCAAAGTCTGGGCTTTTCATTGAGTCGCACGTCGACATCGTCTCATCAACCGAAACTGAATCTCCTGAATGCATAGGGGAGACGAAGCTGCTGCAGGGTACAGTGACAGGTGCAGGTGCAGCAGTTGGAACAATTCTAAGCACTTTAGGAGGAAGAACTGACTCCTTCTGTGGGGCGCTCTCATGGCGGGATATGGCCGAAGCTGGCTTGGTGGAAGCTGATTTCACCGCCGAGACCCGATTCGTGCCCACATTGCGGCCACTGGCCAAAGATCCCTTCTTCACAGGTGCAGCCCAGGTAGCTGAATTAAATTTCTGCAGGAGGATTGAAGACAAGAAATCAATTTAGAACTTATATTTCAATCTGTTCATTTGGGATTCCAGACCACAAGCATGAAAAGGAACAAATATTTATTAGAAACATTAGCAGCACGCAAGTATCATATTACCAATAGAAGATTCCAAAGCAAGCAAACATACAAAACACTTAGCGAATACCAAGAAAGCTTTTATTTTGAACTTCTGAAGGTGCCAATAAACCCTCAAGTGAATTTAGCCTGTTGACCTGGATGCTCCCCAAGAAATCAATCAATCAATTAACCATGAAAAGAAACCAGAAAATCAGCAAGAAAAATCTTGTGGATTGGAATAGGAGAATCCTCAAAATCAGCAAGGAAGAATGTGGCAGAGGTCCAAATTTGAATGTGAAGAGCACTGAAAAACCAAAAGGCAAGAATATATTGGGGATTGGAAGAGGAGAATCGTTTGTAGGCTAACCAAGGAGAAATTGAAGAAATGAAAATCTTGTTGTTGGCTGAAAGAAAGAACTCAAGAAGACGAATTCAAGAAACACTATTTATATTTGCTTGAAACCAACAGATCGAGGCGTATGTCCTCCACAAACAAGATGGAAAAAAACCAAAAAAGGAAAAAATCATACACAGATCGCTTCGGCCATTTCCGCATCAACAGCGACTCACTTGTGCCCCAAGAGGAACCAAGAAGCAAAAAAAAAAAAAAAAAAAGCCACCCCCAAACCATTCCAACCACCTCACACACCAAAAGATCTCCACCCAAACCGCGCAAAGCAAAGAACAAATCTTGGAGAGAAAAAAAAAAAAGGAAAAAAGAAGAAGAAGAAGCAGCAGCAAGCGATCCTTCACGTACCGCATTGTTGGCGGCGGCGGCAACGTTGGTGATGTTACCGAGCGCGACGCGCTTCTTGGCCGCCGCGGCGCCCGCGGCCGCCTTCCCTCCTCCCTCCCCCGCCGCGGGCCGCTTCGCCGCCGACGACGACGACGAGCGGCGGGAGGCTAGGCTGCTCGACATCGGCCGACGGCAACCACCACCTGAACCCTCCTCCTCCTGCTGCTGCTGCGAGGGTTGCGAGGGCGGCGGCGGCCGGCGGGGATCAGAGGCGGAGCAGGGCGAGGGCTTGGATCCTTCCCTTCCCGACAGAGGAGGGGAGAGCCGGAGAGGAGAGGACTCAGAGGAGCGGAGGAGGAGAAGAGAGAAAATGGCGACGACTCTTTCGATTATTTCCAGTTTTTGGGGAAACTATTCTAATCC More
CDS seq		ATGTCGAGCAGCCTAGCCTCCCGCCGCTCGTCGTCGTCGTCGGCGGCGAAGCGGCCCGCGGCGGGGGAGGGAGGAGGGAAGGCGGCCGCGGGCGCCGCGGCGGCCAAGAAGCGCGTCGCGCTCGGTAACATCACCAACGTTGCCGCCGCCGCCAACAATGCGAAATTTAATTCAGCTACCTGGGCTGCACCTGTGAAGAAGGGATCTTTGGCCAGTGGCCGCAATGTGGGCACGAATCGGGTCTCGGCGGTGAAATCAGCTTCCACCAAGCCAGCTTCGGCCATATCCCGCCATGAGAGCGCCCCACAGAAGGAGTCAGTTCTTCCTCCTAAAGTGCTTAGAATTGTTCCAACTGCTGCACCTGCACCTGTCACTGTACCCTGCAGCAGCTTCGTCTCCCCTATGCATTCAGGAGATTCAGTTTCGGTTGATGAGACGATGTCGACGTGCGACTCAATGAAAAGCCCAGACTTTGAGTATATTGATAATGGGGATTCCTCCTCAGTTCTAGGTTCCTTGCAGCGAAGAGCAAACGAGAACCTGCGTATCTCAGAGGATAGAGATGTTGAAGAAACTAAGTGGAAGAAGGATGCTCCTTCCCCAATGGAAATCGACCAAATTTGTGATGTTGACAATAACTACGAGGATCCGCAGTTGTGTGCTACTCTTGCTTCTGATATCTACATGCACTTGCGCGAGGCCGAGACCAGGAAACATCCATCAACCGATTTTATGGAAACACTCCAAAAGGATGTAAACCCAAGCATGAGAGCGATCCTGATAGACTGGCTTGTGGAAGTCGCTGAAGAATATCGTCTTGTTCCTGATACATTATACCTGACAGTTAACTACATTGACCGTTATCTTTCTGGCAATGAGATCAATCGTCAAAGACTGCAATTACTTGGAGTTGCTTGTATGCTTATTGCTGCAAAATACGAGGAGATATGTGCACCTCAAGTAGAAGAATTCTGCTATATAACTGACAACACATACTTCAGAGATGAGGTTTTGGAAATGGAAGCTTCTGTCCTGAATTACCTGAAGTTTGAAATGACTGCACCTACAGCAAAATGCTTTTTGAGGAGATTTGTCCGTGTTGCACAAGTATCTGATGAGGATCCAGCATTGCATCTTGAGTTCCTAGCCAATTATGTTGCTGAGCTATCACTGCTGGAGTACAATCTACTTTCTTACCCTCCTTCACTAGTAGCGGCATCAGCTATTTTCCTGGCCAAATTCATACTGCAGCCAGCAAAGCACCCTTGGAATTCCACCCTTGCTCACTACACACAATACAAGTCGTCAGAGTTAAGCGACTGCGTTAAGGCATTGCACCGCCTTTTCTGTGTTGGTCCTGGGAGTAACCTTCCTGCAATCAGGGAGAAGTATACCCAACATAAGTACAAATTTGTGGCGAAGAAGCCCTGCCCACCCTCAATACCGACCGAATTCTTTCGCGACTCAACATGCTGA More
Protein seq		MSSSLASRRSSSSSAAKRPAAGEGGGKAAAGAAAAKKRVALGNITNVAAAANNAKFNSATWAAPVKKGSLASGRNVGTNRVSAVKSASTKPASAISRHESAPQKESVLPPKVLRIVPTAAPAPVTVPCSSFVSPMHSGDSVSVDETMSTCDSMKSPDFEYIDNGDSSSVLGSLQRRANENLRISEDRDVEETKWKKDAPSPMEIDQICDVDNNYEDPQLCATLASDIYMHLREAETRKHPSTDFMETLQKDVNPSMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNEINRQRLQLLGVACMLIAAKYEEICAPQVEEFCYITDNTYFRDEVLEMEASVLNYLKFEMTAPTAKCFLRRFVRVAQVSDEDPALHLEFLANYVAELSLLEYNLLSYPPSLVAASAIFLAKFILQPAKHPWNSTLAHYTQYKSSELSDCVKALHRLFCVGPGSNLPAIREKYTQHKYKFVAKKPCPPSIPTEFFRDSTC
Function		Cyclin-A1-3 [UniProtKB/Swiss-Prot:Q0INT0]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsZS97_12G0181000	OsZS97_12T0181000.1	Chr12	11179925	11184356	-	makerRMon
CDS seq	ATGTCGAGCAGCCTAGCCTCCCGCCGCTCGTCGTCGTCGTCGGCGGCGAAGCGGCCCGCGGCGGGGGAGGGAGGAGGGAAGGCGGCCGCGGGCGCCGCGGCGGCCAAGAAGCGCGTCGCGCTCGGTAACATCACCAACGTTGCCGCCGCCGCCAACAATGCGAAATTTAATTCAGCTACCTGGGCTGCACCTGTGAAGAAGGGATCTTTGGCCAGTGGCCGCAATGTGGGCACGAATCGGGTCTCGGCGGTGAAATCAGCTTCCACCAAGCCAGCTTCGGCCATATCCCGCCATGAGAGCGCCCCACAGAAGGAGTCAGTTCTTCCTCCTAAAGTGCTTAGAATTGTTCCAACTGCTGCACCTGCACCTGTCACTGTACCCTGCAGCAGCTTCGTCTCCCCTATGCATTCAGGAGATTCAGTTTCGGTTGATGAGACGATGTCGACGTGCGACTCAATGAAAAGCCCAGACTTTGAGTATATTGATAATGGGGATTCCTCCTCAGTTCTAGGTTCCTTGCAGCGAAGAGCAAACGAGAACCTGCGTATCTCAGAGGATAGAGATGTTGAAGAAACTAAGTGGAAGAAGGATGCTCCTTCCCCAATGGAAATCGACCAAATTTGTGATGTTGACAATAACTACGAGGATCCGCAGTTGTGTGCTACTCTTGCTTCTGATATCTACATGCACTTGCGCGAGGCCGAGACCAGGAAACATCCATCAACCGATTTTATGGAAACACTCCAAAAGGATGTAAACCCAAGCATGAGAGCGATCCTGATAGACTGGCTTGTGGAAGTCGCTGAAGAATATCGTCTTGTTCCTGATACATTATACCTGACAGTTAACTACATTGACCGTTATCTTTCTGGCAATGAGATCAATCGTCAAAGACTGCAATTACTTGGAGTTGCTTGTATGCTTATTGCTGCAAAATACGAGGAGATATGTGCACCTCAAGTAGAAGAATTCTGCTATATAACTGACAACACATACTTCAGAGATGAGGTTTTGGAAATGGAAGCTTCTGTCCTGAATTACCTGAAGTTTGAAATGACTGCACCTACAGCAAAATGCTTTTTGAGGAGATTTGTCCGTGTTGCACAAGTATCTGATGAGGATCCAGCATTGCATCTTGAGTTCCTAGCCAATTATGTTGCTGAGCTATCACTGCTGGAGTACAATCTACTTTCTTACCCTCCTTCACTAGTAGCGGCATCAGCTATTTTCCTGGCCAAATTCATACTGCAGCCAGCAAAGCACCCTTGGAATTCCACCCTTGCTCACTACACACAATACAAGTCGTCAGAGTTAAGCGACTGCGTTAAGGCATTGCACCGCCTTTTCTGTGTTGGTCCTGGGAGTAACCTTCCTGCAATCAGGGAGAAGTATACCCAACATAAGTACAAATTTGTGGCGAAGAAGCCCTGCCCACCCTCAATACCGACCGAATTCTTTCGCGACTCAACATGCTGA More
Protein seq	MSSSLASRRSSSSSAAKRPAAGEGGGKAAAGAAAAKKRVALGNITNVAAAANNAKFNSATWAAPVKKGSLASGRNVGTNRVSAVKSASTKPASAISRHESAPQKESVLPPKVLRIVPTAAPAPVTVPCSSFVSPMHSGDSVSVDETMSTCDSMKSPDFEYIDNGDSSSVLGSLQRRANENLRISEDRDVEETKWKKDAPSPMEIDQICDVDNNYEDPQLCATLASDIYMHLREAETRKHPSTDFMETLQKDVNPSMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNEINRQRLQLLGVACMLIAAKYEEICAPQVEEFCYITDNTYFRDEVLEMEASVLNYLKFEMTAPTAKCFLRRFVRVAQVSDEDPALHLEFLANYVAELSLLEYNLLSYPPSLVAASAIFLAKFILQPAKHPWNSTLAHYTQYKSSELSDCVKALHRLFCVGPGSNLPAIREKYTQHKYKFVAKKPCPPSIPTEFFRDSTC More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	4.41812	4.563375	28.826993

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_12g0298950	RBH	0.133810	0.307938	0.811817
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os12g20324	RBH	0.067006	0.163688	0.274996
Nipponbare \| IRGSP 1.0 \| RAP-db	Os12g0298950	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_12g0010240	RBH	0.000000	2.360382	2.724404
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_12g0010440	RBH	0.000000	0.000000	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_12g0010370	RBH	0.000000	0.000000	0.000000
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_12g0010110	RBH	0.000000	0.000000	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0009100	SBH	1.091347	5.510009	7.886757
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_12G0161800	RBH	0	0	2.1673505
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_12g0010040	RBH	0.000000	0.000000	0.200784
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0119900	SBH	2.126998	0.440994	21.666849
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_12g0009950	RBH	0.000000	0.156203	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_12g0010200	RBH	0.000000	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_12g0010160	RBH	0.0	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_12g0010110	RBH	0.0	0.0	0.263927
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_12g0010230	RBH	0.074568	1.476678	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_12G009970	RBH	0.147944	0.800406	0.768216
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_12g0009900	RBH	0.000000	0.000000	2.496611

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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