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
OsN22_09G014180		OGI:09053030 \| 15/16			N22 \| OsN22RS2 \| Gramene(+IsoSeq)			Chr09:19392952-19398179		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		DUA1, OsDUA1
DNA seq		ACCCACCCCACCTGATCCACGGCCGCGGCGAACGGCGGTTTCCTCCCGTCTTCCCGGTGGCCGGGGGCCGGAGCCCCGGGCGCGCCGCGCTCACCGTCGCCGACCGGCGGCCGCGAACCCGCGACCCAGCCGCCGACGCACGCCGCTGCAAGTAACTATGCCTCCTCCCACCGTCCCCTTCTTCCTCACCTCCACCACGCTCGCCGCTGCGGCCGCGAAGCCGCAGCGGCCCGGGCCGCCCTCGCCACCGGCGCAGCAGCAGCAGCCGCGCGAGGCGCGGGATGGTTCTCGGGACGCGTGCGCGTCGTACACCGCGCGCATGCGGCTCAACCCGCAGCTCGCGCTCCGCCTGTTCGACCACCTGCTCCGCTCGGGCGCCGACCCGGACCACGTGGCGTACGCCCTCGCGCTGGGCCGCTGCGCGCGCGGGCGGGACCGCCGCGCCGCCGCGCAGCTCCACTCGCACGCCGCTAAGCGAGGGGCCGCGTCCCACCGTCGCGTCTGCAACGGGCTCATCCACGCGTACGCCGTCTGCGGGTCGCTGCTCGACGCGCGCAAGGTGTTCGACCGCGGGCACGAGGGTGACGCGGTGGCATGGAACTCCCTGCTGCGCGGGTACGCGGCTGCTGGGGACGTGAACGCGCTCCGGGAGTTCTTCGTGGGGATGCAAGCCCGGGACACGGTTTCGTGGAACACGATCATCGCGTGGTGCGTTGAGAATGGGGAATATGAGGAGGCAATTGCGGTGTTCCGTGAGATGCTGGCAAGCATGGAGTGTCTTCCTGACAGAGTCACACTGGTGAGCGTCATCTCAGCGATTACATATTTGGGTGCACTAGCCCAGGGGCTGTGGGCGCATGCATATGTTTGCAGGAAAGGTATCGAAGTCGAGGAGAGGCTGAGCTCAGCTCTCATAAACATGTATTCAAAGTGCGGTTGCATTGAAGGTGCAGTTCATGTGTTTGAAAATCTGGGTGCACAGATGAATGTGGACACATGGAACGCTATGTTAGCTGGCTTCACAGCAAATGGATGCAGTGAGAAAGCTCTGGAGCTTTTCGCTAGGATGGAGATAACAGGTTTGGTGCCTAACAAGATTACTTTCAACACTGTGCTGAATGCTTGTAGTCATGGTGGTTTTGTTGAGGAAGGTATGGGGTGTTTCGAGAGAATGACCAAGGTTTATGGTATTGAGCCTGACATTGCCCACTATGGTTGCATGGTGGATCTGTTCTGTCGTGCAGGGCTTTTTGACAAGGCTGAAAAGATGATCCAAATGATGCCTATGAAACCAGATGCTGCTGTGTGGAAGGCCCTAGTGGGTGCTTGTAAAACTCACAGGAACTTTGAACTGGGAAGGAAAGCAGGCCATATGCTTATTGAGGCTGCACCAAATGATCACGCAGGGTATGTGCTGCTATCCAACATATATGCACTAGATGGAAACTGGACAGGAGTGCATAAGGTGAGGAAGCTGATGCTTGATCGTGGTGTGCAGAAGGTACCTGGAAGCAGCTCAATAGAAATTGATGGTGTAATTCATGAGTTCATATCTGGGGATAAAAGCCATTCAAGCAAGGAGGACATATACGAGATGCTAAGTGAAATGTGTCAGCAATTGAAAGTTGCAGGATATGTTCCAGATACTTCACATGTGCTACTAGATATTGATGATGAGGATGTGAAGGAGAGCTCACTAGCTCTTCACAGCGAGAAGCTTGCAATTGCCTTTGGATTGATAAGCACTGCACCAGGCACGCCTATTAGGATAGCAAAGAACCTCCGGGTTTGTGGAGATTGTCATAATGCCGTTAAACTTCTAAGCAAGATTTATGGGAGGTGCATAATTGTTAGGGATGCAAATCGATTTCATCATTTCAGAGAAGGATCATGCTCTTGCGGGGATTTCTGGTAACTTCAGTTGAGCTACAATTCTATTTCTTTGTAGTTGTAAATGTTAACACAAAAATATATGGCATGTGGGAAAAGTTTTGGAAATGGTTATAGTTGTTCGTCTGAGAACAGTTGAGGGTCTTTACTTGATTCCACGTCTCTATTAAAAGCTAAGGTATCCATAAACCAACACCATGATTACTACCCTCTTGTGTCTCAGCAACTTGAAACCTAATTATTGTTCCTTTTCAGTCTCCATGATCCAGTACTGAACATGAATCTGAGATGTATGTCCTACGCAAAAGTTCAATTAAAAATAAATTCAACTCCTTCCATATGGTAGGGGCTACAAATCATCAATAACCTGATACATACTTAATGCTTTTTTTCTCTAGTGTTGTTACTGTAATTGTTGAGATGGCAGCTTCACATGAACTTGCATTTTAAAGAGGGAAAATAGTAGGTGTCTAGGTGATAGGGACAACTTGGGCAGGCATCTGCTTGCCTTTTTAGTGAGTAAGTCCTGTTTTTAGCTTCTGCTTGCCAATGAAAACCTTCTTCATTCATCTATTCTTCCACACAATCCATTGCCTTTTATGCCAATTCATTTATATTGTTTGCTCATGTTAGATTCTTCTACTTTGTCTGTGCATCTATTCTGTTCTTTGCGCACTATACATTCATCCATGACATCCTACATATGTAATGCAAGTATTGAATATGTTATTGAACAATTGAGTTATACTACAGCTTATTTGTGTCACAAAAAAGTCTTTCAAGTTACAATAGTCTGGAAACAAATCTAGTAATAGAGTACTTTACAAGTACAGTGATAAAGTGGGATTAGTTGTCCCTGGGTTATACCTTTCGTATTCTTTGGCAAAGGCCCAGATGACAGATTTATTCTACTGTTATGTTCTTAACTGTCCTTCAGGGTCTGAAAATTCATGTACTAGGAAAGCTATACCCCTGGGAGAACAGTTACCCACTAGATTTGCTAGTTCTTTTATCTTGCTTGTTGCCTGTTGTTGATGTTGAATGAGACATGAAGTGCTCTGCGCAAGAAATGGTAGCAGTTGTTTAATTCACAAACAAAGTAAAGTGCGAGTTTGTGACACTATTTGGCAGAAGTAATCACTTCCACCATGCTGTTGTTATTACTTCCTGGTGGTCTGGTCGATGTAGGGCCTTTGATTTGAACATATGACAAGGGAGTGTCTTTGACGCAATTGCATGTTTATTGGGCATTTGCAAGCTTACAGCATAGATATTATCTAATGTCACATTCATGAAGATGGAGTTGTAGTTGCTAGTAGCCTAGTACAGAGGTTGCATTAAATCCTCTAAATAGGAAAAGTTTAGATCTTCATGGTGTCAAATTCGAATGTTTATGCCCTTGAGAAACACTGAACCTTTGCAACTTTATATAGCATTCCGTAAGGACATCATCATGGTAAAAGGGAAGGATACAAAGAATCATGTGCGATCTTCTCATATTGTGATGTCTAGAGAGAACACATAAATTTAAATTAAATCAACACTTTCCCATGTAAAGTAGAAAGATTTGAAACATTACTGAGTTCTTAACCTTTAAGAGAAAACTCACTACACTTCTACAGTTCTATGTGAACTATCATGGCCACCACTCCACCAGCACTCTGTTCAACTGGTTAGTTTACAGCTTTGCATTCTGTAGGCACCACAAATGCATATACTGCAATATTAGTTATCCAGATCTGGTACATTACAACTAGGAATTGGTAGCCTTTTTTCCTTCACACACAAGGCAACACAGACACGCATGCATACGCATATGCACACGCACATAATGTTATATGATGTATAGTAGAAATGCAGCTCCATGCCAATCATTAATAGGTTGGCCTTGACAAAATAAGCTGCCTGCTGCCCTTATCAACTCTACTTGTTTATTTTCTCTTGGGAGAAGTTTTTTAGTGTTCCCCAGATATGTAATTTGTGGCCTAGGCCCTAGTTTATAACTCTAATCACTACTCTAGGAGTATAATAAGACCATTAGCGCATGGCACAATGCATAATTATGGTTTGGAATAATCGGTAATACATATGCATGGTTTGGATTATATAGCCCGCAAGATGGTTTTCACCTAACATAGACCTTTACCAAAAATATACTCACTTGCATCTCGCGTGCAGCTGGCTTTGCCACGGACTGTGCTTTGTTTATGGTTTACAGAAAGGTGTAACATACGCTTTCCTAAGCAAAATTAGAGATCCTGTACCCTAGCACATGGGAACCGAATGCTGAATTAACACACAGGTGTACTCACAATGCTGAGATACTATGGGCCAACTTGTACTGTAATCAAATCATCCATGTTCAATTCTAATCATCCATTCTTGGTAATGATCCCATTAAGACTGCTTTTCTGTTCTTTGCTTCTCGATACATCTTTCTAGTAACTGTTTGCACAAACTTTTTTAGCATGTAGTACAAATTATGATAGGCATGGGGGTTTGGTTTGATCGTTCTTTTAATTTGAGTAAGCTTAGAATGTATTGAAAACCTTTCTATTCTGTTCTAGATCTTAGTTTTTTTTTTTTTGCTTATGAATCAACACCAAAAATCATATGTTGAATGCTTTCCTGTTAAGCTTAGAATGTATTGAAAACCTTTCTATTCTGTTCTAGATCTTTTTTTTTTTTTTTTTTTTTTGCTTATGAATCAACACCAAAAATCATATGTTGAATGCTTTCCTGTTAAGCTTAGAATGTATTGAAAACCTTTCTATTCTGTTCTAGATCTTAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTTATGAATCAACACCAAAAATCATATGTTGAATGCTTTCCTGTTAATTTCTGAGTTTTGAAGGACAAGAGTGCAATTATATTGTAGTGACAAAAATAAAATTTGGTGTAAACTAGTTAATCAGGACAGTCTACTCAGGGAGCAGGGTCTGCGAGATGAACGAATCCGATGCTGAAACTCTTATCTTCATTAACATGGATATGTTTTTTAGCTTTAGACTTACCCCAAAAGAGACGATTGCCAGCTAATCTCATGCAGACATTGTTCCATTTTTTTACTTTGAGTTCTTTGGCTGTTATTTCTTGGAGCTGTTTTGTTTGCAGGAATCCTCTGCTCTTACTAGCACCAGATGGCCCGCTGCCGACAGGTAGGACCTAAAAACAAGAAGTCCCATCCATATCAACACTGCATTTCCATTTCCTCTCGTTTTTTTTCTTTCGAGAAAGAAAGCGAAAATGACTATGTTGCTCTTGTTTTCAGCTCATACCCTGCTCCTGTTGACAACAAGCTCTGA More
CDS seq		ATGCCTCCTCCCACCGTCCCCTTCTTCCTCACCTCCACCACGCTCGCCGCTGCGGCCGCGAAGCCGCAGCGGCCCGGGCCGCCCTCGCCACCGGCGCAGCAGCAGCAGCCGCGCGAGGCGCGGGATGGTTCTCGGGACGCGTGCGCGTCGTACACCGCGCGCATGCGGCTCAACCCGCAGCTCGCGCTCCGCCTGTTCGACCACCTGCTCCGCTCGGGCGCCGACCCGGACCACGTGGCGTACGCCCTCGCGCTGGGCCGCTGCGCGCGCGGGCGGGACCGCCGCGCCGCCGCGCAGCTCCACTCGCACGCCGCTAAGCGAGGGGCCGCGTCCCACCGTCGCGTCTGCAACGGGCTCATCCACGCGTACGCCGTCTGCGGGTCGCTGCTCGACGCGCGCAAGGTGTTCGACCGCGGGCACGAGGGTGACGCGGTGGCATGGAACTCCCTGCTGCGCGGGTACGCGGCTGCTGGGGACGTGAACGCGCTCCGGGAGTTCTTCGTGGGGATGCAAGCCCGGGACACGGTTTCGTGGAACACGATCATCGCGTGGTGCGTTGAGAATGGGGAATATGAGGAGGCAATTGCGGTGTTCCGTGAGATGCTGGCAAGCATGGAGTGTCTTCCTGACAGAGTCACACTGGTGAGCGTCATCTCAGCGATTACATATTTGGGTGCACTAGCCCAGGGGCTGTGGGCGCATGCATATGTTTGCAGGAAAGGTATCGAAGTCGAGGAGAGGCTGAGCTCAGCTCTCATAAACATGTATTCAAAGTGCGGTTGCATTGAAGGTGCAGTTCATGTGTTTGAAAATCTGGGTGCACAGATGAATGTGGACACATGGAACGCTATGTTAGCTGGCTTCACAGCAAATGGATGCAGTGAGAAAGCTCTGGAGCTTTTCGCTAGGATGGAGATAACAGGTTTGGTGCCTAACAAGATTACTTTCAACACTGTGCTGAATGCTTGTAGTCATGGTGGTTTTGTTGAGGAAGGTATGGGGTGTTTCGAGAGAATGACCAAGGTTTATGGTATTGAGCCTGACATTGCCCACTATGGTTGCATGGTGGATCTGTTCTGTCGTGCAGGGCTTTTTGACAAGGCTGAAAAGATGATCCAAATGATGCCTATGAAACCAGATGCTGCTGTGTGGAAGGCCCTAGTGGGTGCTTGTAAAACTCACAGGAACTTTGAACTGGGAAGGAAAGCAGGCCATATGCTTATTGAGGCTGCACCAAATGATCACGCAGGGTATGTGCTGCTATCCAACATATATGCACTAGATGGAAACTGGACAGGAGTGCATAAGGTGAGGAAGCTGATGCTTGATCGTGGTGTGCAGAAGGAATCCTCTGCTCTTACTAGCACCAGATGGCCCGCTGCCGACAGCTCATACCCTGCTCCTGTTGACAACAAGCTCTGA More
Protein seq		MPPPTVPFFLTSTTLAAAAAKPQRPGPPSPPAQQQQPREARDGSRDACASYTARMRLNPQLALRLFDHLLRSGADPDHVAYALALGRCARGRDRRAAAQLHSHAAKRGAASHRRVCNGLIHAYAVCGSLLDARKVFDRGHEGDAVAWNSLLRGYAAAGDVNALREFFVGMQARDTVSWNTIIAWCVENGEYEEAIAVFREMLASMECLPDRVTLVSVISAITYLGALAQGLWAHAYVCRKGIEVEERLSSALINMYSKCGCIEGAVHVFENLGAQMNVDTWNAMLAGFTANGCSEKALELFARMEITGLVPNKITFNTVLNACSHGGFVEEGMGCFERMTKVYGIEPDIAHYGCMVDLFCRAGLFDKAEKMIQMMPMKPDAAVWKALVGACKTHRNFELGRKAGHMLIEAAPNDHAGYVLLSNIYALDGNWTGVHKVRKLMLDRGVQKESSALTSTRWPAADSSYPAPVDNKL
Function		Pentatricopeptide repeat-containing protein At5g48910 [UniProtKB/Swiss-Prot:Q9FI80]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsN22_09G014180	OsN22_09G014180_01	Chr09	19393109	19398179	+	NAM
CDS seq	ATGCCTCCTCCCACCGTCCCCTTCTTCCTCACCTCCACCACGCTCGCCGCTGCGGCCGCGAAGCCGCAGCGGCCCGGGCCGCCCTCGCCACCGGCGCAGCAGCAGCAGCCGCGCGAGGCGCGGGATGGTTCTCGGGACGCGTGCGCGTCGTACACCGCGCGCATGCGGCTCAACCCGCAGCTCGCGCTCCGCCTGTTCGACCACCTGCTCCGCTCGGGCGCCGACCCGGACCACGTGGCGTACGCCCTCGCGCTGGGCCGCTGCGCGCGCGGGCGGGACCGCCGCGCCGCCGCGCAGCTCCACTCGCACGCCGCTAAGCGAGGGGCCGCGTCCCACCGTCGCGTCTGCAACGGGCTCATCCACGCGTACGCCGTCTGCGGGTCGCTGCTCGACGCGCGCAAGGTGTTCGACCGCGGGCACGAGGGTGACGCGGTGGCATGGAACTCCCTGCTGCGCGGGTACGCGGCTGCTGGGGACGTGAACGCGCTCCGGGAGTTCTTCGTGGGGATGCAAGCCCGGGACACGGTTTCGTGGAACACGATCATCGCGTGGTGCGTTGAGAATGGGGAATATGAGGAGGCAATTGCGGTGTTCCGTGAGATGCTGGCAAGCATGGAGTGTCTTCCTGACAGAGTCACACTGGTGAGCGTCATCTCAGCGATTACATATTTGGGTGCACTAGCCCAGGGGCTGTGGGCGCATGCATATGTTTGCAGGAAAGGTATCGAAGTCGAGGAGAGGCTGAGCTCAGCTCTCATAAACATGTATTCAAAGTGCGGTTGCATTGAAGGTGCAGTTCATGTGTTTGAAAATCTGGGTGCACAGATGAATGTGGACACATGGAACGCTATGTTAGCTGGCTTCACAGCAAATGGATGCAGTGAGAAAGCTCTGGAGCTTTTCGCTAGGATGGAGATAACAGGTTTGGTGCCTAACAAGATTACTTTCAACACTGTGCTGAATGCTTGTAGTCATGGTGGTTTTGTTGAGGAAGGTATGGGGTGTTTCGAGAGAATGACCAAGGTTTATGGTATTGAGCCTGACATTGCCCACTATGGTTGCATGGTGGATCTGTTCTGTCGTGCAGGGCTTTTTGACAAGGCTGAAAAGATGATCCAAATGATGCCTATGAAACCAGATGCTGCTGTGTGGAAGGCCCTAGTGGGTGCTTGTAAAACTCACAGGAACTTTGAACTGGGAAGGAAAGCAGGCCATATGCTTATTGAGGCTGCACCAAATGATCACGCAGGGTATGTGCTGCTATCCAACATATATGCACTAGATGGAAACTGGACAGGAGTGCATAAGGTGAGGAAGCTGATGCTTGATCGTGGTGTGCAGAAGGAATCCTCTGCTCTTACTAGCACCAGATGGCCCGCTGCCGACAGCTCATACCCTGCTCCTGTTGACAACAAGCTCTGA More
Protein seq	MPPPTVPFFLTSTTLAAAAAKPQRPGPPSPPAQQQQPREARDGSRDACASYTARMRLNPQLALRLFDHLLRSGADPDHVAYALALGRCARGRDRRAAAQLHSHAAKRGAASHRRVCNGLIHAYAVCGSLLDARKVFDRGHEGDAVAWNSLLRGYAAAGDVNALREFFVGMQARDTVSWNTIIAWCVENGEYEEAIAVFREMLASMECLPDRVTLVSVISAITYLGALAQGLWAHAYVCRKGIEVEERLSSALINMYSKCGCIEGAVHVFENLGAQMNVDTWNAMLAGFTANGCSEKALELFARMEITGLVPNKITFNTVLNACSHGGFVEEGMGCFERMTKVYGIEPDIAHYGCMVDLFCRAGLFDKAEKMIQMMPMKPDAAVWKALVGACKTHRNFELGRKAGHMLIEAAPNDHAGYVLLSNIYALDGNWTGVHKVRKLMLDRGVQKESSALTSTRWPAADSSYPAPVDNKL More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsN22_09G014180	OsN22_09G014180_02	Chr09	19392952	19394944	+	IsoSeq
CDS seq	ATGGTTCTCGGGACGCGTGCGCGTCGTACACCGCGCGCATGCGGCTCAACCCGCAGCTCGCGCTCCGCCTGTTCGACCACCTGCTCCGCTCGGGCGCCGACCCGGACCACGTGGCGTACGCCCTCGCGCTGGGCCGCTGCGCGCGCGGGCGGGACCGCCGCGCCGCCGCGCAGCTCCACTCGCACGCCGCTAAGCGAGGGGCCGCGTCCCACCGTCGCGTCTGCAACGGGCTCATCCACGCGTACGCCGTCTGCGGGTCGCTGCTCGACGCGCGCAAGGTGTTCGACCGCGGGCACGAGGGTGACGCGGTGGCATGGAACTCCCTGCTGCGCGGGTACGCGGCTGCTGGGG More
Protein seq	MVLGTRARRTPRACGSTRSSRSACSTTCSARAPTRTTWRTPSRWAAARAGGTAAPPRSSTRTPLSEGPRPTVASATGSSTRTPSAGRCSTRARCSTAGTRVTRWHGTPCCAGTRLLG

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.227405	1.109779	0.965687

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_09g0474051	RBH	0.978617	1.202647	0.746775
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os09g29825	RBH	0.469599	1.011960	0.436901
Nipponbare \| IRGSP 1.0 \| RAP-db	Os09g0474051	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_09g0013840	RBH	0.392773	2.590455	1.543405
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_09g0013790	RBH	0.000000	1.423432	1.088692
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_09g0014050	RBH	0.639980	5.645256	1.120918
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_09g0013880	RBH	0.319489	0.153608	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_09g0013990	RBH	9.560941	2.747098	4.524216
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_09G0303100	RBH	1.9483915	4.3539605	2.0422935
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_09g0013890	RBH	0.230156	0.000000	0.285404
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_09G0233100	SBH	0.584706	1.0468395	3.0809045
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_09g0013880	RBH	0.283188	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_09g0013680	RBH	0.416862	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_09g0013770	RBH	4.494446	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_09g0013650	RBH	0.411854	0.0	1.142458
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_09g0013710	RBH	0.187232	1.937511	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_08G019330	RBH	0.084543	0.0	0.000000
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_09g0013960	RBH	0.957400	0.0	5.645951

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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