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
OsCMeo_09g0008770		OGI:09037980 \| 16/16			CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)			Chr09:13006401-13011463		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		cgccgccagtcccctcctccctctcgttcattgctcagtatgtatcatcgagaatggtcagttgtattgtcaggttaatgacgtgatagtatttgtagcactgacattacctactgttttcctgttgtattgagtggttttggcaatgtttgcaggtacggattcccaataaactgatgttgggtgatctaataactgaaggcaaaatgaagtaatataatcgcatcaatttgtaatgttgtggggagttgattttgtttttgtttttctgtactgatgaggtgtaggctagcagcgcccgccaaccggcactgaggtaaggagttccacaaccacagcactcagatgcaaataatgggcatgcctctgtctaagctactaagcagagaagcacactgcaaataagagctgagtgagctgggagctgccaatctctgttttctctttttcttggattgcaatttttgattttagattggatatttgagagaatgcataggaaagggaaaggaaaagggaaagggatgcctttacattgtacttatctttccttacgttacctatctcagatgtggtcatagtaatatacttttttctttgtgccacttatctttcctttctatgctccactgatatatcagctggtccatgtgccatttggtgattgctgcttacatagttatttttatttatctccgtacgctatgtgatgttatattcccttctcgatatatgttcagccattcaatcagttttgattagttaatgttcatgcatcagatttgttaatacaaaatgttctctgatctggtattcagcttggctaccagtacatgttacaagttcaatcttccacaagcaattgagaaaggttgcaggtgagaggcaagcagaagcatgacaggaatattgatttacttacatgataaccgttgtgccattaggtactaatactaacactattattttaaatcatgccccttctatagcttgcttctttggctgcatgtactatagctgattctttgctgttatatgatattttgaacttcctacagatgttgtatatgctatttaattttcatttttgttttcatgctctgcagtttcatctgcatgtaacctaaataatttcacggtgctcaactggatcactgtgggtgtagtttcattgctcatttcccatgtgaatattaatttattggcaatcctaattgtagctgccatttgatctcctttgtgatgttttacctgtccaaatttttatcccaacgggcatccttgaggtatatctgtgtttatgttataggtgcgcgctgatgcttggttctgcttcatttaatggcttagcttgattaacctgaaaatgtgaattgtgctcttaggggtttttataccatataatgtaatctcttatctttttcagccttggacaatcggaggtcattgagattaaactctgcttgcttcgcatcctccagtaagtgtaagacttaaaaaaaatccatgggtattttttcacttcccagtcgtaacatacatgtcataatgttaagcactaattgatttagttataaactatgtttgagattacactagcaggtcccattaatcaatggaaaatattcttttttttcgcacatagacaagttatatttccaagtaaatttcttcattcaaaaatcacttattttggtatcaatggctagcgtaaccaactcagatgatcttcttgttgataaaatgcagtatgttcagcatggatggtgactttggtccattgcttgagcttatcaagttacacagaatgtatgggcttttgttggtcatggacgttgttagtgtttttctctcccttgaaatacatatttttttcctgactattggtaatcaagtaatgttgtaattttccttttcaaggcacacagttctcacttgtttgtggtggtgatggtggtggtttttaacatataatgtgatatcttttctttttcagccttggacagttggagatcattgtgatgttggtgtaattgggcttactaagtgctctggtactcatgggcttcttccctgttttgacacctttttgttagtatcaattcagagagagacaatttgcgtacatcccttggatttcatgatctgggtaaattttccactcaattctactcttacttctagccgctgtattatgttttcagtttggccataacataatcgaggtttcagttaatatgtaatttgtggtgtattacttgctacctacagtcccattaaattgatgttttcttaccgcctatgctcagactacaatcactggcagtccaagcagcctgcttcttgcctcttttaataagattacacatatatacatggattaattgtgtgattcttctcaaaatgcacttgaaatctgaaggtgtattctacatagtttgtgtatatggatttattcactaattcttctgcaagcagacaatcttggtttgcagccccaagtaaagggcaagtgtacgaatttagccacaaaagcgacgccaacgaggatcgccatcgacggtgaccgctgctccatcgatccttcttcccccgtttgctactctcacttcacaggttcaaataccatccccgcgagatctcatctccaaaccacatgcctttactattaccacactatttcgctctctttctattcttttcattccccattttctctataccgaatatatgtttttagatcatcgagcgtcacacccttcctcgagtcaatcaaactatcatagatctaccattaaccctaagtactgttgacagccctaatcagtgattatgcttaagtgatctaacctacaaaccctctttgatattagctgacccaaaaaatcctttctataaccattttattataggggtagactatttgattgtatcatttaactatgtagatttggcatcctaaatatacacctattctattacatattctctcactcatccttatttcagttcagatataaatgttatactttttggcttgcccattattgaaacatgtatactcgtactttagcccctttcaattccttatattttatatttgtgtcatgacttgctaatatcggattcagttcctaatatttctaatataaaaatttccctttttccatacattagaacaataccattacacgaaagtacaataaataattaatactctttcacataaatcctttaactactatactgaaaaaaaaatacttacatcaactgtaaattattaagctttttcacggctatttagtcctattcctgcatcataattatcttatatcttatcgtagtatagccacttaacccagcacattatcttcttaccatatatatctttccagctacaactaagatttacaccacataaatacttacatacatcaagttatagatcatatacttcattgcatttctacatatcccaaaatactcaccctgtttaaaaataaaaaaattataataaaaactctaataactagctgagcctctcataactttttttatttatcaaatacatctaactacatgtgtatatatattgtagccacaatcatgtcttccgcagtgttcgcatcaatgaggctgaatgcaacaaatcaaagctacttggtaagctcaaagtcaaacaaaactttctatggacaatatgctgttagcaccagtgcggatatgatattttctttctacagcctgtgccaatcacacttgcgacagcatataagatgcagcatggagataatctgaagttaaaaacttcccatggcttgaagataaagatcaaaatcaaggaagtagctagcacactgtacatgacgacaggatggagataatctgaagttagaaactggagaaacgattcttttcaggatgccatcaaggtctaaagcgtgtgttatgatactgaacagacaaggccttattagatgtccagtgaagaccccatccaacagctcatcagctaacaaaaggtcccctgatccatcaggtcaattaaccagagcaagcacatttgaccatgcatcttctagcaaaagcgttccatttctgaggaatggaacaggtacaaagcttgcctcatcacattttttcaacttacactacccattaacatgtctattctgttttcgccgggtaatagaagatatacaattaaatcagccagatactcctccaacttacattggctaaaaacactgctatattgcctcctgcaaaattgcacatgctggacaagtgatttaaatctttctatctatgtttctattcatatgtaatcattttctgtgtcattttttactagcaggcagtaacaaaagaaaacctagcagacacctccttctgccaccagattaagctcacagctgaattgaagagttacatcaaagagattgcagattgtctagaagaatcaaacaagttctatgtcgtgcgtatgaacagaacattcatggaacaggacagagtggtaatttttgacacaacatttccatcttcttatacccatactgagcatataaatgtcacttttctttttcagtactttgcgactgagttttcaaagaaatacattgtgaacttggttcgaggcaagacagcaaacattagagtgcagattgcaggtcgaccctcaacaacttaacatcagggtggttagctttgcagcagccaacagcatcaacttacacaatctgcatcttccacttttataggacacaagtcacctcatgctcaccatagatgctctgtgaaagttacctgcatcttcagtagtcgctgctattatctaccctggaacagctactataattctctctattatcctttgcttgcggtctatctaacttcacttgctcagtaagcacgtgacctataactgcttatcattgtcctcagctccttttgttattcataagctgagtgaacaattaaccactttatgtacaaacagctggcttgttatactacaggttactatggtactatttgttgtttctttttaccatatgctt More
CDS seq		atgacaggaatattgatttacttacatgataaccgttgtgccattagccttggacaatcggaggtcattgagattaaactctgcttgcttcgcatcctccatatgttcagcatggatggtgactttggtccattgcttgagcttatcaagttacacagaatgtatgggcttttgttggtcatggacgttccttggacagttggagatcattgtgatgttggtgtaattgggcttactaagtgctctggtactcatgggcttcttccctgttttgacacctttttgttagtatcaattcagagagagacaatttgcgtacatcccttggatttcatgatctggccccaagtaaagggcaagtgtacgaatttagccacaaaagcgacgccaacgaggatcgccatcgacggtgaccgctgctccatcgatccttcttcccccgtttgctactctcacttcacagccacaatcatgtcttccgcagtgttcgcatcaatgaggctgaatgcaacaaatcaaagctacttgcctgtgccaatcacacttgcgacagcatataagatgcagcatggagataatctgaagttaaaaacttcccatggcttgaagataaagatcaaaatcaaggaagtagctagcacactgatgccatcaaggtctaaagcgtgtgttatgatactgaacagacaaggccttattagatgtccagtgaagaccccatccaacagctcatcagctaacaaaaggtcccctgatccatcaggtcaattaaccagagcaagcacatttgaccatgcatcttctagcaaaagcgttccatttctgaggaatggaacagtaacaaaagaaaacctagcagacacctccttctgccaccagattaagctcacagctgaattgaagagttacatcaaagagattgcagattgtctagaagaatcaaacaagttctatgtcgtgcgtatgaacagaacattcatggaacaggacagagtgtactttgcgactgagttttcaaagaaatacattgtgaacttggttcgaggcaagacagcaaacattagagtgcagattgcaggtcgaccctcaacaacttaa More
Protein seq		MTGILIYLHDNRCAISLGQSEVIEIKLCLLRILHMFSMDGDFGPLLELIKLHRMYGLLLVMDVPWTVGDHCDVGVIGLTKCSGTHGLLPCFDTFLLVSIQRETICVHPLDFMIWPQVKGKCTNLATKATPTRIAIDGDRCSIDPSSPVCYSHFTATIMSSAVFASMRLNATNQSYLPVPITLATAYKMQHGDNLKLKTSHGLKIKIKIKEVASTLMPSRSKACVMILNRQGLIRCPVKTPSNSSSANKRSPDPSGQLTRASTFDHASSSKSVPFLRNGTVTKENLADTSFCHQIKLTAELKSYIKEIADCLEESNKFYVVRMNRTFMEQDRVYFATEFSKKYIVNLVRGKTANIRVQIAGRPSTT
Function		Putative B3 domain-containing protein Os10g0158600 [UniProtKB/Swiss-Prot:Q7XGM6]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsCMeo_09g0008770	OsCMeo_09g0008770.02	Chr09	13007076	13011463	+	NAM
CDS seq	atgacaggaatattgatttacttacatgataaccgttgtgccattagccttggacaatcggaggtcattgagattaaactctgcttgcttcgcatcctccatatgttcagcatggatggtgactttggtccattgcttgagcttatcaagttacacagaatgtatgggcttttgttggtcatggacgttccttggacagttggagatcattgtgatgttggtgtaattgggcttactaagtgctctggtactcatgggcttcttccctgttttgacacctttttgttagtatcaattcagagagagacaatttgcgtacatcccttggatttcatgatctggccccaagtaaagggcaagtgtacgaatttagccacaaaagcgacgccaacgaggatcgccatcgacggtgaccgctgctccatcgatccttcttcccccgtttgctactctcacttcacagccacaatcatgtcttccgcagtgttcgcatcaatgaggctgaatgcaacaaatcaaagctacttgcctgtgccaatcacacttgcgacagcatataagatgcagcatggagataatctgaagttaaaaacttcccatggcttgaagataaagatcaaaatcaaggaagtagctagcacactgatgccatcaaggtctaaagcgtgtgttatgatactgaacagacaaggccttattagatgtccagtgaagaccccatccaacagctcatcagctaacaaaaggtcccctgatccatcaggtcaattaaccagagcaagcacatttgaccatgcatcttctagcaaaagcgttccatttctgaggaatggaacagtaacaaaagaaaacctagcagacacctccttctgccaccagattaagctcacagctgaattgaagagttacatcaaagagattgcagattgtctagaagaatcaaacaagttctatgtcgtgcgtatgaacagaacattcatggaacaggacagagtgtactttgcgactgagttttcaaagaaatacattgtgaacttggttcgaggcaagacagcaaacattagagtgcagattgcaggtcgaccctcaacaacttaa More
Protein seq	MTGILIYLHDNRCAISLGQSEVIEIKLCLLRILHMFSMDGDFGPLLELIKLHRMYGLLLVMDVPWTVGDHCDVGVIGLTKCSGTHGLLPCFDTFLLVSIQRETICVHPLDFMIWPQVKGKCTNLATKATPTRIAIDGDRCSIDPSSPVCYSHFTATIMSSAVFASMRLNATNQSYLPVPITLATAYKMQHGDNLKLKTSHGLKIKIKIKEVASTLMPSRSKACVMILNRQGLIRCPVKTPSNSSSANKRSPDPSGQLTRASTFDHASSSKSVPFLRNGTVTKENLADTSFCHQIKLTAELKSYIKEIADCLEESNKFYVVRMNRTFMEQDRVYFATEFSKKYIVNLVRGKTANIRVQIAGRPSTT More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsCMeo_09g0008770	OsCMeo_09g0008770.01	Chr09	13006672	13011463	+	NAM
CDS seq	atgttcagcatggatggtgactttggtccattgcttgagcttatcaagttacacagaatgtatgggcttttgttggtcatggacgttccttggacagttggagatcattgtgatgttggtgtaattgggcttactaagtgctctgccacaatcatgtcttccgcagtgttcgcatcaatgaggctgaatgcaacaaatcaaagctacttggcagtaacaaaagaaaacctagcagacacctccttctgccaccagattaagctcacagctgaattgaagagttacatcaaagagattgcagattgtctagaagaatcaaacaagttctatgtcgtgcgtatgaacagaacattcatggaacaggacagagtgtactttgcgactgagttttcaaagaaatacattgtgaacttggttcgaggcaagacagcaaacattagagtgcagattgcaggtcgaccctcaacaacttaa More
Protein seq	MFSMDGDFGPLLELIKLHRMYGLLLVMDVPWTVGDHCDVGVIGLTKCSATIMSSAVFASMRLNATNQSYLAVTKENLADTSFCHQIKLTAELKSYIKEIADCLEESNKFYVVRMNRTFMEQDRVYFATEFSKKYIVNLVRGKTANIRVQIAGRPSTT

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsCMeo_09g0008770	OsCMeo_09g0008770.03	Chr09	13006401	13011455	+	IsoSeq
CDS seq	atggaacaggcagtaacaaaagaaaacctagcagacacctccttctgccaccagattaagctcacagctgaattgaagagttacatcaaagagattgcagattgtctagaagaatcaaacaagttctatgtcgtgcgtatgaacagaacattcatggaacaggacagagtgtactttgcgactgagttttcaaagaaatacattgtgaacttggttcgaggcaagacagcaaacattagagtgcagattgcaggtcgaccctcaaca More
Protein seq	MEQAVTKENLADTSFCHQIKLTAELKSYIKEIADCLEESNKFYVVRMNRTFMEQDRVYFATEFSKKYIVNLVRGKTANIRVQIAGRPST

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
A3	Chr09	13008549	13008896	+	OsCMeo_09g0008770.03	OsCMeo_09g0008770.03,OsCMeo_09g0008770.02	All
A3	Chr09	13010514	13010762	+	OsCMeo_09g0008770.03	OsCMeo_09g0008770.03,OsCMeo_09g0008770.02	All
RI	Chr09	13010144	13010514	+	OsCMeo_09g0008770.03	OsCMeo_09g0008770.03,OsCMeo_09g0008770.02	All
SE	Chr09	13010063	13010758	+	OsCMeo_09g0008770.03	OsCMeo_09g0008770.03,OsCMeo_09g0008770.01	All
SE	Chr09	13007880	13008397	+	OsCMeo_09g0008770.01,OsCMeo_09g0008770.02	OsCMeo_09g0008770.03,OsCMeo_09g0008770.02,OsCMeo_09g0008770.01	All
A5	Chr09	13006716	13007827	+	OsCMeo_09g0008770.03	OsCMeo_09g0008770.03,OsCMeo_09g0008770.01	All
AF	Chr09	13006672	13007827	+	OsCMeo_09g0008770.01	OsCMeo_09g0008770.02,OsCMeo_09g0008770.01	All

Expression

	Leaf	Root	Panicle
FPKM	0.558553	0.986714	2.973516

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_09g0381300	RBH	0.000000	0.000000	1.114078
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os09g21360	RBH	0.000000	0.000000	0.137079
Nipponbare \| IRGSP 1.0 \| RAP-db	Os09g0381300	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_09g0008560	RBH	0.132401	0.000000	0.731625
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_09g0008540	RBH	0.000000	0.000000	0.845160
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_09g0008580	RBH	0.064084	0.088704	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_09g0008780	RBH	0.000000	3.741453	2.085528
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_09G0218800	RBH	1.053879	2.027086	1.2889065
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_09g0008720	RBH	0.000000	0.000000	0.161981
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_09G0200200	RBH	1.446848	2.083942	10.7809815
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_09g0008700	RBH	0.0	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_09g0008510	RBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_09g0008420	RBH	0.000000	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_09g0008460	RBH	0.000000	0.0	0.657574
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_09g0008450	RBH	0.223167	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_09G008990	RBH	0.152225	2.012675	0.375081
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_09g0008760	RBH	0.305625	2.542152	2.630813

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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