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
OsMH63_04G0478400		OGI:04089800 \| 16/16			Minghui 63 \| MH63RS3 \| HZAU			Chr04:32141315-32146860		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		DLN66, OsDLN66
DNA seq		CCTCTCCATCCTTATCTCCTCCCCTTTGTCATCTCTCTCTCCCTCTCTCTCTCTCTCTTTCAGCTCAACTCCAACCTCCACCCCTCGCCAAGCTCCTTCCTGACCATGCCCACCTCCTTCTCCTCCTCCTCCACCATCCATCACGGCCTTGATCACCTCCTCCATCAGATCCAACAGCATGGATCACGATAACCACTAGGGCGGCCAGATCTAGCGGCGGCGGTGGAGGAGGCTAGATCCCCAAATCCCTCCTCTCCTCTTTGGTCGGCGTCCCTGGAGCCCAAGGTGTCGGGAATGTGTCAGAGTCCGCCAGCAGGGAGTCAAGTATGAGTAATCCTTATTGTGCCCAAGTAGGCTCTGCTTCACTTTCCTTATCTAGAACACCTTCCGTATACAATATTTTATTTTGTATAAGACTTAGAACATGATGGGCTCTATCAAGCCTAACACAAAAGTATTAGGTATGTCTTATCCGTAACACTGATAAATATTGTAGCATTACTTATGATAAACAAGTCCATATATTACCCAGGATTGTATCTAAAAATTAGAGACCCTGGTGCGAAATGTATTTGGACCCTAAAATTTGATAGCCAAATCCCATGATCCTGTTATCATAATCAATGTGATATGACTTGTAGAACGTGATTATATCTAGTTCTAGTCGATTTAACTTTAGGTATTAGGCATGTTGTGGCCTTTTACTTTTAGTACTGAATCTTAGATCTTAGTTCTGACATTCTGGTTCTGGCTTTATCATTCTAGTTATTATATCGCTAACTAAGTATACTTAGTACTTCATATAATTAAAATTTGAGTCCCCTAACTTTAGGGGCCCTAAACAATTGTACACTTTGCACATGCCAGTACGATCCTGATTTTACTAATTACTCTCTTTTGATGTAAAAAAGTTTTTAGCTACGAATTTAGACATATGCTACATCCAAGCTTATAACTAAAAGTCCTTTTCTTATATAGTGAGTACTAAGGACATGCCCAATGCAGGATGCACCCCACCATCCACATGAGCAAAAGTGACCAAGCACCTAGCTAGAGATATGCCTCACACAGTGCAAGCCATACTCCTATGGAATTTTTATGTTTCAGCGCCTATCAGTCTGTCACATTTTGCATTTAAATCCTTGGATTATTATTATTTGCATATACATCCAATATTTGCAGTATACCCCCTAAAAATCACAAAGATATATATACATCAACCCCTCCTCAATCCTCTCATCACCATCTCTCCTCCCAATCTCTCCCCGCGTCTCCTCCCTCTCCGACTCTCCCTTCGCCGGCGCCGCCTCTCCCCTCCCCGGCCCTCTCTCCCCGGCGCTCCCCTCCCCAGCGCCGCCGCCTCTCTCCCCGCCGCTGGATCGAGGCGGAGGTGGCGGATCAAGCGGCGGAGGAGGCGGATCGAGCGGCGGTGGCGCCGGATAGAGGCGCGGCGGCAACGGATGGAGACGGAGGCGGCGGATCGAGCGGCGACGGGTACGGATTAGGGATGGCTATTGTGCCCGTTTGCCCGTTTACTCGCGGGTAAAAACCCTATTAGGGTTGGCTTTGTTCTCCATTTTATACCCATGGGTATTTTATTGGGTCAAAAGCTATGCCCGATGGGTAAATGGGCATGGGTATGGGTAAACACTACCCATACCCGTTTTGCCCGTTTACCCGCGAAATCTAACTTACATGTAGGTTAGGAGCAAAATCCACTAGAATACATAAGCCACGTTCTTTGTTTTCTACGGTTTCCCTTTTATTTCCCTTATTATTTCTCTCCTCTTACTCTATCGCCGCCAGAGGAGAGACACGACACCAAGGCGGAGAATATTTGATGTTTTAAGTTCGATTTGAACTTAGTAGCTTGTAGACTTTTTGTTCCACTGCTTTTGTTGTGGCGGGTAAACTGGCACGCCCGCGGGCATAAGGTGCCCGCGGGCAATGGGCATGGGCAACCATCCTTACCCGTCATGTAGTAATGGGTATACCCACAGGCACAAATAATCTCACGGGCATGGGTATGGGTAGGCACTACCCGTGCCCGTCGCGTCCGATTGCCATCCCTAGTGCGGATGAAGCCGCGGTGGTGGCGGATCGAGGCGCGGAGGCGCCAGATGGAGGCGGAGGCGGTAGATCGAGTGGCGGCGGGGGCGAATCGAGGCGGGGCGGCACGGATTGACGCCGCGGCCGTGGATCGACGCAGCGGCGGCCGGGATCGACGCATCTTCTTCCCTTCTCTCCAGTCCACCCCCTCTCCATCTTCTTCCCGGCACGGGAGCAGCAACGGTGTGGGGGCAACGTCTCTCCCCCAACGCGGCTCCTCGCCTGTTCCTCGCCGAAAAGCTACCGAAACCACTCGACGCTCTGCAGAGGGTCGCAGCGCTAGGTGAGGGTGCGGTCCCGGTCGACGTGGCGTGAATATTCCCCTCGGGAGCGGTGAGACCACTCTCCAGCGTGGAGCGTTGAAAATAGCCTAAGGAAAGGAAAATGGGCAGATAAAGATTAGTGAAATACGGAGCAGGCGAAATCGGCCAGCTGCCAGTCACAGGAGCGAGAAGTCAAGAAGCAAAGCTGGCGCGAATATTCGCGCGACATCAACGCCAACATCTTCCCCGTCTCTCTCGCTACCCATCGGCTCCACCGCTACCCTCTCCGCCCTGCCACCTGGCACCCGAATATTCCTTCCGCCCGAACTGTTGCGTTTACATGGCCCCACATCGCTCCGCGTCATTAGATTTAGCACTTTATCTTCTTCCACAAAGATTCGAATTTTCTTTTCGGTTTGGATAATCGCAAGCGATCTTTTCACTTTGAGCTACTGTACCTTTTTTTGTCGGCATAGTTGGACTAACGATGCTCGTGCCAATTGCAACGCAGCGCTCGTGCTACGCATCAGTAAGCTGTAGTAAAAGTATCTAGTCTAGTCGTCTAAACAAAGCACGTAGAAATCAACACGGTTTGTGCGCCGTGCTCGTGCCAATAGGGGGAGCATTTTTATCCATCTCGTGTACGTGCCGGCGCCGCCGTGTTGGTGGCGAGCGCGCGGCGGCCACGCACGTACGTGGCCCCGCGCGGTTGGCGCGGGCGTTTAGCCGAGAGATGCTCTCTGGTTGGTTTGTTGGGTTCTTTTACTTTTTTTTGTTTCTTGCGCCGTTGCATTGCACCCCAGCTCAAGCCTCCCTAGATTCCGCGCGCGCACACATGGATGCTTTCTCCTTCCTCCGCGCCACCGTCTCCGCTTCCCTCGCGTCCTCTTGTCCTCACGCAGAGAGTAGACTTGCACTGCTCTTTTATCTCTTTCTCTGGCCACCAAGCTGGTTGTTGTATATTACTAGTAGTAATCCGTCGCCGATAGCTGCTTCGTGTTGCTCGATCTTTGACCAGCCAGTGGGGTTGGAGGAGGGAGGGAGCTAGCTATAGTTGCTAGCGTGTTTACGTTTTTGCCGGCGAGGCGATCGACGGAGATGTTTGAGGGGTGCTACGGCGGAGTCGGGTCGGCGGCGGCGGCGGCGACGCGGGACCCGAAGCCGCGGCTGCGGTGGACGCCGGACCTCCACGAGCGCTTCGTCGACGCCGTCACCAGGCTCGGCGGCCCGGACAGTGAGTCCTCTTTGCCCATCAGTCAGTTCGTTTCCTGCTTAATTTTCTCTTCGCGGCACGGTGACGACAACTTCGTAGTCCTCTAGCTCTGTTTCGGTTGGCACTTGGCAAAGGCAAATAGTCTGCTGATTTCTCTAAACTGCAATGTTTATTGCATTGTTCATCCAAATCCTTTTCCTCTGCGTGACTCTGCAGCTTGGCACATAACTATGTAGAGCTGCATGGTTAATTTTGGGCATGCAAACTGGTTTTCAATTTCAGTGTCAAGAATTTCATTCGAAGAATAGTACGCAAACATCATTTGTCATGCTAAATAAAAATATCACGCATAATCCAGTTTGAACCTGCTTCCTTTATCCTTTATCATAGAATAATTGATTGTCTCCATTCTGATCGTGCTTCCTGCAACAGAAGCAACACCCAAGTCGGTGCTCAGATTAATGGGCATGAAAGGCCTCACCCTGTACCATCTAAAAAGCCACCTCCAGGTTTGAACTCATTTTCATAGATAAAACATTCCATATAGCTGCTCTTTTATTTTCTGTTTTTTTTCGCTCAGTTATATTAACACAGTGCTACTTGTATTGTAACTAGAAATATAGACTGGGAAGGCAAAGCAAGAAATCAGCAGGCCTGGAGCTAGCAGTAGCAGATAGTGGTGGTATGTGCCTACCTTGAAATATTACTGTCATGACTCATGAGCAGAATCAAAAGTATCATGCCTTAAAGCTAAGATTTGTCCACACTTCCTACCTTTATTTTATCAGAATTTACAGCGGAAGGCATCAGTTTTTCTATCGGAGCGCCTCCAAGGAATCCTGCCGGAGGAAACAACACGGGGTAACTAGCAATTGCCCTTCTGCTTGTCCTCATAATGCACTACAATAGAATCATCATAGTCTATTACAGCTACAATGGTATATTTGTAATGGGATGTAAATCCTACTGAATGCCTTTTGTTATGTGATCTTTGGGGATTTTTAATTTCCTTCAGTGGAAGTTCTATGAGTGTCTGACATCTTTAGAACATTTCTCTTGTGAAGCAGAGAAATACCGCTTGCAGATGCGCTAAAGTATCAAGTCGAAGTCCAAAGAAAACTGCAAGAACAACTTGAGGTTAGACCATCGACAGCTTTTGCATCAATCCATGAGCTTCTACTTGCCAATGTTTTCTTCCATTATTGCTAAAAGTGCTTGTCTACACTCAGGTTCAAAAGAAGCTGCAGATGCGAATAGAAGCCCAAGGGAGGTATTTAAAGGAAATACTAGAGAAAGCTCAGAAAAACATTTCCCTGGATGCAAATGGGTCTGCTAACCTCTCATCAACCAGATCACAGATTACAGACATCAACCTAGCTCTTTCAGGTTTCATGGACAATGCAACACAAGTTCAGGAGGAAAACAATGAACTGATGAAACCTATATCTGATGACAACCTAAAAGTTAATAATTTGGGCTTTCAGCTCTACCATTTAGGAAGTCAGGAGAGTAAGGATGTTAAGTGCACTCCAAAAACTGAAGAGTTGCTTCTACTAGACTTGAATATTCAAGGAGGATATGAACTCTCTTCTAGAGGAATGCAAGGGTGTGAGTTGGATCTGAAGATCAACCAGCAGAGAAGATAGAGAGTTGTTTCACAAACCTAACAGTTTTGGAAAGTTGACCGTTCGCTATTAGTTTATTCTTTTTCCATGTGCCAGTGTTGAGCATGCTTGTGTTCACAAGTTTGTTTTTTCTGTCTGCTAATGTTAAATTTCCTGAAAGGAACTTCTGAATAAATATGGTATTATTTAGTTATTTGAAGCTTCAATTGTATATACGAGTGAAGTGTGCAAAATGAGGGAAAATCCAACACAGATGTGTATATTCTATCCAAGTATCCTATAAATTGATGTTTTACTTTTGTTCTTATTATCCTATAAACTGATGTTTTGTTTTTG More
CDS seq		ATGGGCATGAAAGGCCTCACCCTGTACCATCTAAAAAGCCACCTCCAGAAATATAGACTGGGAAGGCAAAGCAAGAAATCAGCAGGCCTGGAGCTAGCAGTAGCAGATAGTGGTGAATTTACAGCGGAAGGCATCAGTTTTTCTATCGGAGCGCCTCCAAGGAATCCTGCCGGAGGAAACAACACGGGAGAAATACCGCTTGCAGATGCGCTAAAGTATCAAGTCGAAGTCCAAAGAAAACTGCAAGAACAACTTGAGGTTCAAAAGAAGCTGCAGATGCGAATAGAAGCCCAAGGGAGGTATTTAAAGGAAATACTAGAGAAAGCTCAGAAAAACATTTCCCTGGATGCAAATGGGTCTGCTAACCTCTCATCAACCAGATCACAGATTACAGACATCAACCTAGCTCTTTCAGGTTTCATGGACAATGCAACACAAGTTCAGGAGGAAAACAATGAACTGATGAAACCTATATCTGATGACAACCTAAAAGTTAATAATTTGGGCTTTCAGCTCTACCATTTAGGAAGTCAGGAGAGTAAGGATGTTAAGTGCACTCCAAAAACTGAAGAGTTGCTTCTACTAGACTTGAATATTCAAGGAGGATATGAACTCTCTTCTAGAGGAATGCAAGGGTGTGAGTTGGATCTGAAGATCAACCAGCAGAGAAGATAG More
Protein seq		MGMKGLTLYHLKSHLQKYRLGRQSKKSAGLELAVADSGEFTAEGISFSIGAPPRNPAGGNNTGEIPLADALKYQVEVQRKLQEQLEVQKKLQMRIEAQGRYLKEILEKAQKNISLDANGSANLSSTRSQITDINLALSGFMDNATQVQEENNELMKPISDDNLKVNNLGFQLYHLGSQESKDVKCTPKTEELLLLDLNIQGGYELSSRGMQGCELDLKINQQRR
Function		Myb family transcription factor PHL11 [UniProtKB/Swiss-Prot:C0SVS4]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsMH63_04G0478400	OsMH63_04T0478400.1	Chr04	32141346	32146860	+	maker
CDS seq	ATGGGCATGAAAGGCCTCACCCTGTACCATCTAAAAAGCCACCTCCAGAAATATAGACTGGGAAGGCAAAGCAAGAAATCAGCAGGCCTGGAGCTAGCAGTAGCAGATAGTGGTGAATTTACAGCGGAAGGCATCAGTTTTTCTATCGGAGCGCCTCCAAGGAATCCTGCCGGAGGAAACAACACGGGAGAAATACCGCTTGCAGATGCGCTAAAGTATCAAGTCGAAGTCCAAAGAAAACTGCAAGAACAACTTGAGGTTCAAAAGAAGCTGCAGATGCGAATAGAAGCCCAAGGGAGGTATTTAAAGGAAATACTAGAGAAAGCTCAGAAAAACATTTCCCTGGATGCAAATGGGTCTGCTAACCTCTCATCAACCAGATCACAGATTACAGACATCAACCTAGCTCTTTCAGGTTTCATGGACAATGCAACACAAGTTCAGGAGGAAAACAATGAACTGATGAAACCTATATCTGATGACAACCTAAAAGTTAATAATTTGGGCTTTCAGCTCTACCATTTAGGAAGTCAGGAGAGTAAGGATGTTAAGTGCACTCCAAAAACTGAAGAGTTGCTTCTACTAGACTTGAATATTCAAGGAGGATATGAACTCTCTTCTAGAGGAATGCAAGGGTGTGAGTTGGATCTGAAGATCAACCAGCAGAGAAGATAG More
Protein seq	MGMKGLTLYHLKSHLQKYRLGRQSKKSAGLELAVADSGEFTAEGISFSIGAPPRNPAGGNNTGEIPLADALKYQVEVQRKLQEQLEVQKKLQMRIEAQGRYLKEILEKAQKNISLDANGSANLSSTRSQITDINLALSGFMDNATQVQEENNELMKPISDDNLKVNNLGFQLYHLGSQESKDVKCTPKTEELLLLDLNIQGGYELSSRGMQGCELDLKINQQRR More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsMH63_04G0478400	OsMH63_04T0478400.2	Chr04	32141315	32146860	+	maker
CDS seq	ATGGGCATGAAAGGCCTCACCCTGTACCATCTAAAAAGCCACCTCCAGAAATATAGACTGGGAAGGCAAAGCAAGAAATCAGCAGGCCTGGAGCTAGCAGTAGCAGATAGTGGTGAATTTACAGCGGAAGGCATCAGTTTTTCTATCGGAGCGCCTCCAAGGAATCCTGCCGGAGGAAACAACACGGGAGAAATACCGCTTGCAGATGCGCTAAAGTATCAAGTCGAAGTCCAAAGAAAACTGCAAGAACAACTTGAGGTTCAAAAGAAGCTGCAGATGCGAATAGAAGCCCAAGGGAGGTATTTAAAGGAAATACTAGAGAAAGCTCAGAAAAACATTTCCCTGGATGCAAATGGGTCTGCTAACCTCTCATCAACCAGATCACAGATTACAGACATCAACCTAGCTCTTTCAGGTTTCATGGACAATGCAACACAAGTTCAGGAGGAAAACAATGAACTGATGAAACCTATATCTGATGACAACCTAAAAGTTAATAATTTGGGCTTTCAGCTCTACCATTTAGGAAGTCAGGAGAGTAAGGATGTTAAGTGCACTCCAAAAACTGAAGAGTTGCTTCTACTAGACTTGAATATTCAAGGAGGATATGAACTCTCTTCTAGAGGAATGCAAGGGTGTGAGTTGGATCTGAAGATCAACCAGCAGAGAAGATAG More
Protein seq	MGMKGLTLYHLKSHLQKYRLGRQSKKSAGLELAVADSGEFTAEGISFSIGAPPRNPAGGNNTGEIPLADALKYQVEVQRKLQEQLEVQKKLQMRIEAQGRYLKEILEKAQKNISLDANGSANLSSTRSQITDINLALSGFMDNATQVQEENNELMKPISDDNLKVNNLGFQLYHLGSQESKDVKCTPKTEELLLLDLNIQGGYELSSRGMQGCELDLKINQQRR More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsMH63_04G0478400	OsMH63_04T0478400.3	Chr04	32144916	32146860	+	maker
CDS seq	ATGGGCATGAAAGGCCTCACCCTGTACCATCTAAAAAGCCACCTCCAGAAATATAGACTGGGAAGGCAAAGCAAGAAATCAGCAGGCCTGGAGCTAGCAGTAGCAGATAGTGGTGAATTTACAGCGGAAGGCATCAGTTTTTCTATCGGAGCGCCTCCAAGGAATCCTGCCGGAGGAAACAACACGGGAGAAATACCGCTTGCAGATGCGCTAAAGTATCAAGTCGAAGTCCAAAGAAAACTGCAAGAACAACTTGAGGTTCAAAAGAAGCTGCAGATGCGAATAGAAGCCCAAGGGAGGTATTTAAAGGAAATACTAGAGAAAGCTCAGAAAAACATTTCCCTGGATGCAAATGGGTCTGCTAACCTCTCATCAACCAGATCACAGATTACAGACATCAACCTAGCTCTTTCAGGTTTCATGGACAATGCAACACAAGTTCAGGAGGAAAACAATGAACTGATGAAACCTATATCTGATGACAACCTAAAAGTTAATAATTTGGGCTTTCAGCTCTACCATTTAGGAAGTCAGGAGAGTAAGGATGTTAAGTGCACTCCAAAAACTGAAGAGTTGCTTCTACTAGACTTGAATATTCAAGGAGGATATGAACTCTCTTCTAGAGGAATGCAAGGGTGTGAGTTGGATCTGAAGATCAACCAGCAGAGAAGATAG More
Protein seq	MGMKGLTLYHLKSHLQKYRLGRQSKKSAGLELAVADSGEFTAEGISFSIGAPPRNPAGGNNTGEIPLADALKYQVEVQRKLQEQLEVQKKLQMRIEAQGRYLKEILEKAQKNISLDANGSANLSSTRSQITDINLALSGFMDNATQVQEENNELMKPISDDNLKVNNLGFQLYHLGSQESKDVKCTPKTEELLLLDLNIQGGYELSSRGMQGCELDLKINQQRR More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	1.180716	10.6696015	4.3425465

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_04g0600000	SBH	0.000000	0.151193	0.000000
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os04g51130	RBH	0.000000	0.101080	0.000000
Nipponbare \| IRGSP 1.0 \| RAP-db	Os04g0600000	SBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_04g0025350	RBH	0.0	3.691105	0.000000
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_04g0026130	RBH	0.0	0.0	0.0
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_04g0025860	RBH	0.0	0.0	1.182318
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_04g0025580	RBH	0.056688	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_04g0025840	RBH	0.189567	0.0	0.000000
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_02G0468900	RBH	2.348841	5.163827	1.6753405
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_04g0024580	RBH	0.0	0.253193	0.097273
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_04G0482400	RBH	1.406429	4.7038105	3.469807
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_04g0025050	RBH	0.0	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_04g0024880	RBH	0.000000	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_04g0024970	RBH	0.0	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_04g0025390	RBH	0.145482	0.376839	0.000000
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_04g0025570	RBH	0.0	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_04G024800	RBH	0.000000	0.0	1.126409
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_04g0024690	RBH	0.0	0.000000	0.000000

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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