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_03G0026400		OGI:03004600 \| 8/16			Minghui 63 \| MH63RS3 \| HZAU			Chr03:1726581-1731599		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		PHR1, OsPHR1
DNA seq		CTACGAGTCAAGCGTGGAGAGCGACAAGTCGAGGCTGATCCGGCTTCCCGACGACGACGACGTCGTCGACGAGACCAGGCTGCCGCCGGCGCCGGCGCCGGCGCCGCCGCATCCCGTGTCCAACGCCAGCGAGAGCGAGAGCGAGCAGCCGTCGTCGTGCTCGCCGTCCGGCGCCACGCCGTTGTTGCTCGCGGCGGCGGCGGCGGCCGGTTCGAACCACACCGAGCGATACGACGACGAGGGGCGCGCCTCCGTGCGGCCGCCGCCGCCGCCGCCGCAGCTCGCCGTTGGCGGCGCGACGCGGTGTGGGGCAAACGTGCCGACCTACATGAACAGCGCCACGTGGTAATTAATCAGCGGTTAAAGTGAACTTTTACTGTTGATTTTTTTTTTCTTACGACAAAAAGGGAAAGGTAGGGACTATCCGGCTGTTCACTTCGAGCTTTTGTGACTTTTTGGAGTGATTGGAGGGAAGCAAGCTACTGTGAATGTTTTATGTGTCGCAAAGCTGCAGAGACTAGACATGCAAAGACATGAAAAAAAAAAGAAAAGAAAAAGGCACTACCATGCATCACCAATTCACCATGGGTTTGTGCATGGCTGCATGCATGCACTGCACGAACGTCGACGCACACAAACACTTTAATTTGCAGGGGAACGGTCTAGCTACTGCGTTTGGACAGACTGAGACAGAGTAGTGGATTGATGATCCATCCATCCATCCATACGATTTGTCCCTCTGAATCTCTGATCGATCACTAGTGAATCACATCCATGGATAGCCGAGAAAGACTACTACTAGTACTATTACTGGGAGTAGGATATGAGGAGGCCGGAGTACCTGAAAAGGGATGTTGTCATCGCTGCCGCAGCAGCAGGCAGCAGGAGGAGGAAGAGGAGGAGGAGGAGGCCCCGATGTCACCACGAACCCCAAGAATTTCAGCTTGGAGGAAGAGCTGTACCGAGGTGCGGCGTAGCACTGTGATCCGCCATCGCCGCCGGCTGCTGCAGCAGCAGCGCCCGGCGGCATCGTCGTCGTCCTCTGGCTGCGTACATAGTAGCACTGCAGGCTCGTCGACGGTGACATGTCGCTCTCACGTATTCCATGGCCTCTGAGACGCAGCAGCTGCAGCTGGCTAATTCTGGGGCTCGCGCTCGCGTTCGCGTCGTCGTCTACCTCCTCCGGCCTCCCACCACGTCGTCGTCGCGTCTCCGTCGCAGATGCTGCGGCGTCGTCCCTGCAGCTGCGTACATTGGGCGCGGCAATGCGTGCGCGCGTGCCTGGTTCGTCAATATTCATGCCACTGCTGCAGGAGAGAGAGAGAGATAGAGGAAAAAGGGAATAGAAATGGGAAACATGCATGCGTGTGTGCAGCGTGCCAGCGTGCAAAACTAGTGTCGCACTAGTGACAAATGGGGCTAACTATGCATGCAGATCTAGTTTCAGTGTGACTGACTTTGTGTGTTCGAGATGTTTTTAACTTTCTATGGTGTTTGAGATGCCACTTTGTCCATTACTTTCTGCAACTTAATTTGTATTGGGATATAGTAGTATATGTGGAAGTACTTCAAATAACAAATCTGACGATATAATTCTCAAAAAGAAAATCTTGATGTTTTAAATTAGATTGGTGGACATATTCTAGGGTGTCAAGTAGTTCTATAATACCTAGTGCATTTTAGTTATGTAAAATTCACCAAAGGAAAAGAAGAATATAAGAAGCTCGTTCAATAAAACAATAATACGTTAGGCCCTGTTTGAGAGGCTTCTGACAGTTGTAATTTGTCTTATAAAAACCTATATCTTTCCAAACAGTATAGATACTCAGATTCTGAGTAACCAATAGCTACAAGATCTACAAAATGCACTAGAATTCATAAGCTAAAAAACTAAGCCCTTCTCATATTTTCATCAGCTGTATCTGTGAATTTTAAGCTCCATCTAAATAATCATTGTGTTTTAAGGTTTCTAGTTATTTTAAATTGTACTAATGGGGTCCACAACTATAAATGCTCCTATAACAGAACAAAGTTTGTCAAAACATTCTAATAAAAGAACTAGTACCACTATATTCTTCTCAAAACATACCCGTGGATATAATACGAATTGCTTGTTATAGCCATGCAAACATCTCGGCTTTGTTCACTTTATAGTCATTTTCAATCTTTCCAAAATTTATCATTGCCAAAATTTTAACAAGTTAGAAACATTAATTACCAAGATTTAGTAGGATAGGCTAATATAATGTAGTCAATTATCTAGGCATGACAAATATTTTATAACAAAATAAATTTTGTCACACAGTTGTCAATTTTATTAAATAATGATATGAGTTAAAATGACATGAATCTGAACAGGCCCCACATCAAGTAGGTATTACTATGTCCATTCTAAAATAATACAAGAATTTGTGGCTACACAAATGGATACAAGTAAGACATCCCTTTGCTTATTACTAGTAGCCTTTTTTTTTTCAAGTTTTTCACTTATCTAGAAATATTGATGGGATGCCTCAAGATGTTGCATCCTAGAAAAAATCAACTTCTAACAACGTATATAGTTAGATATTTAGGGGGTGTTTACATCTAGGGGTGTAAAGTTTTGGCGTATCACATCGGGTATTATATAGGGTGTCACATAGGGTATTTGGGCACTGGTAAAAAAACTAATTATAGAATCCGTCAGTAAACCGCGAGACGAATTTATTAAGCCTAAATAACTTGTCATTAGCAAATGTTTACTGTAGCACCACATTGTTAAATCATGGAGCAACTAGGCTTAAAAGATTCATCTCGTAAATTAGTCGCAATCTGTGTAATTAGTTATATTTTTAGCCTATATTTAATACTTCATGCAAGTGTTCAAACATTCGATGTGATAGTTTAATTCACACCAAACTTTCCCCAAACTTAACTTTCCATCACATCACATCACATCACATCTAAAATTTTTCTACTCACATAAACTCCTAACTTTTTTTTCCAAACTATCAACTTTCCTCAAACTTCTCCCTAATTTTAGGAACTAAACACAATCTAATTGAATATTTGAATTAGAGGGTAAAGTGAATGCAAAATGATGGTTTTAAACTGTTGACATTATTCGTGATAAGAATTGCTCATGATGTGACTGATGGCTCATAGATTGACAGAGCATAAACTGATTGCTCCAAATAAAGGGCAATGACCTTTTCAGTTGGAGGTGAAGCAGTGGCTCCTTTCTAGGCTTTGGGGAGTGGCAGCTGCAGCAAGGGACATCACACTCATCATGATCACACTGCTGCATATCAGTCCAAACTTCCACACCACCTCCATATGTGTGCTCCTGATCCACCTGTTGCACCTGTATCCCTGATCACAAGATTGGCAAAAGAAGAATGGTTTTAGGTGGTGTTTAGATCAGGGACTTAACTTTAGTCCATGTTTTTAGACACTAATTTAGAGTATTAAATATAGACTACTTACAAAACTAATTACATAAATAAAAGCTAATTCACGAGACAAATTTTTTAAACCTAATTAATCTATAATTAGAGAATGTTTACTGTAGCATCACATAGGCTAATCATGGATTAATTAGGCTCATTAGATTCGTCTCGCAAATTAGTCCAAGATTATGGATGAGTTTTATTAATAGTCTACATTTAATATTTATAATTAATTTTCAAACATCCGATGTGATAGGGACTTAAAAGTTTTAGTCCCATCTAAACAGGGCCTTAGGTTTTTCTTTCCTTAGCTTTCCTCCTCTCATGGAGTACTGGAGTTACTAGTAGCAGCTGCATGCAGCATTAGGATAAAGGAACTAACACTGTATAGCCCAAAGAATTAGTATAAAAAATTTCAAAGAATTGTTATATTTTGAGAAGTGTGCCATCCATGCACACATGCATCTGCATACAAGCAAGTGTGCCCAACAGTTCTTCTTTAATGGCGAAATAAGGTGCTTAAGACCTTAACACTACTCTGACTAGCCTGTGATTAACAACCTTCAAGACTAGTAGCATCGACAAGAAAATGCATCTTCCTGCATTATGTATGCATCGGTGGTTAATAAGAATTGTGACTAACTGGGGTCTGTATATTCTTCACAGTTTTAGCAGTGAGGAATGTAGAGTACTGTAGTAGCTATATTTGGAGACTCTGCAGTTCAGGACCAACAAGATAGACACGTCTCGGGGAATATATCCTTTTTACTTCAAACTTTTGTTTGTTGAAAAAAGCAGAGCTCTGCCTGAACCATTCCTGGCAGGCAAAAATACCTATAGAAGTAGCTAGTCAAAGCCAACACATTGCAAAGCAAAGTTAAAAGAAAAAAACAAAAGAATGTACGTGTATAAAAGTATGTACGTAATGTTTATAATACATATATAAACATTCCAAGATCATTCAAAGCAAAGTACCTTGCATTCCAAGATCATTCCTCATGTTCCTGTACATCTGCTCCAAAGAACATAAAACAACATTAGTGATACTACTAAAAAGGAAGCAGGAGAAGCAACCGAAGAAGAAGACAAGTCACAAGGACATGAGACATATAAGGCCAACACTGATAATTAAACTACACCTGAAGATGGCTTTTGACATGAGATATGGTGAGTCCTCCCACTCCCATCAGCTGCAAAACTCGCTTCGGTGTAGCCTCTGCACATCACACCCACACACCAACATGAGAAAGATAAAAACCTCTGGTACTCATATGAAAATGGAGCTTAGAACTAGCTATAGAGAAGAAACATGCAAACAAATATATAGAACTAGAAAGAGAGTAGGAAAAGATGCAGATAAACCCCAAGCTAGTATGATCAAGACACATCACACATATGAGATGAGCTAGATGAGGATGAGGTCGACGAAGAACATACTGTCCTGGCCGCCGAGCTTGTGAATGGCATGGACGAAGCAGTGGTGCAGGTCAGGCGTCCAGCGTAGCCGCGGCACCTTGGATCGGTTGTACTGCCTGACGCCGCCGTTCCTCTCCCTGCCGCCGCCCACCATTGCCGCCCTCACCATGGTCAT More
CDS seq		ATGGTGGGCGGCGGCAGGGAGAGGAACGGCGGCGTCAGGCAGTACAACCGATCCAAGGTGCCGCGGCTACGCTGGACGCCTGACCTGCACCACTGCTTCGTCCATGCCATTCACAAGCTCGGCGGCCAGGACAAGGCTACACCGAAGCGAGTTTTGCAGCTGATGGGAGTGGGAGGACTCACCATATCTCATGTCAAAAGCCATCTTCAGATGTACAGGAACATGAGGAATGATCTTGGAATGCAAGGGATACAGGTGCAACAGGTGGATCAGGAGCACACATATGGAGGTGGTGTGGAAGTTTGGACTGATATGCAGCAGTGTGATCATGATGAGTGTGATGTCCCTTGCTGCAGCTGCCACTCCCCAAAGCCTAGAAAGGAGCCACTGCTTCACCTCCAACTGAAAAGCAGTGGCATGAATATTGACGAACCAGGCACGCGCGCACGCATTGCCGCGCCCAATGTACGCAGCTGCAGGGACGACGCCGCAGCATCTGCGACGGAGACGCGACGACGACGTGGTGGGAGGCCGGAGGAGGTAGACGACGACGCGAACGCGAGCGCGAGCCCCAGAATTAGCCAGCTGCAGCTGCTGCGTCTCAGAGGCCATGGAATACGTGAGAGCGACATGTCACCGTCGACGAGCCTGCAGTGCTACTATGTACGCAGCCAGAGGACGACGACGATGCCGCCGGGCGCTGCTGCTGCAGCAGCCGGCGGCGATGGCGGATCACAGTGCTACGCCGCACCTCGGTACAGCTCTTCCTCCAAGCTGAAATTCTTGGGGTTCGTGGTGACATCGGGGCCTCCTCCTCCTCCTCTTCCTCCTCCTGCTGCCTGCTGCTGCGGCAGCGATGACAACATCCCTTTTCAGGTCGGCACGTTTGCCCCACACCGCGTCGCGCCGCCAACGGCGAGCTGCGGCGGCGGCGGCGGCGGCCGCACGGAGGCGCGCCCCTCGTCGTCGTATCGCTCGGTGTGGTTCGAACCGGCCGCCGCCGCCGCCGCGAGCAACAACGGCGTGGCGCCGGACGGCGAGCACGACGACGGCTGCTCGCTCTCGCTCTCGCTGGCGTTGGACACGGGATGCGGCGGCGCCGGCGCCGGCGCCGGCGGCAGCCTGGTCTCGTCGACGACGTCGTCGTCGTCGGGAAGCCGGATCAGCCTCGACTTGTCGCTCTCCACGCTTGACTCGTAG More
Protein seq		MVGGGRERNGGVRQYNRSKVPRLRWTPDLHHCFVHAIHKLGGQDKATPKRVLQLMGVGGLTISHVKSHLQMYRNMRNDLGMQGIQVQQVDQEHTYGGGVEVWTDMQQCDHDECDVPCCSCHSPKPRKEPLLHLQLKSSGMNIDEPGTRARIAAPNVRSCRDDAAASATETRRRRGGRPEEVDDDANASASPRISQLQLLRLRGHGIRESDMSPSTSLQCYYVRSQRTTTMPPGAAAAAAGGDGGSQCYAAPRYSSSSKLKFLGFVVTSGPPPPPLPPPAACCCGSDDNIPFQVGTFAPHRVAPPTASCGGGGGGRTEARPSSSYRSVWFEPAAAAAASNNGVAPDGEHDDGCSLSLSLALDTGCGGAGAGAGGSLVSSTTSSSSGSRISLDLSLSTLDS
Function		Putative Myb family transcription factor At1g14600 [UniProtKB/Swiss-Prot:Q700D9]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsMH63_03G0026400	OsMH63_03T0026400-mRNA-1	Chr03	1726581	1731578	-	maker
CDS seq	ATGGTGGGCGGCGGCAGGGAGAGGAACGGCGGCGTCAGGCAGTACAACCGATCCAAGGTGCCGCGGCTACGCTGGACGCCTGACCTGCACCACTGCTTCGTCCATGCCATTCACAAGCTCGGCGGCCAGGACAAGGCTACACCGAAGCGAGTTTTGCAGCTGATGGGAGTGGGAGGACTCACCATATCTCATGTCAAAAGCCATCTTCAGATGTACAGGAACATGAGGAATGATCTTGGAATGCAAGGGATACAGGTGCAACAGGTGGATCAGGAGCACACATATGGAGGTGGTGTGGAAGTTTGGACTGATATGCAGCAGTGTGATCATGATGAGTGTGATGTCCCTTGCTGCAGCTGCCACTCCCCAAAGCCTAGAAAGGAGCCACTGCTTCACCTCCAACTGAAAAGCAGTGGCATGAATATTGACGAACCAGGCACGCGCGCACGCATTGCCGCGCCCAATGTACGCAGCTGCAGGGACGACGCCGCAGCATCTGCGACGGAGACGCGACGACGACGTGGTGGGAGGCCGGAGGAGGTAGACGACGACGCGAACGCGAGCGCGAGCCCCAGAATTAGCCAGCTGCAGCTGCTGCGTCTCAGAGGCCATGGAATACGTGAGAGCGACATGTCACCGTCGACGAGCCTGCAGTGCTACTATGTACGCAGCCAGAGGACGACGACGATGCCGCCGGGCGCTGCTGCTGCAGCAGCCGGCGGCGATGGCGGATCACAGTGCTACGCCGCACCTCGGTACAGCTCTTCCTCCAAGCTGAAATTCTTGGGGTTCGTGGTGACATCGGGGCCTCCTCCTCCTCCTCTTCCTCCTCCTGCTGCCTGCTGCTGCGGCAGCGATGACAACATCCCTTTTCAGGTCGGCACGTTTGCCCCACACCGCGTCGCGCCGCCAACGGCGAGCTGCGGCGGCGGCGGCGGCGGCCGCACGGAGGCGCGCCCCTCGTCGTCGTATCGCTCGGTGTGGTTCGAACCGGCCGCCGCCGCCGCCGCGAGCAACAACGGCGTGGCGCCGGACGGCGAGCACGACGACGGCTGCTCGCTCTCGCTCTCGCTGGCGTTGGACACGGGATGCGGCGGCGCCGGCGCCGGCGCCGGCGGCAGCCTGGTCTCGTCGACGACGTCGTCGTCGTCGGGAAGCCGGATCAGCCTCGACTTGTCGCTCTCCACGCTTGACTCGTAG More
Protein seq	MVGGGRERNGGVRQYNRSKVPRLRWTPDLHHCFVHAIHKLGGQDKATPKRVLQLMGVGGLTISHVKSHLQMYRNMRNDLGMQGIQVQQVDQEHTYGGGVEVWTDMQQCDHDECDVPCCSCHSPKPRKEPLLHLQLKSSGMNIDEPGTRARIAAPNVRSCRDDAAASATETRRRRGGRPEEVDDDANASASPRISQLQLLRLRGHGIRESDMSPSTSLQCYYVRSQRTTTMPPGAAAAAAGGDGGSQCYAAPRYSSSSKLKFLGFVVTSGPPPPPLPPPAACCCGSDDNIPFQVGTFAPHRVAPPTASCGGGGGGRTEARPSSSYRSVWFEPAAAAAASNNGVAPDGEHDDGCSLSLSLALDTGCGGAGAGAGGSLVSSTTSSSSGSRISLDLSLSTLDS More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsMH63_03G0026400	OsMH63_03T0026400-mRNA-2	Chr03	1730970	1731599	-	maker
CDS seq	ATGACCATGGTGAGGGCGGCAATGGTGGGCGGCGGCAGGGAGAGGAACGGCGGCGTCAGGCAGTACAACCGATCCAAGGTGCCGCGGCTACGCTGGACGCCTGACCTGCACCACTGCTTCGTCCATGCCATTCACAAGCTCGGCGGCCAGGACAAGGCTACACCGAAGCGAGTTTTGCAGCTGATGGGAGTGGGAGGACTCACCATATCTCATGTCAAAAGCCATCTTCAGATGTACAGGAACATGAGGAATGATCTTGGAATGCAAGGTACTTTGCTTTGA More
Protein seq	MTMVRAAMVGGGRERNGGVRQYNRSKVPRLRWTPDLHHCFVHAIHKLGGQDKATPKRVLQLMGVGGLTISHVKSHLQMYRNMRNDLGMQGTLL

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.710107	0.031133	0.3812735

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_03g0325500	SBH	3.592712	7.256366	2.119022
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os03g03760	RBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os03g0329900	SBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_03g0002350	RBH	0.094906	0.000000	0.283762
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_03g0002320	RBH	0.000000	0.0	0.0
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_03g0002350	RBH	0.783305	0.0	1.010556
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_03g0002330	RBH	0.000000	0.000000	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_03g0002370	RBH	0.000000	1.454222	0.000000
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_10G0348300	RBH	0.078195	0	0.1851385
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_03g0002310	RBH	0.034185	0.0	0.109991
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_03G0027300	RBH	0.4912775	0.0171155	1.903623
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_03g0002400	RBH	0.000000	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_03g0002400	RBH	0.0	0.959110	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_03g0002370	RBH	2.132202	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_03g0002410	SBH	0.131473	0.170277	0.596675
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_03g0002390	RBH	0.000000	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_03G002390	RBH	0.000000	0.000000	0.000000
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_03g0002220	RBH	0.000000	0.0	0.000000

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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