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
Os06g0526100		OGI:06053880 \| 16/16			Nipponbare \| IRGSP 1.0 \| RAP-db			Chr06:19490529-19494500		Homologues MicroCollinearity RGI-JBrowse RAP-DB Ricevarmap2
Gene Symbol		BHLH54, OsbHLH054, bHLH054, bHLH54, OsSPCH1, SPCH1, SPCH
DNA seq		ACATACCACCCTGCGCTTGTCATCAAACAACGGTCGACCTCAAACCACCATCAGATCGATCGAGCTTGAAACAAATTAAGCCACCAAAAGCAACATTCCCTTGGTGACCGTAGCTAGACTCATCCATCATCCATGGGAGACGCGCTGTGTGATCAGCTCCTCTTGGTGGACAGCGACGGCGGCGAGTTCATCCCCCACCACGCCGACGCCGACGCCGACGACCTCTTCACCATCCTCGAGACGTGGGAGGGCTGCGCCAACGTCGTCGCCGGCGGCGCCCCCGCGACCACGACGACGTTAGGTAGTCCTATTGCCGCCGCTGCCTGCATCTCCGGCGTTGTTGGTGGGCAGAATCATCAGCAGCTGCCGGAACCTGCCGCCGCGAAGACCGTGCCAGCCACCAATAACAAGCGGCGGGAGGAGGAGGTGGCGGACCGTGACGGCGACGGAGACGACGACGACGGTTCGCCGCAGAAGAGGCGCAAGTGCTGCTCGCCGGAGTCTTCGACGACGGACGTGGCGGCGGCGACGACGCCCAAGACGGCGCACATCGCCGTGGAGCGCAACCGGAGGAAGCAGATGAACGAGAACCTCGCCGTGCTTCGCTCCCTCATGCCATGCTTCTACGTCAAGCGGGTAAGATCGTCTACACATCGATATAAGCCTCTAACTATAAGTGATCTACCCCATGTGTCTTAAAAAACCAATGTATACAAACTTTCTTGCTATGAATCTGGACATAGCCTACGGTTACTTCTAATTAGAAGCTATTTTTTTCACGACAAAGAAAGTATATAATATATAGCCTGAGTTGAACTTTTGGAATAGCATAGTTTACTTCTAGTCAGAAGTTCATTTTTTTAGATTGAGAAAGTATGTAATATCTAGCTAGCTAATGTGATTGGTGCACGAACAAGTTAGATTCTCCAACTAGTCTCCATGGATTGGGTATCAATCATTTATGATCCTACACGCACTATGCCATCTATCTGCTAGCTAGTCGATCATATCACATCACTTATTGGCACAGGCATCCGGTCCTACGTAACGTAGTACGACAGTACTACCAATACTGTCTCATGCATCAATGCATATGGTATATGGACCGACCTACTCCGTGAAAATTCTCAGTTTAGACTTTAATTCAATCAGCTGTACAGGCAAAGAGCAGGGATTCTACGAATGCATATACTCAAGTAGAGAATCTCAATTGAAACTAACACTCCTATAGATAGCATGTTTTTTTTGCCTTGCCAGCGCTGGAATATAATGCAACCATGCATATATATATATATATATATATATATATATATAGTTAACATCTTAGGCTCTATTTATTTATTTGGTGCAATAGATAACTACTCTGAGATAATATACATATATATAGTTATGTTAGACCAAGTTACACTATTTGTTTCTCTGAAATAATATACATATATATAGTTATGTTTGACATGTATTAATTTGAAATTTTGAATTGATCAGGGAGACCAGGCATCCATCATAGGAGGAGTGGTGGACTACATCAAGGAGCTGCAGCAAGTATTGCACTCGCTGGAGGCCAAGAAGCAGCGCAAGGTCTACACCGACCAGGTGCTCAGCCCACGGCCGCCGGCGACGGTGGCGGCGTCGTGCTGCAGCCCGCGCCCACCGCAGCTCAGCCCCAGGCTGCCGCCGCAGCTGCTCAAGTCCACGCCGCCGCTCAGCCCGCGGCTCGCCGTGCCGATCAGCCCCAGGACGCCGCCGACGCCCGGTAGTCCCTACAGGCTCCTCCGGCTGCCGCCGCCGCCGCCCCCGGCGTCCGGCTCCAACTACGCGTCCCCGGCGATGACGCCGACCCACCACGAGACGGCGGCGCCGTCGCTGGACGCCATCGCCGCCGAGCTGTCGGCGTACGCCAGCAGGCAGGCGCTGGGCGGCGGCCTCCTCCTCCCCGACGTGAAGGTGGAGTTCGCCGGCGCGAACCTGGTGCTGAAGACGGTGTCGCAGCGGTCGCCGGGGCAGGCGGTGAAGATCATCGCCGCCCTGGAGGGCCGATCGCTGGAGATTCTTCACGCCAAGATCAGCACCGTCGATGACACCGCCGTCAACTCCTTCACTGTCAAGGTGTGTACTGCTAGTCTGCTACTGCATGGCACAGCTATTTCAGCTCTTGCGCTCATTATGTGATTATTATTACCCCCTTCATTTTTAAATGATTGACACCGGATACGTGCACTATTTATTTTTAAAATTTTGAAAAATTGTCTTCTTTGCAAAATATTTACAAACACTATAAGGGTTATTAAGTGTGAAACTTTTGATCACTTTAATCTAACAATTTAAGAGTAATTAGTGGTCAAAGTTCTAATAGTACACTGAAAGTTGCTAGATTTTTTAAAATGGAGAGAGTATGTGTCCTAATCACAATTATTTAAAAAAATTAAAACTGAATTAATGTTTAACAAATTTTTCTCATAATTAGTATTTTTTTTAAATAAAGGTACGAGCTCTGCATTTCATTTAGAAAAGAAAATCAAAAGTCGCAAGTGTAATCGTTGCAACATTTTCAGCTCTACCATTTATAATTAACAGAAGCCTTCATATAATTAACCATATTATTGTCACTAAGATTGTTGATATGTACACATGAACAAAAGATCTCATAGATGAGTGCACTGCTTGAGGCCGTGTGGAGGACACAGTAAATGTGAATGGAACATTTGAAAGGAAACTGTTTAGGGTACAGTGCCGTATCAAAAGAAATGCATTTGTTTCATGTGAGTTTCCCATGAAGTGCATGTATGGCTAGCTTAACAGCTAGTACTGCCCAAGCATGTTGAAGCAATGAAGCTGCACTGCTCATAAATGTGGTAGGGTATACAAATGTCTATGTTCTGCCCGGACATCTGTATGGTAGTATAGTATATATATCAGAGACCAGACAGTGTACTGGTACTTCACTGCATGCCTTCACTGTTACATGGTGGTATATCTGCATTTTCACAGTTCTTCAGGATGGGTGCCAATTGGTAACATACATTAATTCATGGTATAATATATTGGTACACTTGTATTGGAAACAAATTTAATACTAAAATTTGTGGCATCTTCGAGTATCTAGGAGTGAAAGTTTATCATGACATTGACAAATCTTACACGTAACATTTTTTATCCTACGGTAGTTTTCAGGTTTCCGCTGCATATTTCTCCTATATATTTTTCCTATATAGGCATTCTTACAAAAATTCCTCGGGTTTCTTCGCTTCCATCCTATTTAATTAGATTATACTGGGCTGAATTTTAGTTTATTTTCATAAATAGGGCCATAACATCATGCATCAATTAAATATGACCTATGTAAATCATGTAAACATATATATGTCAGTTTCCATTTAGTGCAGTGTTGTCACGCTTTCACGTCATCTTATTTAGTTTTTGGACCATTAGATTGTAATTGTTTTGCTCTTGGGTTGATGCATGAAAGCACTTCCTTTCTGTGAAGAAACTATATATGGAATGCTATGTGATAAGTTTTAGTTTATAAGATGAAATTAACATTCCTATGATTTAATATTTTGGTAAATTATAAAATCTTCACTGTGCTTACATTTTTCTAGTATATCTTTGGGCAGATTGGAATTGAGTGCGAGCTCAGCGCTGAAGAGTTGGTACAGGTGATTCAGCAAACGTTCACATGACTCACGCATGTTTCGACCGACCAACTGTTGAAGCTGAAATTAATTAAGTATAGCATGCAGCAGAAACAGAGCGAACAGCCAAGGGAGCACTAGAGTCGACAATACGTGTTGGGCTCTCTGTGTACGAGTGTGTCTGCATTTGCGAGATGAAATTCAATTTAGTTTCAATTCAGATTTGCCTCTAGTGCTCATCATGCACGTGCTAATTTTGCATTTATTTTTGTCTTTTTGTTAATTCTCGTGCAAATTGATTTTTCTACATATATAGGACTATCGGATTCAATATTATGTC More
CDS seq		ATGGGAGACGCGCTGTGTGATCAGCTCCTCTTGGTGGACAGCGACGGCGGCGAGTTCATCCCCCACCACGCCGACGCCGACGCCGACGACCTCTTCACCATCCTCGAGACGTGGGAGGGCTGCGCCAACGTCGTCGCCGGCGGCGCCCCCGCGACCACGACGACGTTAGGTAGTCCTATTGCCGCCGCTGCCTGCATCTCCGGCGTTGTTGGTGGGCAGAATCATCAGCAGCTGCCGGAACCTGCCGCCGCGAAGACCGTGCCAGCCACCAATAACAAGCGGCGGGAGGAGGAGGTGGCGGACCGTGACGGCGACGGAGACGACGACGACGGTTCGCCGCAGAAGAGGCGCAAGTGCTGCTCGCCGGAGTCTTCGACGACGGACGTGGCGGCGGCGACGACGCCCAAGACGGCGCACATCGCCGTGGAGCGCAACCGGAGGAAGCAGATGAACGAGAACCTCGCCGTGCTTCGCTCCCTCATGCCATGCTTCTACGTCAAGCGGGGAGACCAGGCATCCATCATAGGAGGAGTGGTGGACTACATCAAGGAGCTGCAGCAAGTATTGCACTCGCTGGAGGCCAAGAAGCAGCGCAAGGTCTACACCGACCAGGTGCTCAGCCCACGGCCGCCGGCGACGGTGGCGGCGTCGTGCTGCAGCCCGCGCCCACCGCAGCTCAGCCCCAGGCTGCCGCCGCAGCTGCTCAAGTCCACGCCGCCGCTCAGCCCGCGGCTCGCCGTGCCGATCAGCCCCAGGACGCCGCCGACGCCCGGTAGTCCCTACAGGCTCCTCCGGCTGCCGCCGCCGCCGCCCCCGGCGTCCGGCTCCAACTACGCGTCCCCGGCGATGACGCCGACCCACCACGAGACGGCGGCGCCGTCGCTGGACGCCATCGCCGCCGAGCTGTCGGCGTACGCCAGCAGGCAGGCGCTGGGCGGCGGCCTCCTCCTCCCCGACGTGAAGGTGGAGTTCGCCGGCGCGAACCTGGTGCTGAAGACGGTGTCGCAGCGGTCGCCGGGGCAGGCGGTGAAGATCATCGCCGCCCTGGAGGGCCGATCGCTGGAGATTCTTCACGCCAAGATCAGCACCGTCGATGACACCGCCGTCAACTCCTTCACTGTCAAGATTGGAATTGAGTGCGAGCTCAGCGCTGAAGAGTTGGTACAGGTGATTCAGCAAACGTTCACATGA More
Protein seq		MGDALCDQLLLVDSDGGEFIPHHADADADDLFTILETWEGCANVVAGGAPATTTTLGSPIAAAACISGVVGGQNHQQLPEPAAAKTVPATNNKRREEEVADRDGDGDDDDGSPQKRRKCCSPESSTTDVAAATTPKTAHIAVERNRRKQMNENLAVLRSLMPCFYVKRGDQASIIGGVVDYIKELQQVLHSLEAKKQRKVYTDQVLSPRPPATVAASCCSPRPPQLSPRLPPQLLKSTPPLSPRLAVPISPRTPPTPGSPYRLLRLPPPPPPASGSNYASPAMTPTHHETAAPSLDAIAAELSAYASRQALGGGLLLPDVKVEFAGANLVLKTVSQRSPGQAVKIIAALEGRSLEILHAKISTVDDTAVNSFTVKIGIECELSAEELVQVIQQTFT
Function		Transcription factor SPEECHLESS [UniProtKB/Swiss-Prot:Q700C7]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
Os06g0526100	Os06t0526100-01	Chr06	19490529	19494500	+	irgsp1_rep
CDS seq	ATGGGAGACGCGCTGTGTGATCAGCTCCTCTTGGTGGACAGCGACGGCGGCGAGTTCATCCCCCACCACGCCGACGCCGACGCCGACGACCTCTTCACCATCCTCGAGACGTGGGAGGGCTGCGCCAACGTCGTCGCCGGCGGCGCCCCCGCGACCACGACGACGTTAGGTAGTCCTATTGCCGCCGCTGCCTGCATCTCCGGCGTTGTTGGTGGGCAGAATCATCAGCAGCTGCCGGAACCTGCCGCCGCGAAGACCGTGCCAGCCACCAATAACAAGCGGCGGGAGGAGGAGGTGGCGGACCGTGACGGCGACGGAGACGACGACGACGGTTCGCCGCAGAAGAGGCGCAAGTGCTGCTCGCCGGAGTCTTCGACGACGGACGTGGCGGCGGCGACGACGCCCAAGACGGCGCACATCGCCGTGGAGCGCAACCGGAGGAAGCAGATGAACGAGAACCTCGCCGTGCTTCGCTCCCTCATGCCATGCTTCTACGTCAAGCGGGGAGACCAGGCATCCATCATAGGAGGAGTGGTGGACTACATCAAGGAGCTGCAGCAAGTATTGCACTCGCTGGAGGCCAAGAAGCAGCGCAAGGTCTACACCGACCAGGTGCTCAGCCCACGGCCGCCGGCGACGGTGGCGGCGTCGTGCTGCAGCCCGCGCCCACCGCAGCTCAGCCCCAGGCTGCCGCCGCAGCTGCTCAAGTCCACGCCGCCGCTCAGCCCGCGGCTCGCCGTGCCGATCAGCCCCAGGACGCCGCCGACGCCCGGTAGTCCCTACAGGCTCCTCCGGCTGCCGCCGCCGCCGCCCCCGGCGTCCGGCTCCAACTACGCGTCCCCGGCGATGACGCCGACCCACCACGAGACGGCGGCGCCGTCGCTGGACGCCATCGCCGCCGAGCTGTCGGCGTACGCCAGCAGGCAGGCGCTGGGCGGCGGCCTCCTCCTCCCCGACGTGAAGGTGGAGTTCGCCGGCGCGAACCTGGTGCTGAAGACGGTGTCGCAGCGGTCGCCGGGGCAGGCGGTGAAGATCATCGCCGCCCTGGAGGGCCGATCGCTGGAGATTCTTCACGCCAAGATCAGCACCGTCGATGACACCGCCGTCAACTCCTTCACTGTCAAGGTGTGTACTGCTAGTCTGCTACTGCATGGCACAGCTATTTCAGCTCTTGCGCTCATTATGTGA More
Protein seq	MGDALCDQLLLVDSDGGEFIPHHADADADDLFTILETWEGCANVVAGGAPATTTTLGSPIAAAACISGVVGGQNHQQLPEPAAAKTVPATNNKRREEEVADRDGDGDDDDGSPQKRRKCCSPESSTTDVAAATTPKTAHIAVERNRRKQMNENLAVLRSLMPCFYVKRGDQASIIGGVVDYIKELQQVLHSLEAKKQRKVYTDQVLSPRPPATVAASCCSPRPPQLSPRLPPQLLKSTPPLSPRLAVPISPRTPPTPGSPYRLLRLPPPPPPASGSNYASPAMTPTHHETAAPSLDAIAAELSAYASRQALGGGLLLPDVKVEFAGANLVLKTVSQRSPGQAVKIIAALEGRSLEILHAKISTVDDTAVNSFTVKVCTASLLLHGTAISALALIM More

Gene	Transcript	Chromosome	Start	End	Strand	Source
Os06g0526100	Os06t0526100-02	Chr06	19490529	19494500	+	irgsp1_rep
CDS seq	ATGGGAGACGCGCTGTGTGATCAGCTCCTCTTGGTGGACAGCGACGGCGGCGAGTTCATCCCCCACCACGCCGACGCCGACGCCGACGACCTCTTCACCATCCTCGAGACGTGGGAGGGCTGCGCCAACGTCGTCGCCGGCGGCGCCCCCGCGACCACGACGACGTTAGGTAGTCCTATTGCCGCCGCTGCCTGCATCTCCGGCGTTGTTGGTGGGCAGAATCATCAGCAGCTGCCGGAACCTGCCGCCGCGAAGACCGTGCCAGCCACCAATAACAAGCGGCGGGAGGAGGAGGTGGCGGACCGTGACGGCGACGGAGACGACGACGACGGTTCGCCGCAGAAGAGGCGCAAGTGCTGCTCGCCGGAGTCTTCGACGACGGACGTGGCGGCGGCGACGACGCCCAAGACGGCGCACATCGCCGTGGAGCGCAACCGGAGGAAGCAGATGAACGAGAACCTCGCCGTGCTTCGCTCCCTCATGCCATGCTTCTACGTCAAGCGGGGAGACCAGGCATCCATCATAGGAGGAGTGGTGGACTACATCAAGGAGCTGCAGCAAGTATTGCACTCGCTGGAGGCCAAGAAGCAGCGCAAGGTCTACACCGACCAGGTGCTCAGCCCACGGCCGCCGGCGACGGTGGCGGCGTCGTGCTGCAGCCCGCGCCCACCGCAGCTCAGCCCCAGGCTGCCGCCGCAGCTGCTCAAGTCCACGCCGCCGCTCAGCCCGCGGCTCGCCGTGCCGATCAGCCCCAGGACGCCGCCGACGCCCGGTAGTCCCTACAGGCTCCTCCGGCTGCCGCCGCCGCCGCCCCCGGCGTCCGGCTCCAACTACGCGTCCCCGGCGATGACGCCGACCCACCACGAGACGGCGGCGCCGTCGCTGGACGCCATCGCCGCCGAGCTGTCGGCGTACGCCAGCAGGCAGGCGCTGGGCGGCGGCCTCCTCCTCCCCGACGTGAAGGTGGAGTTCGCCGGCGCGAACCTGGTGCTGAAGACGGTGTCGCAGCGGTCGCCGGGGCAGGCGGTGAAGATCATCGCCGCCCTGGAGGGCCGATCGCTGGAGATTCTTCACGCCAAGATCAGCACCGTCGATGACACCGCCGTCAACTCCTTCACTGTCAAGATTGGAATTGAGTGCGAGCTCAGCGCTGAAGAGTTGGTACAGGTGATTCAGCAAACGTTCACATGA More
Protein seq	MGDALCDQLLLVDSDGGEFIPHHADADADDLFTILETWEGCANVVAGGAPATTTTLGSPIAAAACISGVVGGQNHQQLPEPAAAKTVPATNNKRREEEVADRDGDGDDDDGSPQKRRKCCSPESSTTDVAAATTPKTAHIAVERNRRKQMNENLAVLRSLMPCFYVKRGDQASIIGGVVDYIKELQQVLHSLEAKKQRKVYTDQVLSPRPPATVAASCCSPRPPQLSPRLPPQLLKSTPPLSPRLAVPISPRTPPTPGSPYRLLRLPPPPPPASGSNYASPAMTPTHHETAAPSLDAIAAELSAYASRQALGGGLLLPDVKVEFAGANLVLKTVSQRSPGQAVKIIAALEGRSLEILHAKISTVDDTAVNSFTVKIGIECELSAEELVQVIQQTFT More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	None	None	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_06g0526100	RBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os06g33450	RBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os02g0257500	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_06g0017990	RBH	0.0	0.0	0.0
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_06g0017820	RBH	0.0	0.0	0.0
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_06g0017920	RBH	0.0	0.0	0.0
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_06g0017800	RBH	0.0	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_06g0018010	RBH	0.0	0.0	0.0
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_06G0303600	RBH	0.218182	0.007479	0.7236945
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_06g0017520	RBH	0.0	0.0	0.0
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_06G0278600	RBH	0.222205	0	3.234233
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_06g0017880	RBH	0.0	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_06g0017810	RBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_06g0017520	RBH	0.0	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_06g0018220	RBH	0.000000	0.0	0.0
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_06g0017660	RBH	0.0	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_06G017640	RBH	0.0	0.0	0.0
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_06g0017820	RBH	0.0	0.0	0.0

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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