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
OsPr106_04g0018560		OGI:04074630 \| 13/16			PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)			Chr04:25731344-25738086		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		PTR
DNA seq		cgattaaagttttttttggacgaaaatttttagaaaaaagtgtgcgctagtaacggacgtttgactaataatagcactataggcaaaatcacatctacgcaaaacttgactaatcctttggcacggtttgaccaacactacaggcgcggtatttttcaaggtgaatcgtgatccgccgatggctcgacgtcgacgacgacgcgtgggtcttgccggtatatgtacctgctcgcccagtagaggtagttgacgaagccaagcagcccgacggcggcgacgacccagtagaagaggtcgaggcggctggtgttgagggtggcgccctcgagccacCCGccgccgccgccgccgccgccgtgccgcctcgtggccctgttcaccacctgcaccagcagcgtggcgagccacgacgagaggccgagctcgcaccagaacagcgccgacgcgatggacttcatgccacggggcgcctcgctgctgaagagctcgaggaggcccgggaacgacgtcacgtcggagacgccgagcaggaagaactgcggcgccagccagaacagcgacatctgccccgccgccgcggcgtcggcccgccgcttcctctccacgacggcggcgatggccgacgccaggatcacggcggcgaacccggcgccgacgcgctgcaggtgggtgacgccgctggcgtagcccgtgcgccgccgcaggagcggcacgaggaagcggtcgtacaccgggagcagcgccatctggaacgcgctggggatgatgaagagcgtcgccggcgagacgtggatcctccccagccgggtgttggtcaagccgccctgctgcacggtgaaggtgaagaggagcgggttcgacatgtagccgatcagggagctgatgaagacggggagcacgcggagcacggcctttgtctcctccacgttcttcgtgctgcagactgaccaggccccgtctttgcctccattgatgcaagctttgtcaaggaatctgccaagatgcatgcaaagacaaaattttagtattgcactctgccaagaggacaatgctcaattgccaatattttctgctttgtattcaaagtagtctagaaaaagtactcagtatttcgttgaacatacttcagactactgtttgtttgagaagctatttcagttacttcagtagagcctccttgctcagtgcttctttcttcctgtgcttcttccagcttctcaggaagttgaagcttcctgttcttgaatgcaaccacaagaacctgggatagatagatcagaatgcagtcaactaacatgcacaggatctcttttcttgagaattgatgttgacatcatgttttgacccaacaaggagcacaacctacctggagtatccgagttagcggacttccttcgggtacatggttgcggtacaaagggagaccagcagcaaccacaagcagcccaagcaggatcaggaacgcgcacaccccaaacccgacatcccaccctttgctgttctccagccaaactatgaggatcaatcctatgaaacccccaaaggagattccgaaggtgtaccaattgaagaagctggactgctggcgggactcggaggggtcttcatggtcgaactggtctgctccgaggggcggcatacaagcacgcatgaagccatcgccaaaagcgctgatgtacagcgctgcgtaaagtaggacggcattcctgccatggacctctctgcagctgcttacctctgcttccgcgttgcaaggcggtggacggagagagggaaggtaagcttgcagtgcgagcaaaccgtagccctgcatatatgattgccaataattcgttagatggttgaatagaccaagaagcagattaccagAaaaaaatgccaatttctttattattggtaggtttgcgcacagtaattggcaacggagaattaaacaaaaatagtttcttttgatcatattaggcttgatgtagatagttgagtaaaccaaaaagcgaattaccaaaaattccaatggaccaaagaggagtattgttctagctcgagttatgtaagagtctgagaggaaagctcctaacagagcaaacccagatgtggcaccaagaacattagtgactgtagttgaagagcttgagattcccatatgcattgttccatggagataggtaaccatattcagcatgtttgggacattgactgtgcttgtcaccacagtcagaactgtaagagatcgaaacatgtataaaatgcttcagtgatttaaagaaagaaaagaagcttgaaatggaaagagtaactcgtcacatgtctgcatattactagtaactagacaaaatcacataattcaggaaacatggataaagcaagtcaactggcaatcacttacaatatacaaaccatgctgctctgactcctccatgcacctttctattaataggatttcccctccagtccaaaaagcctccgactgccatggtttttctgatgagttcaaatatttctctcttgattactgcctggccattgcagcataagggggtataaatcatagtagatagacagttgaagtcagggactcaggacccaggggtattgatcacagatggataagtcaaatttgaagaagtcagaaaaacaaaatgacAaaaaaatattcttgaatagtatagccgtcacctaccacttgcaagcaccaacagtccaacactaaagttgactatcagattcagagttcctactccctactaaccaaaatatggaggtgtatcctgacaatttttttaagcaatctgtcaaatggcatgcattgacactgatgtacaaatatcttagataaaatgcatgccttcaagtccaagccatcattctggactatcttgaaactaagctcttaatttattaattgttctgagaagtcgtctttaaagacgcttcctatgagaatcattgctgctcaaattatgagcacgaaatgcttatgcatgagttacataataaactctaccaattaggttaacctactattactcttgattatcagtccaaaactcaggtttgtaacttacagttgatttcctccatattaaccatcatggaacaacccaattgtggttttaccttttaacctaagcatccactactctacaatgcgtcttcaaggagatggcatcagctcgaacaggatacgcatatgaaaagtataaacaagagaaattaaaacctaaaaccctaaaaattattggtttaaaaagataaccaaaacatatttgctactcccattattcccttttacttgtcactgtttacaagtttgattttatctttgaccaataaaaacttttaagttatgatgttttgatgaatgcaagtagttaattatatttaacatgcaaagtactttgataatataatatctccttaaataTttttaaatattttttataaaaaagacgaatggtcaaagtttgtacatgaatagtatctagtgtcaagtgaaagggagcatagggagtagctattatttttaatcatgggccgatgcaattaatacagattgtctgaaatgcacatcagtagcaaaaagaaaaggtttcaaattcaaccacacccttaaacatactagattagagaggtcatggtggctaaaacaatgatttacttgtccattggcagctgaatgggtgattgtccaaaagcaattaaatttcatcaagctgaacttcgagcatgcaacacatatacagagaaaatcaacttctttgtattgttgattggtttcaatttgaaagaaacaaatataattttctgctaaggtttgtggtgtcctgctgacatccttgtttcattggaaggcattcattgagcacaatgttttcaacttttcattcttagtataaaattacatatttttattatgatatgacataattgaagcttgaagaccaagcagaaatgatacttttatgtcagtacagtacatactctcattcttcagtaaactagtcagctatactatttttacaaaccttgttagtcatcagtttaggtaccacaaatattgatgttcttcctaagacacagtttacgcaactactttcaatattgaaaatctattttctggccttgcaagatagcgacagatagagataacatcactgtacgctagattgcattgattgtaacttgtaagttctgtcaagctgccataagccaatggagattataggatatctttgttacgatctatacaacacagacaggctaacaaaagaaaattaatcacaactctttgttttctcttacctatctattgcatactgtttggatctttaagctccaaaattgtcgccgtctgatctaacagtactgacccttttcttgttggcatatctcctagcccagaatgcataattgataaatgccaccagctcgaaggttgccaataacaagaagaagcgatcaaggcgtgtcctgttgaagtttgttccatctaaccatcctcttccattgtctccaagccttgtcattctgttgacgagctggacaaaggcacatcctgaccaggctgctattccgaccagaagagactgcactgctggtgcaatatgctttgcttcaggtgcctcgctctttatgaactgaaccagcccaccaatatatgctatatccatgatgcttagcaggaagaactgcatcaccagccagaagacggacattgggacaccgtcagctactaatgttagcccttgctgctccacgaccatcagcctctttgcttccaccaacatggcaatgcatgctgccattatcccacacgcagaggcaacaccgatgtgctgcagaggggtgataccattggtgtggcctgtgaatatcctcagcagtggtatcaagattctcctgtagcacggttgcatcagcatgtgaaatgttgttgggattgcgatgagagaggcagagggtatctggatcattcctatccctgagtccatcgtgctgccaacttgtatggttaacgtcatgagcaatgtgaagggcaagtaggcgaatatgcagctgatgaagattggaagcatctgagtaatagcctctgttttctcatcaactcgagtagtgctgcagaaaatacaaattgttttttcccgtcatgtattcaggatttgtccacaaatatattagggtattatggagattatgatttccacaaaaataggaattattatactcttggttctcaacatttatttaaaagttaaaagttcatacattgttttcagaaatacattgttttctggggatttttttattatcagggaacttaccaaatatttttgctgtcacatttgtcttccccgtcctcatctacatgatctgatgtactgatctcttgcagctcaataacatcaataacagcagcctgcctcttctttgatgatgtgacaagaacctggaaaggtaccagtaatacaacttcaaaacaatatgatcttctgttttccttgctttgtcttgctacattcaattttgttttagattgatgtgtggaaggactgccctaatttctttattgcttgtaattaatctgttatctgaaatttctagaaataggcatggtgactttccagcaataagcatggaaggtagaataatgcaatgtaatgctatcagacaaaagagtataaaacataacttggataacagcatccttcttgtatatatttgacttccacaaaatggatcgTggatAatataaagcaacactaaccagTtggcgtcaaaataaatcaatcatacacaaattcgttataattaacatgcataccaaattagaCcgacaaacgtatataattgtggcatatgattttttacctgcaatattctagttagaggacttccattgagcttgcgcattccatagaaaggcagtccactggctgctatgagcagccctacaataacaataagggcacacaacaaaaagccaatgtcccaacccagattcttctcgATCCacactaGgaataccaatccaataagtgctccaagagagtttgcagacttgagccagcttaagaagttactcctgagatgtgatgcttctggatcatcattgctgaactgatcttcaccaagggctggtacgcaatcgcgcatgcagccctccccaatggcaaacattaataagctcaagtagagcagtgttaagttccagccttgcgctggctcacatttgcttggatctttgtttatctcacaaatcggaggatggagtgaaggcaagtgcgcttgcaatgctagcaacatatagccctgcatttaaacacattgattataactcagcattttaaaaaaccctacctcctcatcttagaagcttaaaatgtcctgaaagcatatactatctccctcgtcttaaaatcctgtactaaTTCTTttCTTTTAGGCGAATAAAAGCTTCGATTTGATTACTCATTCGAACAAAATGTTAGCAAATCGAAAGTGACACGAAAAATATGCTTCCAAAGTGTTCGATTCTAACATTTGGGGATGCCATTGTAAACTCACCTCCACCCTAGTACGATTTTCTCCCAATTCTGCCTATTACATCTTCCTTAACCTCGCCGGCTCGTCCTCACCCACCCACCCCCCCCCCGGCTCCCTCCTGCTGCTCCTCCTCCGGCGAACTCTTCTCGTAGCCATCGGTGATCGCCCTGCTTCTCCGCTCTCGCTTGATCCCACGTCAT 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CDS seq		atggcagtcggaggctttttggactggaggggaaatcctattaatagaaaggtgcatggaggagtcagagcagcatggtttgtatattttctgactgtggtgacaagcacagtcaatgtcccaaacatgctgaatatggttacctatctccatggaacaatgcatatgggaatctcaagctcttcaactacagtcactaatgttcttggtgccacatctgggtttgctctgttaggagctttcctctcagactcttacataactcgagctagaacaatactcctctttggtccattggaatttttgggctacggtttgctcgcactgcaagcttaccttccctctctccgtccaccgccttgcaacgcggaagcagaggtaagcagctgcagagaggtccatggcaggaatgccgtcctactttacgcagcgctgtacatcagcgcttttggcgatggcttcatgcgtgcttgtatgccgcccctcggagcagaccagttcgaccatgaagacccctccgagtcccgccagcagtccagcttcttcaattggtacaccttcggaatctcctttgggggtttcataggattgatcctcatagtttggctggagaacagcaaagggtgggatgtcgggtttggggtgtgcgcgttcctgatcctgcttgggctgcttgtggttgctgctggtctccctttgtaccgcaaccatgtacccgaaggaagtccgctaactcggatactccaggttcttgtggttgcattcaagaacaggaagcttcaacttcctgagaagctggaagaagcacaggaagaaagaagcactgagcaaggaggctctactgaagtaactgaaatagcttctcaaacaaacagtagtctgaaattccttgacaaagcttgcatcaatggaggcaaagacggggcctggtcagtctgcagcacgaagaacgtggaggagacaaaggccgtgctccgcgtgctccccgtcttcatcagctccctgatcggctacatgtcgaacccgctcctcttcaccttcaccgtgcagcagggcggcttgaccaacacccggctggggaggatccacgtctcgccggcgacgctcttcatcatccccagcgcgttccagatggcgctgctcccggtgtacgaccgcttcctcgtgccgctcctgcggcggcgcacgggctacgccagcggcgtcacccacctgcagcgcgtcggcgccgggttcgccgccgtgatcctggcgtcggccatcgccgccgtcgtggagaggaagcggcgggccgacgccgcggcggcggggcagatgtcgctgttctggctggcgccgcagttcttcctgctcggcgtctccgacgtgacgtcgttcccgggcctcctcgagctcttcagcagcgaggcgccccgtggcatgaagtccatcgcgtcggcgctgttctggtgcgagctcggcctctcgtcgtggctcgccacgctgctggtgcaggtggtgaacagggccacgaggcggcacggcggcggcggcggcggcggCGGgtggctcgagggcgccaccctcaacaccagccgcctcgacctcttctactgggtcgtcgccgccgtcgggctgcttggcttcgtcaactacctctactgggcgagcaggtacatataccggcaagacccacgcgtcgtcgtcgacgtcgagccatcggcggatcacgattcaccttga More
Protein seq		MAVGGFLDWRGNPINRKVHGGVRAAWFVYFLTVVTSTVNVPNMLNMVTYLHGTMHMGISSSSTTVTNVLGATSGFALLGAFLSDSYITRARTILLFGPLEFLGYGLLALQAYLPSLRPPPCNAEAEVSSCREVHGRNAVLLYAALYISAFGDGFMRACMPPLGADQFDHEDPSESRQQSSFFNWYTFGISFGGFIGLILIVWLENSKGWDVGFGVCAFLILLGLLVVAAGLPLYRNHVPEGSPLTRILQVLVVAFKNRKLQLPEKLEEAQEERSTEQGGSTEVTEIASQTNSSLKFLDKACINGGKDGAWSVCSTKNVEETKAVLRVLPVFISSLIGYMSNPLLFTFTVQQGGLTNTRLGRIHVSPATLFIIPSAFQMALLPVYDRFLVPLLRRRTGYASGVTHLQRVGAGFAAVILASAIAAVVERKRRADAAAAGQMSLFWLAPQFFLLGVSDVTSFPGLLELFSSEAPRGMKSIASALFWCELGLSSWLATLLVQVVNRATRRHGGGGGGGGWLEGATLNTSRLDLFYWVVAAVGLLGFVNYLYWASRYIYRQDPRVVVDVEPSADHDSP
Function		Protein NRT1/ PTR FAMILY 4.6 [UniProtKB/Swiss-Prot:Q8H157]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_04g0018560	OsPr106_04g0018560.01	Chr04	25731499	25738086	-	NAM
CDS seq	atggcagtcggaggctttttggactggaggggaaatcctattaatagaaaggtgcatggaggagtcagagcagcatggtttgtatattttctgactgtggtgacaagcacagtcaatgtcccaaacatgctgaatatggttacctatctccatggaacaatgcatatgggaatctcaagctcttcaactacagtcactaatgttcttggtgccacatctgggtttgctctgttaggagctttcctctcagactcttacataactcgagctagaacaatactcctctttggtccattggaatttttgggctacggtttgctcgcactgcaagcttaccttccctctctccgtccaccgccttgcaacgcggaagcagaggtaagcagctgcagagaggtccatggcaggaatgccgtcctactttacgcagcgctgtacatcagcgcttttggcgatggcttcatgcgtgcttgtatgccgcccctcggagcagaccagttcgaccatgaagacccctccgagtcccgccagcagtccagcttcttcaattggtacaccttcggaatctcctttgggggtttcataggattgatcctcatagtttggctggagaacagcaaagggtgggatgtcgggtttggggtgtgcgcgttcctgatcctgcttgggctgcttgtggttgctgctggtctccctttgtaccgcaaccatgtacccgaaggaagtccgctaactcggatactccaggttcttgtggttgcattcaagaacaggaagcttcaacttcctgagaagctggaagaagcacaggaagaaagaagcactgagcaaggaggctctactgaagtaactgaaatagcttctcaaacaaacagtagtctgaaattccttgacaaagcttgcatcaatggaggcaaagacggggcctggtcagtctgcagcacgaagaacgtggaggagacaaaggccgtgctccgcgtgctccccgtcttcatcagctccctgatcggctacatgtcgaacccgctcctcttcaccttcaccgtgcagcagggcggcttgaccaacacccggctggggaggatccacgtctcgccggcgacgctcttcatcatccccagcgcgttccagatggcgctgctcccggtgtacgaccgcttcctcgtgccgctcctgcggcggcgcacgggctacgccagcggcgtcacccacctgcagcgcgtcggcgccgggttcgccgccgtgatcctggcgtcggccatcgccgccgtcgtggagaggaagcggcgggccgacgccgcggcggcggggcagatgtcgctgttctggctggcgccgcagttcttcctgctcggcgtctccgacgtgacgtcgttcccgggcctcctcgagctcttcagcagcgaggcgccccgtggcatgaagtccatcgcgtcggcgctgttctggtgcgagctcggcctctcgtcgtggctcgccacgctgctggtgcaggtggtgaacagggccacgaggcggcacggcggcggcggcggcggcggCGGgtggctcgagggcgccaccctcaacaccagccgcctcgacctcttctactgggtcgtcgccgccgtcgggctgcttggcttcgtcaactacctctactgggcgagcaggtacatataccggcaagacccacgcgtcgtcgtcgacgtcgagccatcggcggatcacgattcaccttga More
Protein seq	MAVGGFLDWRGNPINRKVHGGVRAAWFVYFLTVVTSTVNVPNMLNMVTYLHGTMHMGISSSSTTVTNVLGATSGFALLGAFLSDSYITRARTILLFGPLEFLGYGLLALQAYLPSLRPPPCNAEAEVSSCREVHGRNAVLLYAALYISAFGDGFMRACMPPLGADQFDHEDPSESRQQSSFFNWYTFGISFGGFIGLILIVWLENSKGWDVGFGVCAFLILLGLLVVAAGLPLYRNHVPEGSPLTRILQVLVVAFKNRKLQLPEKLEEAQEERSTEQGGSTEVTEIASQTNSSLKFLDKACINGGKDGAWSVCSTKNVEETKAVLRVLPVFISSLIGYMSNPLLFTFTVQQGGLTNTRLGRIHVSPATLFIIPSAFQMALLPVYDRFLVPLLRRRTGYASGVTHLQRVGAGFAAVILASAIAAVVERKRRADAAAAGQMSLFWLAPQFFLLGVSDVTSFPGLLELFSSEAPRGMKSIASALFWCELGLSSWLATLLVQVVNRATRRHGGGGGGGGWLEGATLNTSRLDLFYWVVAAVGLLGFVNYLYWASRYIYRQDPRVVVDVEPSADHDSP More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsPr106_04g0018560	OsPr106_04g0018560.02	Chr04	25731344	25731525	-	IsoSeq
CDS seq	catcggcggatcacgattcaccttgaaaaataccgcgcctgtagtgttggtcaaaccgtgccaaag
Protein seq	HRRITIHLEKYRACSVGQTVPK

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	1.151093	7.849608	4.446796

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_04g0491500	SBH	0.220163	0.000000	0.623486
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os04g41400	RBH	0.0	0.044105	0.088274
Nipponbare \| IRGSP 1.0 \| RAP-db	Os04g0491500	SBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_04g0018160	RBH	0.0	1.166167	0.000000
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_04g0018940	RBH	0.026084	0.964924	0.429396
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_04g0018650	RBH	0.0	0.000000	0.554377
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_04g0018360	RBH	0.0	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_02g0022280	SBH	7.545002	0.000000	7.586216
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_04G0383700	RBH	9.0941355	23.128197	28.875256
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_04g0017350	RBH	0.000000	0.962984	0.395520
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_04G0338900	SBH	7.76006	10.5775585	1.5837065
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_04g0017850	RBH	0.062070	0.064055	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_04g0017690	RBH	0.100468	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_04g0017770	RBH	0.000000	0.559480	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_04g0018190	RBH	0.000000	0.131494	0.470778
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_04g0018350	RBH	0.000000	0.706599	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_04G017650	RBH	0.0	0.294610	0.267948
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_04g0017590	RBH	0.000000	4.372428	1.183992

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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