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
OsNaBo_08g0002880		OGI:08007540 \| 16/16			NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)			Chr08:2490816-2496111		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		ctaaaccgggatgggcttgattttaattgcagggagagggctaatattcgcaatcaagatcctcacaatgatgtgcactctttcatcaccctgtgggtagaatattgtgatcttcctgagttttacacaattgaacatttcttctatttctctgcgagtaggatcaattgctgcagcagcatctgggtaatcctcatagtcatcagatccatactgataacaagaatgaaagacaccatcaaactcaagccatgagcacaaatagcaatatggaaggggctgaggtattatatcttaccttgttaagttgcaggtgaagtttttctatgttaggtgagcgccgaagcaagaaaagtagaggatagcaaccatctctcaaaaaccactcacctagcttcaaatatttcaggttgctgaatgtcttacaccttggaaaactacggattaacacatttggcaccacctgccaacaagtccgaccatgttttaggaaaaccatataaaaaacacatataagaaactgttaaaaggaggtcacatacatcttcataggcagttggagaaaccaactccaagcttgtgacattggaaagagcagggataatattgcagtcaacagcagaattttggaaagagagttcaaaaaagtaaaatgtggcctttttcactgatgacacgtccacgagctgaatatttctgtttggaatctcatctagatgcagggtaactaggtttggcatatctatcataagatgctcaaattttggtgggaaatgctctgtggtctctgtagagttaatgagcaaattcttcaatgtggtagaggaaaacatggtgacaatgatggcacagtttttcaactccagatcctctaagaccgggcaacaagaagagaggttcttgacaaaactgtcatctataatgaaatggcaaaggtgcaagatagacaagtagaccgaggtgaacggaaagggataaccatcaattgaaagaagattggtgccacaatgctccataatgccaagagcccaggcattgctcctaagggcatgacgaatccatggatggatgtcagaataatcaagggaatcatcagagcagttgcaggtggcaagaatccaaagtgcatccagtggcacaggtttgcggtacaggagcaaattgtcaacgaatttcttgaaacttttcatgctgctgaactttgctgcatcagctttgagccactttgtagatgaccagacgttctgccacctccgcgatagcacgcatgtctgcactgcctcttgcgcggttaaatagagcatgacaaagcgtagcagcccgtctggtagtctgctaatcctgtcaggcgcattctcctcattgttagaggtggtcatccctgtcgctggaagaactcgctctatcagggacattgagtcgagcagcttccgtgcaaggtgttgtctctacaaaattaaatgatcccaagcaagggtagaagagtaagctaaaagactacaccacactagtaaaaatttcatcatgaattcaatattataagcagaaaatggaacgagattcaagcatgaggtaatctaacaatttcggtggcaatttaagaaaagaaccagtagcacccgcataatcttgccatgggttttatccactagaggagaatctgtgtagaatcaaatactccctccgtcccAaaatataaatacctctagactttaaatttgtcccaaactataacaacttctccaacaacattctcttctcaaccaataacaaccctctaccattcaattttcccacgtacctccacttctccgatcacaacactcatttaattctatactttcttaataaccgtatccaactctaaaaatgcttatattcatggacggatggagtattactcatctcaaaggttctttttttttcctcagaataatcccctggttccggaccaagcagcgtcagcaaatctgagacactaggctcaagtgcaacaaaatccaccatactgtaagaaacaacacgacattgatctctaacaccctaacagaggagaaactagaggagcagtggggatgaaaagagaaccctagtagagccgaaaggatggaccaagaagaacaggtaggaggagcagcacgcaccaatagcccgcggggtcgcgcatgcaggcccagccttggtcgcggctcgccggcgttccgccgccgacgggggcctccgggtgtcgccgccggtggccggagctagagtagcgtggaagtgaaatgcgacaccaacgcagaggtcggccggtcccacatgtcagctgcccctcccactgtggtctccctgagccgtacgatcgtatcgtgcggctcagatgcagtagagctggagatgttttcacactggaaccctctgattgtttcgtaattacgacataagcccctggatttttggagcgctaggcgcgtaacgaggcggatgagtctggctggcccacatgtcagtgactaaacgccttgtgggttggctggcctaaggagagttccggcccaacaaatatggacattcacgttccggcccaacttttgctgctccgaaattatcagatgggttgtcgctgcgaggcagcggctgagaagtagccgaacgataattcgatactccatctccaaaatcgaagataaaattgaaataaacaagcaacagcagcagcagcaagcacaagtgttggtcgcacataagaagtttgcaaattgcaatcttgaaatggacaagtgagaaagtaccgtcctacaggaaacaaaaaaaacagctcgattgtaaacaggaatgagaagcttcagaagctgttcagaaactatgaacataattgtttcgtctgatgatgataagctcgatattctgataattggttcctgcagacatgcactatgaacataaaggatagctgagcaagtcttccaaaaacatcatccttggtatcagaatatctaatccaaccagatagacacctcagtcaccaaaatccacagatcacctaacagaatagtttaaatgatgtttgttaaatgcctcaaaacataagccgctgattcaataagcatgaatgggcaattttaagaaacataccatgataatctggaattcggacagggcttgattttaatttcaggtagagggctaatgttcgcaatcaatatcctcacaatgatgtgcacccttttatcgccctgagggtagacgatttcaatctctgtaagtttttcacaatgaaacgttcttgctgcttctttgcatggaggatctattgctgctgcagcagttggaaacttctcatactcctcagctccaagctgataacaagaataaaaaaggaaaccattaaactcaagccgtgaccaaaaacagcaatgtggaaggggggagctgttaaatcttgccttggtaagttgcaggcgaagtttttctatgtgaggcgagtaccgaagcaagaagagtagcggatagcatccatctctcagaaaccactcaccaagcttcaaccttttcaggttgtcaaatgccttacaccttggaagatcacacattaatacctttgacacctgccgacaagtccaaaggtgtatcagaaaaacacataaaaaccgataggagaaaatgttcaaaggaggtagcatacttcatcatagacagaatcacatatcagcttcaagcttgtggcatttgaaagagcactgagaatattgcagtcaacagcggaatttcgaaaagagtcttcaaaaaagtaaattgtggcctctttcactgacgataagtccacaaggtgaatatttcttcttggaatctcctctatatgcagggtaactaagtttggcatttctatgacaagatactcaatttgtttgggcagatgttcaatgtcttctgcattgtgaatgacgaaactcttcaatgtggttgaggaaaacatggtgacatcgatgccacagcttatcaacactagatccttcaaaaccgggcaaccagaagaaagcttcttggaaaaacagtcatctattgtaaacttgaaaagcaccaacttagacaagtgcaccgaggtgaaagcaaagggataaccatctatagaaagaagcttggaaccacaacgaacgaatatgccaacttcgcgtgcattgctcctaagcacatgatgaacccatcgatggatgtcggaataatcaagggaatcatcagagttgtcgcaggcggcagaaatccaaagtcccttcagtggaacagggttgcggtacaggagcacattatcaagaaatttcttgaaacttgtgatgctgctggacttggctgcattagcatgcagaaacatcatagatgaccagacgttctgccacctccgtgacagcacacatgtccgcactgcctcttgcgctgttagataggacatgacatggtgcagcagctcgtcaggtaggttgctgatcctgtcaaaatcattatcctcacagtgagagatggacatccctgtatctagaggaagttgttgtatcaggggcattcaatcgagcaggtgtggagcaaactggtgtctctacaaaattaaacaatccctagcaagggaagataataagtaagacagaaaactacactgcactagtaaatatgccatcatgaattcattgtcgtaagcagaaaatggaaaaggagattgaaacatgatcaaaattaacaacaatttcggtggcaattcaagaacagaaacaccaacacccacacaatcttgccatggcttttagcctttttatccgtgagaggagaatgaatctagatattcgttgcggcaatcgtcatagaaatcaaacatgactaaatcacattattattttttctttttcctcggagcaaccccttccccagtgttccagtcccaggagcctaccaaccacagttgcagcaaagaaaatagccattgccgtggacgtggagagcatctgcaaccaactgacgatttggctcaaatgcaagaatctccgtcaaaaacaactacgggaaaaccctagctttcctgattcagggttcgtagcagaggccgcgaagaaactaaggcggggcaggggcgatggaaaaccctagacgacgaatagaggcggaagaatgaacaactcggagaaaatcagggtaggagcacttctcaccaagaacgacggaggcgcgcgtgcggttccggtcttgatcgcggctgcttgcctccgctcgccggcgttctgcggcccgccggagctccggcctccgggtgtcgccgccggctggagag More
CDS seq		atgtccatctctcactgtgaggataatgattttgacaggatcagcaacctacctgacgagctgctgcaccatgtcatgtcctatctaacagcgcaagaggcagtgcggacatgtgtgctgtcacggaggtggcagaacgtctggtcatctatgatgtttctgcatgctaatgcagccaagtccagcagcatcacaagtttcaagaaatttcttgataatgtgctcctgtaccgcaaccctgttccactgaagggactttggatttctgccgcctgcgacaactctgatgattcccttgattattccgacatccatcgatgggttcatcatgtgcttaggagcaatgcacgcgaagttggcatattcgttcgttgtggttccaagcttctttctatagatggttatccctttgctttcacctcggtgcacttgtctaagttggtgcttttcaagtttacaatagatgactgtttttccaagaagctttcttctggttgcccggttttgaaggatctagtgttgataagctgtggcatcgatgtcaccatgttttcctcaaccacattgaagagtttcgtcattcacaatgcagaagacattgaacatctgcccaaacaaattgagtatcttgtcatagaaatgccaaacttagttaccctgcatatagaggagattccaagaagaaatattcaccttgtggacttatcgtcagtgaaagaggccacaatttacttttttgaagactcttttcgaaattccgctgttgactgcaatattctcagtgctctttcaaatgccacaagcttgaagctgatatgtgattctgtctatgatgaagtgtcaaaggtattaatgtgtgatcttccaaggtgtaaggcatttgacaacctgaaaaggttgaagcttggtgagtggtttctgagagatggatgctatccgctactcttcttgcttcggtactcgcctcacatagaaaaacttcgcctgcaacttaccaaggcaagatttaacagctccccccttccacattgctgtttttggtcacggcttgagtttaatggtttccttttttattcttgttatcagcttggagctgaggagtatgagaagtttccaactgctgcagcagcaatagatcctccatgcaaagaagcagcaagaacgtttcattgtgaaaaacttacagagattgaaatcgtctaccctcagggcgataaaagggtgcacatcattctgctcgactcaatgtccctgatagagcgagttcttccagcgacagggatgaccacctctaacaatgaggagaatgcgcctgacaggattagcagactaccagacgggctgctacgctttgtcatgctctatttaaccgcgcaagaggcagtgcagacatgcgtgctatcgcggaggtggcagaacgtctggtcatctacaaagtggctcaaagctgatgcagcaaagttcagcagcatgaaaagtttcaagaaattcgttgacaatttgctcctgtaccgcaaacctgtgccactggatgcactttggattcttgccacctgcaactgctctgatgattcccttgattattctgacatccatccatggattcgtcatgcccttaggagcaatgcctgggctcttggcattatggagcattgtggcaccaatcttctttcaattgatggttatccctttccgttcacctcggtctacttgtctatcttgcacctttgccatttcattatagatgacagttttgtcaagaacctctcttcttgttgcccggtcttagaggatctggagttgaaaaactgtgccatcattgtcaccatgttttcctctaccacattgaagaatttgctcattaactctacagagaccacagagcatttcccaccaaaatttgagcatcttatgatagatatgccaaacctagttaccctgcatctagatgagattccaaacagaaatattcagctcgtggacgtgtcatcagtgaaaaaggccacattttacttttttgaactctctttccaaaattctgctgttgactgcaatattatccctgctctttccaatgtcacaagcttggagttggtttctccaactgcctatgaagatgtggtgccaaatgtgttaatccgtagttttccaaggtgtaagacattcagcaacctgaaatatttgaagctaggtgagtggtttttgagagatggttgctatcctctacttttcttgcttcggcgctcacctaacatagaaaaacttcacctgcaacttaacaagtatggatctgatgactatgaggattacccagatgctgctgcagcaattgatcctactcgcagagaaatagaagaaatgttcaattgtgtaaaactcaggaagatcacaatattctacccacagggtgatgaaagagtgcacatcattgtgaggatcttgattgcgaatattagccctctccctgcaattaaaatcaagcccatcccggtttag More
Protein seq		MSISHCEDNDFDRISNLPDELLHHVMSYLTAQEAVRTCVLSRRWQNVWSSMMFLHANAAKSSSITSFKKFLDNVLLYRNPVPLKGLWISAACDNSDDSLDYSDIHRWVHHVLRSNAREVGIFVRCGSKLLSIDGYPFAFTSVHLSKLVLFKFTIDDCFSKKLSSGCPVLKDLVLISCGIDVTMFSSTTLKSFVIHNAEDIEHLPKQIEYLVIEMPNLVTLHIEEIPRRNIHLVDLSSVKEATIYFFEDSFRNSAVDCNILSALSNATSLKLICDSVYDEVSKVLMCDLPRCKAFDNLKRLKLGEWFLRDGCYPLLFLLRYSPHIEKLRLQLTKARFNSSPLPHCCFWSRLEFNGFLFYSCYQLGAEEYEKFPTAAAAIDPPCKEAARTFHCEKLTEIEIVYPQGDKRVHIILLDSMSLIERVLPATGMTTSNNEENAPDRISRLPDGLLRFVMLYLTAQEAVQTCVLSRRWQNVWSSTKWLKADAAKFSSMKSFKKFVDNLLLYRKPVPLDALWILATCNCSDDSLDYSDIHPWIRHALRSNAWALGIMEHCGTNLLSIDGYPFPFTSVYLSILHLCHFIIDDSFVKNLSSCCPVLEDLELKNCAIIVTMFSSTTLKNLLINSTETTEHFPPKFEHLMIDMPNLVTLHLDEIPNRNIQLVDVSSVKKATFYFFELSFQNSAVDCNIIPALSNVTSLELVSPTAYEDVVPNVLIRSFPRCKTFSNLKYLKLGEWFLRDGCYPLLFLLRRSPNIEKLHLQLNKYGSDDYEDYPDAAAAIDPTRREIEEMFNCVKLRKITIFYPQGDERVHIIVRILIANISPLPAIKIKPIPV
Function		F-box/LRR-repeat protein At4g14096 [UniProtKB/Swiss-Prot:Q94B46]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNaBo_08g0002880	OsNaBo_08g0002880.01	Chr08	2490816	2495319	-	NAM
CDS seq	atgtccatctctcactgtgaggataatgattttgacaggatcagcaacctacctgacgagctgctgcaccatgtcatgtcctatctaacagcgcaagaggcagtgcggacatgtgtgctgtcacggaggtggcagaacgtctggtcatctatgatgtttctgcatgctaatgcagccaagtccagcagcatcacaagtttcaagaaatttcttgataatgtgctcctgtaccgcaaccctgttccactgaagggactttggatttctgccgcctgcgacaactctgatgattcccttgattattccgacatccatcgatgggttcatcatgtgcttaggagcaatgcacgcgaagttggcatattcgttcgttgtggttccaagcttctttctatagatggttatccctttgctttcacctcggtgcacttgtctaagttggtgcttttcaagtttacaatagatgactgtttttccaagaagctttcttctggttgcccggttttgaaggatctagtgttgataagctgtggcatcgatgtcaccatgttttcctcaaccacattgaagagtttcgtcattcacaatgcagaagacattgaacatctgcccaaacaaattgagtatcttgtcatagaaatgccaaacttagttaccctgcatatagaggagattccaagaagaaatattcaccttgtggacttatcgtcagtgaaagaggccacaatttacttttttgaagactcttttcgaaattccgctgttgactgcaatattctcagtgctctttcaaatgccacaagcttgaagctgatatgtgattctgtctatgatgaagtgtcaaaggtattaatgtgtgatcttccaaggtgtaaggcatttgacaacctgaaaaggttgaagcttggtgagtggtttctgagagatggatgctatccgctactcttcttgcttcggtactcgcctcacatagaaaaacttcgcctgcaacttaccaaggcaagatttaacagctccccccttccacattgctgtttttggtcacggcttgagtttaatggtttccttttttattcttgttatcagcttggagctgaggagtatgagaagtttccaactgctgcagcagcaatagatcctccatgcaaagaagcagcaagaacgtttcattgtgaaaaacttacagagattgaaatcgtctaccctcagggcgataaaagggtgcacatcattctgctcgactcaatgtccctgatagagcgagttcttccagcgacagggatgaccacctctaacaatgaggagaatgcgcctgacaggattagcagactaccagacgggctgctacgctttgtcatgctctatttaaccgcgcaagaggcagtgcagacatgcgtgctatcgcggaggtggcagaacgtctggtcatctacaaagtggctcaaagctgatgcagcaaagttcagcagcatgaaaagtttcaagaaattcgttgacaatttgctcctgtaccgcaaacctgtgccactggatgcactttggattcttgccacctgcaactgctctgatgattcccttgattattctgacatccatccatggattcgtcatgcccttaggagcaatgcctgggctcttggcattatggagcattgtggcaccaatcttctttcaattgatggttatccctttccgttcacctcggtctacttgtctatcttgcacctttgccatttcattatagatgacagttttgtcaagaacctctcttcttgttgcccggtcttagaggatctggagttgaaaaactgtgccatcattgtcaccatgttttcctctaccacattgaagaatttgctcattaactctacagagaccacagagcatttcccaccaaaatttgagcatcttatgatagatatgccaaacctagttaccctgcatctagatgagattccaaacagaaatattcagctcgtggacgtgtcatcagtgaaaaaggccacattttacttttttgaactctctttccaaaattctgctgttgactgcaatattatccctgctctttccaatgtcacaagcttggagttggtttctccaactgcctatgaagatgtggtgccaaatgtgttaatccgtagttttccaaggtgtaagacattcagcaacctgaaatatttgaagctaggtgagtggtttttgagagatggttgctatcctctacttttcttgcttcggcgctcacctaacatagaaaaacttcacctgcaacttaacaagtatggatctgatgactatgaggattacccagatgctgctgcagcaattgatcctactcgcagagaaatagaagaaatgttcaattgtgtaaaactcaggaagatcacaatattctacccacagggtgatgaaagagtgcacatcattgtgaggatcttgattgcgaatattagccctctccctgcaattaaaatcaagcccatcccggtttag More
Protein seq	MSISHCEDNDFDRISNLPDELLHHVMSYLTAQEAVRTCVLSRRWQNVWSSMMFLHANAAKSSSITSFKKFLDNVLLYRNPVPLKGLWISAACDNSDDSLDYSDIHRWVHHVLRSNAREVGIFVRCGSKLLSIDGYPFAFTSVHLSKLVLFKFTIDDCFSKKLSSGCPVLKDLVLISCGIDVTMFSSTTLKSFVIHNAEDIEHLPKQIEYLVIEMPNLVTLHIEEIPRRNIHLVDLSSVKEATIYFFEDSFRNSAVDCNILSALSNATSLKLICDSVYDEVSKVLMCDLPRCKAFDNLKRLKLGEWFLRDGCYPLLFLLRYSPHIEKLRLQLTKARFNSSPLPHCCFWSRLEFNGFLFYSCYQLGAEEYEKFPTAAAAIDPPCKEAARTFHCEKLTEIEIVYPQGDKRVHIILLDSMSLIERVLPATGMTTSNNEENAPDRISRLPDGLLRFVMLYLTAQEAVQTCVLSRRWQNVWSSTKWLKADAAKFSSMKSFKKFVDNLLLYRKPVPLDALWILATCNCSDDSLDYSDIHPWIRHALRSNAWALGIMEHCGTNLLSIDGYPFPFTSVYLSILHLCHFIIDDSFVKNLSSCCPVLEDLELKNCAIIVTMFSSTTLKNLLINSTETTEHFPPKFEHLMIDMPNLVTLHLDEIPNRNIQLVDVSSVKKATFYFFELSFQNSAVDCNIIPALSNVTSLELVSPTAYEDVVPNVLIRSFPRCKTFSNLKYLKLGEWFLRDGCYPLLFLLRRSPNIEKLHLQLNKYGSDDYEDYPDAAAAIDPTRREIEEMFNCVKLRKITIFYPQGDERVHIIVRILIANISPLPAIKIKPIPV More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNaBo_08g0002880	OsNaBo_08g0002880.02	Chr08	2493463	2496111	-	IsoSeq
CDS seq	ctccagccggcggcgacacccggaggccggagctccggcgggccgcagaacgccggcgagcggaggcaagcagccgcgatcaagaccggaaccgcacgcgcgcctccgtcgttcttgggattgtttaattttgtagagacaccagtttgctccacacctgctcgattgaatgcccctgatacaacaacttcctctagatacagggatgtccatctctca More
Protein seq	LQPAATPGGRSSGGPQNAGERRQAAAIKTGTARAPPSFLGLFNFVETPVCSTPARLNAPDTTTSSRYRDVHLS

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.372611	1.583760	2.222442

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_08g0149100	RBH	0.000000	0.0	1.295778
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os08g05470	SBH	0.000000	0.000000	0.000000
Nipponbare \| IRGSP 1.0 \| RAP-db	Os08g0149100	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_08g0003300	RBH	0.073797	0.000000	1.144547
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_08g0003340	RBH	0.038544	0.0	0.256464
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_08g0003310	RBH	0.0	0.000000	2.213237
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_08g0003300	RBH	0.049080	0.047103	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_08g0003130	RBH	0.000000	0.000000	2.042170
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_08G0044000	RBH	0.731311	2.3461565	1.7886605
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_08g0002990	RBH	0.0	0.0	0.161155
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_08G0048900	RBH	0.316679	0.65144	4.4512755
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_08g0003020	RBH	0.0	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_08g0003070	RBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_08g0002870	RBH	0.0	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_08g0003140	RBH	0.074086	0.0	0.0
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_08g0003060	RBH	0.000000	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_08G003000	RBH	0.108677	0.017223	1.984032
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_08g0002800	RBH	0.000000	1.769461	1.231458

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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