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_10g0003440		OGI:10013400 \| 16/16			NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)			Chr10:4363141-4367731		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		ggaattaaactgaaatttctatacaaacaggacttcgaacgaccatataagttcaattaaggtctgaaataattaaacatgtgaaaaacataaactgaattagacatggcacatttgaaatgcatcattacaatttagaaacagggacatggtattcagagcatcactatacatttcaaaaagagcaaccttacaatcaccctaatgagcatcgtaattcaaacttgtggcctattcggttaacaaattatgagcagtctcagttattgtttttcatcccagctagtgtgtactttggtcctctctgcaacaaaaggaaatccattgaattggtgcctaaaagggatttcttagcttcactggttgctatacttccatacatacctataatgcaaaaaaaataaaaatgaaaaatccatctcccaaactgaactgaattatattagacaaagtaatcatacaagtgtggaagcttaacacccaaacctaaaatctagcaaacactgcaattcgtattaaattataaagatttaaatttctgagagaacaatgcaacttacctatttcacttcctgtggggcttttcttttagcataagctctatacctccatgaagattttatggggagatagtaatcaactaattgtcatccctttatataattatgctcgggaaatccttaatgaatacccccctgcctctgatggttagtgagatcttgcatgaagcttggaagctcccttagattggggcattgctcaatcaataaataccgaagagaacccgaggcagaacaaagagtgtcaggaagacgctctagctttggaagtccaatgatctgcaatgatcgaagactccatagcccatccatggcctcctctggatgcatcaaatccagctccgggcaattgtcgatgaacagctctcgcagactggagaggtgtgtcatgctggctgggagagaaggaagctttgggcaatcactgatccacagcatctgtagggcagtcaacgagccaatcccttctggcagtgatgttagttcactacatgagtgaagctgcagggatgttagtgaagcccagccacgaagtcctgcttctggcaactgcttttgcttcgatgtcaaactcaggtacctgaggctgattaacttgtttacatctctcggcaactcgattagttggtcacttcgataaagatcaagtgtctgaaggtttatgagcttgcatagggaattgggaaggtattttatggttttgttccaggtgaggtcaagatacctcaagtgcttcaaatttccaattgaatctgggagttcgtcaattctaactccggatataatcaatacacgtagaagcaataacttggacagcagcacttccagaaattttttgcttaaagaaccatgattacacgaactaataaaagttcgagcttttcttgctttgattaaatgcctgggaaattcttgctcgtgtgtgaaatccttaaggtcccatactagatgcctgactgtttctgagacttgttgcccttcacagttcacaacagctaggtctgtgtccaaaacatatctaccaagatcatgtacaatgtcatgtaacttgcaatgtggcatgcttccatcaaaagtaattagagagtcttgaaaaagggaacttcctatcaattcaataatgtactgattaccaacatctatttcttcactcaatttgttcgagttcagtagcccatgtgccatccaaaacatgattatgcatcttctgtaatattcgaagtccttaggaaatatggataaataggaaagacatggtttaagggcagctggaagagcattgtaacttaactttagcactggcattatatctctgtcaccttgtacaattttgcacaagtggtcttctttaacacgtagccattgagtttcatcacgcatggtaaatagtagagaacccaatgattttattgccagtggtactccagcacacttcttcacaatggactctccaattttcaacaaccacggatatttattttcctcaccttgtctgaatgcaactctggtaaaaatttgcatgcactcatgaaaagggagtgcacccaccttgtacgggtctgaggtaccaaccatagatgcaacaacattttcgcgtgtagtaacaattatcacactaccccttgcaccacttgacaacaaattcctcagctctctccattcatttacatcacgagtccacagatcatccaataccaggaaataatttccattctgcagaattcccctgagcttattttgtaaatgttccaagtttagatgcttgcaactctcaccactggcagactcgattatatcttgtagtatatttttcagattaaatttattagagacacaggcccacatcatcttgctgaacctctccctgatttgttgatcatgatacaccatatttgctagttcagttttcccaatgcctccaagcccaagcagaggaagcacaaaaatatcatgatgttctgctgctcttagtatcttactaacaatctcatctctagcatcatcccttccaattatatcaggttgatacacaaaagaatatgattctctttctggttcttcagaacactgaccacccactgtccaatcggtcagtccaaagtcctttttactagcggctatttcgttaagcttttcatgaacttctcttattctgctgctccatttcttcttccttttgagcaattttcttctcaatttcaatcgagaaatatgtacacaattggtttgagtaaccacatctttgctaactctgcgcttcaaagtttcagttgacgcatcgtccaaaatgtcatctatgtcatacatgacatctttcagttttcgcagccattccttgagtgcactagaagtactctgcttcctctctgcgtctagaagaactccactaatagcttgcaacgaattctgtagcttccccagttcttgatgcacactcctgtctgatttaatccccatcaaaccgtgttcactaacaaacaaaattatttttccaataattgacacggcaaaacttgacagaagtacttcggccatagttgtaagaactgagccttctgaaaaaaagtaaaatatgtgacagacctgtggatgccatacaatataggccactcgataaggaaggaaaatgaatcagcacatgacttttaaggctaaatagtgaacttttgttagaaatgggtgatttcatagaaaaagatattatataagattcaagaacacttgcgttatatttgtgaagattaattgattgacacaaaaacaaatactaaaaaggaacttggtatcaaattaatagagaagaaatagagacccaagttgagtccaagaggtttctgaactttggtgatggtggtgtacatccacacctctcaccaattgatctgggcttagtccctatctgcatgccttatggcaaatatatactatgaactaaattacctgttacctgtgccatgtagctgctagtggtcaaaatttgttaggggatgatgactgttatattatgatccgaattagactggtaattccacttccaaatatgaagttctacttctagtccaattctggatgatgtaactcgtataatataacccttaagagacatagtgcaagacaatgctaaatataaagagcaaacaagttccatttaacatcctcaacatagtgattattattttgtaaacatcagcccccaaacgcacacaagggcacgaatttccttattgcatagtcacctaaaatcctgtatcactaaaccagaaattgcaattcaataaagcagaatctgattacagtagagctttactgaaacttctgttatatatgtatgaaaatcatgctctaatagtataccttttggtgtttgcaggtgctcatagtgcagttagccaaaagaaatatgatttagaaaatgaatgcctcaattacaagagaattaggtggtaaataatctaaattctccaattacaaatacAaaaaaagaaatactctaaaaaaactcagattcatcctcctccctcttccatgttgcttttcacctgggaacctagaatcctgcccctgtgagctgtgatatctttttgaggcatttccacaaacaggtcacaggcaatagaaaaatcctaaatggctttaacagcaaaggtaacaagaaaagcctaccagcaatacaatttacaggaatgatcgacttagagatagggagaaagatagcaagacggagagatgagagatcgatctcaccagtcaccagccctgaacccctcgcctgcttccgcagcctcgctgtcagcaatctccagagagaaacggaagaagattttcagggatcgagcgggcaggtgatgcagattggcctcgccgtggaagcctgatgccaaattgctccatcctctgatgtcaaatcgcgtaaaaattatatataaggaagagaattggcctacggtaagatgagaaaagccgagagcggacagcggtgggtttagcacaattctatgtgcgcatgcccttggtaagttggtatgtcgtaa More
CDS seq		atggccgaagtacttctgtcaagttttgccgtgtcaattattggaaaaataattttgtttgttagtgaacacggtttgatggggattaaatcagacaggagtgtgcatcaagaactggggaagctacagaattcgttgcaagctattagtggagttcttctagacgcagagaggaagcagagtacttctagtgcactcaaggaatggctgcgaaaactgaaagatgtcatgtatgacatagatgacattttggacgatgcgtcaactgaaactttgaagcgcagagttagcaaagatgtggttactcaaaccaattgtgtacatatttctcgattgaaattgagaagaaaattgctcaaaaggaagaagaaatggagcagcagaataagagaagttcatgaaaagcttaacgaaatagccgctagtaaaaaggactttggactgaccgattggacagtgggtggtcagtgttctgaagaaccagaaagagaatcatattcttttgtgtatcaacctgatataattggaagggatgatgctagagatgagattgttagtaagatactaagagcagcagaacatcatgatatttttgtgcttcctctgcttgggcttggaggcattgggaaaactgaactagcaaatatggtgtatcatgatcaacaaatcagggagaggttcagcaagatgatgtgggcctgtgtctctaataaatttaatctgaaaaatatactacaagatataatcgagtctgccagtggtgagagttgcaagcatctaaacttggaacatttacaaaataagctcaggggaattctgcagaatggaaattatttcctggtattggatgatctgtggactcgtgatgtaaatgaatggagagagctgaggaatttgttgtcaagtggtgcaaggggtagtgtgataattgttactacacgcgaaaatgttgttgcatctatggttggtacctcagacccgtacaaggtgggtgcactcccttttcatgagtgcatgcaaatttttaccagagttgcattcagacaaggtgaggaaaataaatatccgtggttgttgaaaattggagagtccattgtgaagaagtgtgctggagtaccactggcaataaaatcattgggttctctactatttaccatgcgtgatgaaactcaatggctacgtgttaaagaagaccacttgtgcaaaattgtacaaggtgacagagatataatgccagtgctaaagttaagttacaatgctcttccagctgcccttaaaccatgtctttcctatttatccatatttcctaaggacttcgaatattacagaagatgcataatcatgttttggatggcacatgggctactgaactcgaacaaattgagtgaagaaatagatgttggtaatcagtacattattgaattgataggaagttccctttttcaagactctctaattacttttgatggaagcatgccacattgcaagttacatgacattgtacatgatcttggtagatatgttttggacacagacctagctgttgtgaactgtgaagggcaacaagtctcagaaacagtcaggcatctagtatgggaccttaaggatttcacacacgagcaagaatttcccaggcatttaatcaaagcaagaaaagctcgaacttttattagttcgtgtaatcatggttctttaagcaaaaaatttctggaagtgctgctgtccaagttattgcttctacgtgtattgattatatccggagttagaattgacgaactcccagattcaattggaaatttgaagcacttgaggtatcttgacctcacctggaacaaaaccataaaataccttcccaattccctatgcaagctcataaaccttcagacacttgatctttatcgaagtgaccaactaatcgagttgccgagagatgtaaacaagttaatcagcctcaggtacctgagtttgacatcgaagcaaaagcagttgccagaagcaggacttcgtggctgggcttcactaacatccctgcagcttcactcatgtagtgaactaacatcactgccagaagggattggctcgttgactgccctacagatgctgtggatcagtgattgcccaaagcttccttctctcccagccagcatgacacacctctccagtctgcgagagctgttcatcgacaattgcccggagctggatttgatgcatccagaggaggccatggatgggctatggagtcttcgatcattgcagatcattggacttccaaagctagagcgtcttcctgacactctttgttctgcctcgggttctcttcggtatttattgattgagcaatgccccaatctaagggagcttccaagcttcatgcaagatctcactaaccatcagaggcaggggggtattcattaa More
Protein seq		MAEVLLSSFAVSIIGKIILFVSEHGLMGIKSDRSVHQELGKLQNSLQAISGVLLDAERKQSTSSALKEWLRKLKDVMYDIDDILDDASTETLKRRVSKDVVTQTNCVHISRLKLRRKLLKRKKKWSSRIREVHEKLNEIAASKKDFGLTDWTVGGQCSEEPERESYSFVYQPDIIGRDDARDEIVSKILRAAEHHDIFVLPLLGLGGIGKTELANMVYHDQQIRERFSKMMWACVSNKFNLKNILQDIIESASGESCKHLNLEHLQNKLRGILQNGNYFLVLDDLWTRDVNEWRELRNLLSSGARGSVIIVTTRENVVASMVGTSDPYKVGALPFHECMQIFTRVAFRQGEENKYPWLLKIGESIVKKCAGVPLAIKSLGSLLFTMRDETQWLRVKEDHLCKIVQGDRDIMPVLKLSYNALPAALKPCLSYLSIFPKDFEYYRRCIIMFWMAHGLLNSNKLSEEIDVGNQYIIELIGSSLFQDSLITFDGSMPHCKLHDIVHDLGRYVLDTDLAVVNCEGQQVSETVRHLVWDLKDFTHEQEFPRHLIKARKARTFISSCNHGSLSKKFLEVLLSKLLLLRVLIISGVRIDELPDSIGNLKHLRYLDLTWNKTIKYLPNSLCKLINLQTLDLYRSDQLIELPRDVNKLISLRYLSLTSKQKQLPEAGLRGWASLTSLQLHSCSELTSLPEGIGSLTALQMLWISDCPKLPSLPASMTHLSSLRELFIDNCPELDLMHPEEAMDGLWSLRSLQIIGLPKLERLPDTLCSASGSLRYLLIEQCPNLRELPSFMQDLTNHQRQGGIH
Function		Putative disease resistance protein RGA1 [UniProtKB/Swiss-Prot:Q7XA42]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNaBo_10g0003440	OsNaBo_10g0003440.01	Chr10	4363141	4367731	-	NAM
CDS seq	atggccgaagtacttctgtcaagttttgccgtgtcaattattggaaaaataattttgtttgttagtgaacacggtttgatggggattaaatcagacaggagtgtgcatcaagaactggggaagctacagaattcgttgcaagctattagtggagttcttctagacgcagagaggaagcagagtacttctagtgcactcaaggaatggctgcgaaaactgaaagatgtcatgtatgacatagatgacattttggacgatgcgtcaactgaaactttgaagcgcagagttagcaaagatgtggttactcaaaccaattgtgtacatatttctcgattgaaattgagaagaaaattgctcaaaaggaagaagaaatggagcagcagaataagagaagttcatgaaaagcttaacgaaatagccgctagtaaaaaggactttggactgaccgattggacagtgggtggtcagtgttctgaagaaccagaaagagaatcatattcttttgtgtatcaacctgatataattggaagggatgatgctagagatgagattgttagtaagatactaagagcagcagaacatcatgatatttttgtgcttcctctgcttgggcttggaggcattgggaaaactgaactagcaaatatggtgtatcatgatcaacaaatcagggagaggttcagcaagatgatgtgggcctgtgtctctaataaatttaatctgaaaaatatactacaagatataatcgagtctgccagtggtgagagttgcaagcatctaaacttggaacatttacaaaataagctcaggggaattctgcagaatggaaattatttcctggtattggatgatctgtggactcgtgatgtaaatgaatggagagagctgaggaatttgttgtcaagtggtgcaaggggtagtgtgataattgttactacacgcgaaaatgttgttgcatctatggttggtacctcagacccgtacaaggtgggtgcactcccttttcatgagtgcatgcaaatttttaccagagttgcattcagacaaggtgaggaaaataaatatccgtggttgttgaaaattggagagtccattgtgaagaagtgtgctggagtaccactggcaataaaatcattgggttctctactatttaccatgcgtgatgaaactcaatggctacgtgttaaagaagaccacttgtgcaaaattgtacaaggtgacagagatataatgccagtgctaaagttaagttacaatgctcttccagctgcccttaaaccatgtctttcctatttatccatatttcctaaggacttcgaatattacagaagatgcataatcatgttttggatggcacatgggctactgaactcgaacaaattgagtgaagaaatagatgttggtaatcagtacattattgaattgataggaagttccctttttcaagactctctaattacttttgatggaagcatgccacattgcaagttacatgacattgtacatgatcttggtagatatgttttggacacagacctagctgttgtgaactgtgaagggcaacaagtctcagaaacagtcaggcatctagtatgggaccttaaggatttcacacacgagcaagaatttcccaggcatttaatcaaagcaagaaaagctcgaacttttattagttcgtgtaatcatggttctttaagcaaaaaatttctggaagtgctgctgtccaagttattgcttctacgtgtattgattatatccggagttagaattgacgaactcccagattcaattggaaatttgaagcacttgaggtatcttgacctcacctggaacaaaaccataaaataccttcccaattccctatgcaagctcataaaccttcagacacttgatctttatcgaagtgaccaactaatcgagttgccgagagatgtaaacaagttaatcagcctcaggtacctgagtttgacatcgaagcaaaagcagttgccagaagcaggacttcgtggctgggcttcactaacatccctgcagcttcactcatgtagtgaactaacatcactgccagaagggattggctcgttgactgccctacagatgctgtggatcagtgattgcccaaagcttccttctctcccagccagcatgacacacctctccagtctgcgagagctgttcatcgacaattgcccggagctggatttgatgcatccagaggaggccatggatgggctatggagtcttcgatcattgcagatcattggacttccaaagctagagcgtcttcctgacactctttgttctgcctcgggttctcttcggtatttattgattgagcaatgccccaatctaagggagcttccaagcttcatgcaagatctcactaaccatcagaggcaggggggtattcattaa More
Protein seq	MAEVLLSSFAVSIIGKIILFVSEHGLMGIKSDRSVHQELGKLQNSLQAISGVLLDAERKQSTSSALKEWLRKLKDVMYDIDDILDDASTETLKRRVSKDVVTQTNCVHISRLKLRRKLLKRKKKWSSRIREVHEKLNEIAASKKDFGLTDWTVGGQCSEEPERESYSFVYQPDIIGRDDARDEIVSKILRAAEHHDIFVLPLLGLGGIGKTELANMVYHDQQIRERFSKMMWACVSNKFNLKNILQDIIESASGESCKHLNLEHLQNKLRGILQNGNYFLVLDDLWTRDVNEWRELRNLLSSGARGSVIIVTTRENVVASMVGTSDPYKVGALPFHECMQIFTRVAFRQGEENKYPWLLKIGESIVKKCAGVPLAIKSLGSLLFTMRDETQWLRVKEDHLCKIVQGDRDIMPVLKLSYNALPAALKPCLSYLSIFPKDFEYYRRCIIMFWMAHGLLNSNKLSEEIDVGNQYIIELIGSSLFQDSLITFDGSMPHCKLHDIVHDLGRYVLDTDLAVVNCEGQQVSETVRHLVWDLKDFTHEQEFPRHLIKARKARTFISSCNHGSLSKKFLEVLLSKLLLLRVLIISGVRIDELPDSIGNLKHLRYLDLTWNKTIKYLPNSLCKLINLQTLDLYRSDQLIELPRDVNKLISLRYLSLTSKQKQLPEAGLRGWASLTSLQLHSCSELTSLPEGIGSLTALQMLWISDCPKLPSLPASMTHLSSLRELFIDNCPELDLMHPEEAMDGLWSLRSLQIIGLPKLERLPDTLCSASGSLRYLLIEQCPNLRELPSFMQDLTNHQRQGGIH More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.147638	1.228037	0.000000

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_10g0161400	RBH	0.233407	0.0	0.285237
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os10g07400	RBH	0.150264	0.0	0.069901
Nipponbare \| IRGSP 1.0 \| RAP-db	Os10g0161400	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_10g0003310	RBH	0.0	2.038005	0.591060
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_10g0003600	SBH	0.000000	0.970145	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_10g0003520	SBH	0.749586	0.0	0.000000
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_10g0003830	SBH	0.126337	0.054133	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_10g0003210	RBH	0.0	4.205642	0.512956
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_10G0064600	RBH	0.151932	1.1586795	0.2345075
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_10g0003430	RBH	0.0	0.0	0.191434
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_10G0072400	RBH	0.2205365	0.4157265	1.611987
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_10g0003260	RBH	0.032501	0.006608	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_10g0003300	RBH	0.0	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_10g0003390	RBH	0.0	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_Ung0056750	RBH	0.0	0.0	0.143032
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_10g0003500	RBH	0.0	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_10G003700	SBH	0.340562	0.276391	0.000000
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_10g0003730	RBH	0.0	4.457654	0.0

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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