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_03g0037140		OGI:03092820 \| 16/16			NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)			Chr03:35553199-35558332		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		acactggcctctcgtcctcactccataacggccatgtcgtcctcgcctctaaccgccacgccttcccctctccttcccgccaaatccaagaacccaccaccccaccaccaccaccacaacccgctcctcgcctacctcccgcactgcacgagcctccgcgcgctcgcgcagctccacgccgtcgccgtcaaggccggcggcggcctccaggcgcacccggccttcgtcacgaggctcctcacgctctgcacggagcagggggcggaggcgcccgcgcacctcgcgtacgcgcgccaggtgttcgacagaatcccccacccgggcgacgtcgtctggtacaacacgctgctgcgcgggtacgcgcgcgggggtgggggcgggggcggcgcggaggaggccgcgcgggtgttcgtccggatgatggaggagggggtggcgcccgacacgtacacgttcgtgtcgctgctcaaggcgtgcgcgtccgcgcgggccggcgaggaagggcagcaggcgcacggcgtggcggtcaaggccggcgccgcggagcacgagtacgtcgcgcccacgctgatcaacatgtacgccgagtgcggggacgtgcgcgccgcgcgcgtgatgttcgacaggatggacggggagtgcgtcgtctcgtacaatgccatgatcaccgcgtccgtcaggagcagcctgcccggcgaggcgctggtgctgttccgggagatgcaggccaaggggctcaagccgacgtccgtgacgttgattagtgtgctctcggcgtgcgcattgctcggagctctggaacttgggaggtggatccacgactatatcaggaagatgaggcttgattcccttgtgaaggtcaacactgcgctgatcgacatgtatgcgaagtgtgggagcttggaggatgccattggcgtgttccaggatatggaatcaagggataaacaagcttggtctgtgatgatggtggcatatgctaaccatggctatggcagagaggccatttcaatgttcgaagagatgaagaaacaaggtatgaaacctgatgatgttacattccttggggtgctctatgcctgcagccactctggtatggtgagcgaagggctccaatactttgacagcatgagggaatatggcattgtttcagggatcaagcactatggttgtgtgactgatttgctggctcgatcaggtcagctagaaagggcttacaagttcattgatgaactgccaataaaaccaactgccatcttatggaggacgctgctttctgcttgtgcgggtcatggagatgtcgatatgggaaaacgtgtctttgagaggattctggagctggatgattctcatggtggtgactatgtaatattctcaaatttgtgtgccaatactgggagatgggaagagatgaacatggtaaggaagcttatgagtgaaaagggggtggtgaaggtgccagggtgtagctcaattgagatagataacatggttcatgagttcttcgcaggagatggaagtcacccacactcacaggaggcacgcagaatggttgatgaagttattgagcagctaaaacttgtcggttatgtccctaatacttcacatgtgtttcatgttgaaatgggtgaggaggagaaagcaacaagcctaagataccatagtgagaagctggcaatctcttttgggcttctaaatacagcaccgggaactacccttcgtattgttaagaatcttcgtgtgtgtccagattgccattcgatggcaaagcttgtttctatggtctttaacaggcgaatcatactcagagacctaaatcgtttccaccactttgaagatggggtctgctcttgtggtgactactggtagagtttaggaacataactgctgtaccaaaataccttatccttccagtaacacaaaggctttatccattcaggtatgattaacttgtacacccatgagaaacttactgatgattgaagattcattttctgaagattgatgataccgagacaataattactgatccaagtttgttaatatctactgcatcgtcatgcctaccacctaatagtttcattgcctggttgcatacttgcatgtatatgttaatccttgaagagcattttttttgttatgccttgcgcatgctcttttttaattacttacgaacacataccacaccaagtcgctaagactaagcttgtgtttgatgttgtagtttgctatttttcttttgcacctttcccccctaaactgatgttcgtttttgatgatgtaagtgctaaaatgagccatcttaaccttgaatttttttccaatccatttcttgtcattgttactcttggacatgagaaaacaacagagaaccaaatgttttacccctttgtgatgaaaatactatgcatttttactattttacgagttagcttaatgatttgcctccaggcaagcagtggagaacagcacactatgccttgccatggagttagatcagatatcaaatgggataaccgcggacagcagaaacttttctctataaaatatttcagataaaggaatacctgctttggtgaatgtcattagcctgattgaacaacttggagtttcagctggtgaaagtgaagagttactttcgatgaatctagttgagattttgatctttagttccccgattgattaggaaattaagtagtgcaaataagctgttaagctgaatcatgttggtttttctatcagtgcatacagaaattggttaaaactcaaaaggcaaatagatctatacaaatgtgtctaagctaaatgatggtaatttggttaggaaagatagtgaaagcttttcagggggaccattgtaccctgaaggtgacagagggaccgagagcgtcttcaagaaacctaagatgataatcttgaagcataagcttctgaatgtcttgaaatacttggctacaaatgctgattcaaggactttggtcttgtttcatatgaccagattttgtaggctatatttgctgcttggattggtatacatgattttgatttatctccattttatcagcaccattttaaatttgctcgggtggtcatggaactgtggtacgacctttagcccactgagtgtccgagaaaaaaaaaaccttcagtccactgagcttcaaatcatatgcaagcatgagacatgtagcaaagctagttttttttgggtgaggtaacactatgtagtgaagttgctgtgcttatttaaacttcattgacaccatgggagatcctgaaaacttgtctgtagataaattctattacttaatgagatcacacttcaacaaagacctagctttaaagatattggctggttaggaaactgtctttaggttggtaatatatctctttctagcctctgccccctactacaaatcggtgtaatgctagccacaacaattctagaaatagtcataatgaatgttcagacctcaaattctgctactgaatactgtatcactttgacttccatcatcaccatactatgccataaatagattaagaaaccacattgtttggatgactgaaaataagaatcactgaagcaagtttgctttttaggattaggatgaaagccaccactaattcatgctgagatatgattagattgtccgtacaccatgtaactaactaacaagaccttgatttcccaccagaaacaatgcatttggttacctgctaccttaagggacttgattatcacataatttgatataggtaactttttactgctgatgaattgaacagtgcggtaagaatgatgcggtaagctttggttttcaataattttatgccaatttgcatgttttacttggtccaatatggcatattcatcctcatcactatacatttatttttacatcttctattatctgcaaatttatccaattcttgcttggttaacatctgtctgtcggtcactcactaaatgatccaatgaaaggtcagccacaccatgccatgctgcatgactactctgtttctaattttgatttcgacgtcttgtatttttcaatcacattgcacatgtcctttctatcttcagaatcatcttcatttaccatctttatggttgctgtccatcattggaaattcattgatgtgctcattataccggatgtacattgacacagtacattatactcttctcagttatctaaatataatctcagtggattgatgtgtgtgactaagacttgaattaaaagttagagagacagagtgtgctggtgaagccgtattgttgagtggcttgcatgaaggaaccacagactgcctggagccagccaatataacaggtaagggaagtttcttctgatcttgtcttttgagttgatcaaccaaagggaaagaacacccttgttcgtagctggaatccatgagaagcacttgctttttattaattcccctttgactaatctttatcaaatgcatttacgtcctttgttgttcatcatttggtgtgcctgagctagaatctttcttaatgtacttactgtgttttctatttcctctatcttctgtcctttttttaaaacttctttttttgactaggacatatattctttctaagatcgaactttttgactaaggtacatgcctgaatcgccagatggcatcaagttaggtactagcttgccatgaatttcccaacattcatatatttgacttagtattaatcgaacttaacagtcatcttttttaaccacttcagagtagatagcaaatcagtacacaTtttttttctcccttcacatttcatcatctctccactttagtggtggtcctatttttgaactgatttctaacatagcatggtccctaatctagctgcatcctagatccatttctggactgatgaaatctgacacagctctaagtatttgacagatgagtaatgtaggttgtacgggaattctagaacactaaaaaaaataaaaaccttttacaagagacaatatgaaaaactgaaataatcttttaccatactttcagttgggttctgcaatgcaatctgtcaatccattattacttttttttctttctgaaaaataaagatttactgtatataccttatgtatacacttgctga More
CDS seq		atgtcgtcctcgcctctaaccgccacgccttcccctctccttcccgccaaatccaagaacccaccaccccaccaccaccaccacaacccgctcctcgcctacctcccgcactgcacgagcctccgcgcgctcgcgcagctccacgccgtcgccgtcaaggccggcggcggcctccaggcgcacccggccttcgtcacgaggctcctcacgctctgcacggagcagggggcggaggcgcccgcgcacctcgcgtacgcgcgccaggtgttcgacagaatcccccacccgggcgacgtcgtctggtacaacacgctgctgcgcgggtacgcgcgcgggggtgggggcgggggcggcgcggaggaggccgcgcgggtgttcgtccggatgatggaggagggggtggcgcccgacacgtacacgttcgtgtcgctgctcaaggcgtgcgcgtccgcgcgggccggcgaggaagggcagcaggcgcacggcgtggcggtcaaggccggcgccgcggagcacgagtacgtcgcgcccacgctgatcaacatgtacgccgagtgcggggacgtgcgcgccgcgcgcgtgatgttcgacaggatggacggggagtgcgtcgtctcgtacaatgccatgatcaccgcgtccgtcaggagcagcctgcccggcgaggcgctggtgctgttccgggagatgcaggccaaggggctcaagccgacgtccgtgacgttgattagtgtgctctcggcgtgcgcattgctcggagctctggaacttgggaggtggatccacgactatatcaggaagatgaggcttgattcccttgtgaaggtcaacactgcgctgatcgacatgtatgcgaagtgtgggagcttggaggatgccattggcgtgttccaggatatggaatcaagggataaacaagcttggtctgtgatgatggtggcatatgctaaccatggctatggcagagaggccatttcaatgttcgaagagatgaagaaacaaggtatgaaacctgatgatgttacattccttggggtgctctatgcctgcagccactctggtatggtgagcgaagggctccaatactttgacagcatgagggaatatggcattgtttcagggatcaagcactatggttgtgtgactgatttgctggctcgatcagatttactgtatataccttatgtatacacttgctga More
Protein seq		MSSSPLTATPSPLLPAKSKNPPPHHHHHNPLLAYLPHCTSLRALAQLHAVAVKAGGGLQAHPAFVTRLLTLCTEQGAEAPAHLAYARQVFDRIPHPGDVVWYNTLLRGYARGGGGGGGAEEAARVFVRMMEEGVAPDTYTFVSLLKACASARAGEEGQQAHGVAVKAGAAEHEYVAPTLINMYAECGDVRAARVMFDRMDGECVVSYNAMITASVRSSLPGEALVLFREMQAKGLKPTSVTLISVLSACALLGALELGRWIHDYIRKMRLDSLVKVNTALIDMYAKCGSLEDAIGVFQDMESRDKQAWSVMMVAYANHGYGREAISMFEEMKKQGMKPDDVTFLGVLYACSHSGMVSEGLQYFDSMREYGIVSGIKHYGCVTDLLARSDLLYIPYVYTC
Function		Pentatricopeptide repeat-containing protein At2g02980, chloroplastic [UniProtKB/Swiss-Prot:Q8LK93]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNaBo_03g0037140	OsNaBo_03g0037140.01	Chr03	35553232	35558332	+	NAM
CDS seq	atgtcgtcctcgcctctaaccgccacgccttcccctctccttcccgccaaatccaagaacccaccaccccaccaccaccaccacaacccgctcctcgcctacctcccgcactgcacgagcctccgcgcgctcgcgcagctccacgccgtcgccgtcaaggccggcggcggcctccaggcgcacccggccttcgtcacgaggctcctcacgctctgcacggagcagggggcggaggcgcccgcgcacctcgcgtacgcgcgccaggtgttcgacagaatcccccacccgggcgacgtcgtctggtacaacacgctgctgcgcgggtacgcgcgcgggggtgggggcgggggcggcgcggaggaggccgcgcgggtgttcgtccggatgatggaggagggggtggcgcccgacacgtacacgttcgtgtcgctgctcaaggcgtgcgcgtccgcgcgggccggcgaggaagggcagcaggcgcacggcgtggcggtcaaggccggcgccgcggagcacgagtacgtcgcgcccacgctgatcaacatgtacgccgagtgcggggacgtgcgcgccgcgcgcgtgatgttcgacaggatggacggggagtgcgtcgtctcgtacaatgccatgatcaccgcgtccgtcaggagcagcctgcccggcgaggcgctggtgctgttccgggagatgcaggccaaggggctcaagccgacgtccgtgacgttgattagtgtgctctcggcgtgcgcattgctcggagctctggaacttgggaggtggatccacgactatatcaggaagatgaggcttgattcccttgtgaaggtcaacactgcgctgatcgacatgtatgcgaagtgtgggagcttggaggatgccattggcgtgttccaggatatggaatcaagggataaacaagcttggtctgtgatgatggtggcatatgctaaccatggctatggcagagaggccatttcaatgttcgaagagatgaagaaacaaggtatgaaacctgatgatgttacattccttggggtgctctatgcctgcagccactctggtatggtgagcgaagggctccaatactttgacagcatgagggaatatggcattgtttcagggatcaagcactatggttgtgtgactgatttgctggctcgatcagatttactgtatataccttatgtatacacttgctga More
Protein seq	MSSSPLTATPSPLLPAKSKNPPPHHHHHNPLLAYLPHCTSLRALAQLHAVAVKAGGGLQAHPAFVTRLLTLCTEQGAEAPAHLAYARQVFDRIPHPGDVVWYNTLLRGYARGGGGGGGAEEAARVFVRMMEEGVAPDTYTFVSLLKACASARAGEEGQQAHGVAVKAGAAEHEYVAPTLINMYAECGDVRAARVMFDRMDGECVVSYNAMITASVRSSLPGEALVLFREMQAKGLKPTSVTLISVLSACALLGALELGRWIHDYIRKMRLDSLVKVNTALIDMYAKCGSLEDAIGVFQDMESRDKQAWSVMMVAYANHGYGREAISMFEEMKKQGMKPDDVTFLGVLYACSHSGMVSEGLQYFDSMREYGIVSGIKHYGCVTDLLARSDLLYIPYVYTC More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsNaBo_03g0037140	OsNaBo_03g0037140.02	Chr03	35553199	35555217	+	IsoSeq
CDS seq	actggcctctcgtcctcactccataacggccatgtcgtcctcgcctctaaccgccacgccttcccctctccttcccgccaaatccaagaacccaccaccccaccaccaccaccacaacccgctcctcgcctacctcccgcactgcacgagcctccgcgcgctcgcgcagctccacgccgtcgccgtcaaggccggcggcggcctccaggcgcacccggccttcgtcacgaggctcctcacgctctgcacggagcagggggcggaggcgcccgcgcacctcgcgtacgcgcgccaggtgttcgacagaatcccccacccgggcgacgtcgtctggtacaacacgctgctgcgcgggtacgcgcgcgggggtgggggcgggggcggcgcggaggaggccgcgcgggtgttcgtccggatgatggaggagggggtggcgcccgacacgtacacgttcgtgtcgctgctcaaggcgtgcgcgtccgcgcgggccggcgaggaagggcagcaggcgcacggcgtggcggtcaaggccggcgccgcggagcacgagtacgtcgcgcccacgctgatcaacatgtacgccgagtgcggggacgtgcgcgccgcgcgcgtgatgttcgacaggatggacggggagtgcgtcgtctcgtacaatgccatgatcaccgcgtccgtcaggagcagcctgcccggcgaggcgctggtgctgttccgggagatgcaggccaaggggctcaagccgacgtccgtgacgtt More
Protein seq	TGLSSSLHNGHVVLASNRHAFPSPSRQIQEPTTPPPPPQPAPRLPPALHEPPRARAAPRRRRQGRRRPPGAPGLRHEAPHALHGAGGGGARAPRVRAPGVRQNPPPGRRRLVQHAAARVRARGWGRGRRGGGRAGVRPDDGGGGGARHVHVRVAAQGVRVRAGRRGRAAGARRGGQGRRRGARVRRAHADQHVRRVRGRARRARDVRQDGRGVRRLVQCHDHRVRQEQPARRGAGAVPGDAGQGAQADVRDV More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	2.104459	1.957925	0.387478

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_03g0795200	RBH	1.832128	1.888040	0.542030
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os03g58100	RBH	1.223202	1.296238	0.153591
Nipponbare \| IRGSP 1.0 \| RAP-db	Os03g0795200	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_03g0037990	RBH	0.822234	0.0	0.796810
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_03g0037680	RBH	0.450152	0.000000	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_03g0037730	RBH	2.198240	1.094481	0.650070
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_03g0038040	RBH	0.059428	0.000000	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_03g0037560	RBH	3.430682	0.000000	3.461622
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_03G0565400	RBH	6.825894	2.427374	3.475839
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_03g0037350	RBH	0.548280	0.079013	0.242847
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_03G0567100	RBH	1.7312945	1.1958805	0.2972075
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_03g0037890	RBH	0.103555	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_03g0037890	RBH	0.463306	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_03g0037500	RBH	0.000000	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_03g0037560	RBH	0.413289	0.178746	0.261122
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_03g0037580	RBH	0.624538	0.000000	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_03G037360	RBH	0.181258	0.000000	0.551260
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_07g0004450	RBH	0.479281	1.503062	0.895341

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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