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
OsLaMu_05g0011100		OGI:05035520 \| 16/16			LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)			Chr05:13699131-13705778		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		ttaccagccagggtcagatgcctcccagctgccatcccatggataactgctagaaaataaaatgtacaactctgattccttatccgtttgtgctacaaatagatgtcaagtcaaaggagtaaaattataaacacataaccatggaaaaatcaGgggaaaacacagcagtccaacaggaaaaaaaaatgagtttaactacagccctcagaacaaacaatggcacaagatatgatggaaatatagaggcaacacatggtcttcaggagaagttaagtgcagttcaacccagggtataaatgatccacatatttctcataatataaaaactaaacaggaataacatagctcctgaagaaaacgatttcagaatttcaggctatctgaacagtataggatatagtaaaatctcatcgatcaccaaaaaatccaaataaagcaatagcagatgttctcatggatagtggtaatcttggacaaatttgaagatcattacagcatgactccaagcatatatacacaaagagacatgcacagaacacagaagatccaggatattatattctaactcagaacacacatagtttgtctaactaaagaaagcatcaacggattagatagacacactagtgagaggtttctgatgtcaaagggtggttcactgaactttacaatctgcaatcaactgtagaacgaaattgctagaattaatatcttctacatttgaacatacctggcatcaagtgtgacatgtgcagtagtatagcccttcatggaatccaaatagaaaaacactaaaaaGgggaagagcttagacatagtcaatcaagaggataaggccattggattgtgaatgtgattcatccatgcaaacaagatttgctatggtcagtactcagtaaacactaaacaatatggaaataatgtaggctaagcaagttgttaacgttgtgaagacgtgtgacatccaaaacctgaaaaatcatgatggatttaaggcaacaggaatatatgctttacagataatctgacagcatgccttatgaacattcgaaatacaacatcaccagtggcggattcactgttggggctggttggtgtgccagccccacctctaatccctgctcttaattagtcattaacaaatctaattagtcttagtgaagaaatttcccgaatagcacaggctaccttagtccttctactgcccaaactgataaaacagaacatccttcgagtataaataacaatatattcacatatatttgtgaatattttaatatagccacaaatcaaaatagagagttttttttatcatatgcacatttggttttcattggaaaatactttagttgatatacctttatttgttttaatcatactctctccatccctaaatatttgatgccgttgacttttttaaatatgtttgaccgttcgtcttattaaaaattttaagtaattattaattcttttcctatcatttgattcattgttaaatatacttttatgtatacatatagttttatatgtttcacaaaagtttttaataagatgaacggtcaaacatgtttaaaaaagtcaacggcgtcaaatatttagggacggagggagtattatattttttacactagcacctcctcaatttacaccctggattcgccactgaacatcactgaaactatagtcttatgttatgtccaaagcattttgtggattcaacaaacatcacatttgtgaggcatctagtcaaatattttttaaaacttcaaaatcatgtgcatagaaaatatgagttttcagatactgacagttgctgaaaggagaagcactctaatcaagaataaatttaacaatcagtctagcgctggcaaggggacaaagaaaacggaatccatgcgaggatagtaatgggactgggttcgcccagggagatggctagagagtaggcagaattttctgggagcaaagtcattaaaaagactttgttaaacgcattaagttgatggacttctgatcaaatcacgaatggccatgatgtcctgtatcatccagcaatcatatatcagaaaattttaaattgatgcctttaaagcacaaattatttgttttggggagatttggaggtaaggatccaacttcaaatatgaggtgtttgatcaaatcaagcgctagctaggactacttgtatcaacgctccatgtatagccaaactgatgctggtgctgttataataaagtatagatacacatctaaattttggtcAaaaaattggaatatccatgatggcatgatgttcatgttgctatttacacgtcaaacagtagtgttgcatggatctcttcacttctggcatatcaggaagcatgtgcagtaactaaacaagttgatgaatacaaaacacagaactatttataattgcaattcccaagctgataagatcaaattggtgaaaatttgcaattgcttttatttacaatcaatgaagtttactaagaacttatgtatatctgtaaggaatcagtaacacaatttctaaagtgctgcagaacagaagcaggtgaatctgaattgaacagtatgcaggtgactttcttcacctcaatattagacaaacaatcgttactttattgtctaagcaattctaagaaaattatatcgcaaaaaggtccaaatttggcatatagtaacgcagtgaaataatttcccatcctgataaagattattgattagtttccatacctgcaaaggcttcctatgcttgcagtgcatgcatttgtcaggaggcaccaacaaggacagctactgatctttgaaagagctagctacatagctacatatgtcagatggtacaagaagcaaccacaattagattgacatgcaaaattcgattaggaccaaaagagtttacaaataccaaacctgtactgcaacagatctgaaagctacaatattactccagaaaaagcagaataatataaatatctgtctccaattctccatgaaatacaaagtgcttgaaatgtttgcagcatacatgacatatttttattccatatataacatatttgctattccatatatgatatatttgtaattccaaacgatagataagccagctctttccatacctaatcagaaactaatacacaaaggtagttagcaaactgagtaactggttttggagaatacaatggccagccggcactgagccgccatatttctaaggcgttgttcgtttaatccccaagagagagggattggaagggaataaatccccttcaaatccacccataagagggattaaacgaacaaggcctaaaggggtttcatgtatgaaggtgtagaacccatagggcccatgagttatatatactaccgccatccttaaaaggatgacatcataaaatgcatgcggtcaaacctcaaaatgttaaacgattaatatatggaaaacatattaggatttgaatatgaaaatatatattagtagatttgctatgaaaaactatttcatatagttatacttttattaagttttataaatacatagtttgaaaaattaatgatcgaacatgtgcatggaagactgacgatatccaaaatataagtaaaaaagaatggaggtaataatatggtggcataagtctcgcactcttacatgatgagtttaataaataggttaaggccagagtataaaattaacagttccaaaaaaataactccggttaatgcaagtgtaagtagggtaaggcctgatagaagggctagagattagtgatcaaagtattgtcttgcaaatatattgtgatagaaattgttatcaaagttatatttaggagaccatgttgatgcccaaaatgataagttttcatggctagagtataaagaatctagattacatcagtattccttactgtgggaaaatatctagtaatacattgttaactacttagtttatgcttctacctctgatgctttcacaaaagaaaccctcaccaatagccaccacatgagcatgaaccattcttgaaatgatgaaaacgactggggtcgcgcactacgatctcatggtccacaatcttggaaatgtaggtgaatgcgctatggcaatcaccacatacacgcaggttctttgtgatccttattgggcaaccagggaaagttgtgaggagaccatatgcaagagcaagtttctcactgtgctcaacaagaagattatttttctcttcctcatcaacatcatgtaatgcgaagtttgtctcaggaacatatcccatagctttgatgcgatcaattagactctccagaagagcataaatttgtggggatagtgggtgtgatcgatctccgacaaagaaagatgctgtgcccttttgaccctggacccagctgcatcctggcctcttcttaattcctgatttcttcatcaagtgcctgatcctcgctacatccttccaccgccctgcagtggcatatatgttggagataagcgtgtaagatccatcattttcagcattcatctcgaccagtttgttcagagcatgttcagcaagttcaacatttgaatgtactctacaggcactcagtaatgcaacccaaactactgcggtgggctccattggcatatccttaactgttttccatgccttatctaatcgcccaaagcgggccagcaagtcaatagcacaggcatagtgctctgcccgaggtgtcaaaccataatctgcactcatgctgtcaaagtacgatagaccttgatcaaccattccacaatgactacaagcataaagaacaaccaggaaggttatatcgtcaggaacaaagcctgctttccgcatcttgtcaaatatgtccagggcctcactaccacgaccgtgcattccataccctatcatcattgatgtccaagaaatagcactcttttgagacatgctatcgaatacatgcctagctgtatcaacatccccacactttgagtacatatcaatgaagcagttcgccacaaagtatgcagatgagtcatatcggtgatgacgaagcacataagcatgaatctgcttacctatacgtatggctgccaaatgtgcacaggccatcaaaatgcacgaaattgtataagcatttggggctactccatatggttccgaaatcatctccacgaaaagcttgagggcatcatttgagtccccatattgtgcatgccccccgatcatgacagtccaggtgacaacattgcgttcctctagaggtatatcatcaaatatggagtgtgcagctttgaagcttctgcactttgagtacatatctattagcgcgttgtacaccataagatcctcatcctcaccaccAaaatcattatccaaggttagaagacagttctttagggagtaggcatgaatttccataccctgagaaaatgctcccaaagaagcgcatgcagacaacacagagatgattgtgacacaatttggcaaggacccagaaaatatcatttgacggaatacattgagtgcttcatggctgcatcccctctgagaatagcctgcaattacagcagtccatgttaccacatctaatgggatattttccttgcgtatgttcttgaaaagctcaaaggctgccttaaagttgccactttgggagtacccagccaccattgcgttccaagaaaccacatctttgaattccatcatgttgaaaacctttaccgcattttccatcaaaccacacttaccgtaagcatcaatcagggcattaccaacaaaaacatctggaaatgtgccattacgaatagcattaccatggacttctttagtttgaggtactgcctttagaagaaccacatgcagggagtatgttgacaatgctaatgatgtctgacctttcatttgtaggcttctcatggacaatcaatgtcatctttgaaaacagatccaatgcagtccaagcattactacttttaacatgggctgaaacaatagagttccatgagataacatcatcaatacccctctgagttatttcatcaaagatcatgctggcttcctccaaagaaccacaacgggaatacattgccaccaacgcattgcatatgaagacattggactcaaagccattgcagcatatcaatccatggaatgcactaccacaacggtatgaaggtagctctccacatgcttttaatacatgtggtagagtAaaatggtccggcctagttccagcacgcagcatgcggcaagagacattaattgcactgtcaaggcggccttgtttgatgtgttctcggataagtagattccaccacactgctggtgacggtgtaacacgttccaacaccaagagagcatagtcggtagcaccacaagcaagataagaagctacgacaccagtacccagagatcttggagatataattggttcggatggcaatcctggcagtgagactgacaataatggtgtgggcaaagaaagaagaccagaagcaattatctgttggtgaatttgatgaactgtatttgcagacttgcattccttcaatagggatgcaaagtgactaggataaacatctacaccaacgcatgctgcccttgcacctgaaaggaaccgtactccaattggttttaccgccttaggcaagttcaaaagcat More
CDS seq		atgcttttgaacttgcctaaggcggtaaaaccaattggagtacggttcctttcaggtgcaagggcagcatgcgttggtgtagatgtttatcctagtcactttgcatccctattgaaggaatgcaagtctgcaaatacagttcatcaaattcaccaacagataattgcttctggtcttctttctttgcccacaccattattgtcagtctcactgccaggattgccatccgaaccaattatatctccaagatctctgggtactggtgtcgtagcttcttatcttgcttgtggtgctaccgactatgctctcttggtgttggaacgtgttacaccgtcaccagcagtgtggtggaatctacttatccgagaacacatcaaacaaggccgccttgacagtgcaattaatgtctcttgccgcatgctgcgtgctggaactaggccggaccatttTactctaccacatgtattaaaagcatgtggagagctaccttcataccgttgtggtagtgcattccatggattgatatgctgcaatggctttgagtccaatgtcttcatatgcaatgcgttggtggcaatgtattcccgttgtggttctttggaggaagccagcatgatctttgatgaaataactcagaggggtattgatgatgttatctcatggaactctattgtttcagcccatgttaaaagtagtaatgcttggactgcattggatctgttttcaaagatgacattgattgtccatgagaagcctacaaatgaaaggtcagacatcattagcattgtcaacatactccctgcatgtgtacctcaaactaaagaagtccatggtaatgctattcgtaatggcacatttccagatgtttttgttggtaatgccctgattgatgcttacggtaagtgtggtttgatggaaaatgcggtaaaggttttcaacatgatggaattcaaagatgtggtttcttggaacgcaatggtggctgggtactcccaaagtggcaactttaaggcagcctttgagcttttcaagaacatacgcaaggaaaatatcccattagatgtggtaacatggactgctgtaattgcaggctattctcagaggggatgcagccatgaagcactcaatgtattccgtcaaatgatattttctgggtccttgccaaattgtgtcacaatcatctctgtgttgtctgcatgcgcttctttgggagcattttctcagggtatggaaattcatgcctactccctaaagaactgtcttctaaccttggataatgatttTggtggtgaggatgaggatcttatggtgtacaacgcgctaatagatatgtactcaaagtgcagaagcttcaaagctgcacactccatatttgatgatatacctctagaggaacgcaatgttgtcacctggactgtcatgatcggggggcatgcacaatatggggactcaaatgatgccctcaagcttttcgtggagatgatttcggaaccatatggagtagccccaaatgcttatacaatttcgtgcattttgatggcctgtgcacatttggcagccatacgtataggtaagcagattcatgcttatgtgcttcgtcatcaccgatatgactcatctgcatactttgtggcgaactgcttcattgatatgtactcaaagtgtggggatgttgatacagctaggcatgtattcgatagcatgtctcaaaagagtgctatttcttggacatcaatgatgatagggtatggaatgcacggtcgtggtagtgaggccctggacatatttgacaagatgcggaaagcaggctttgttcctgacgatataaccttcctggttgttctttatgcttgtagtcattgtggaatggttgatcaaggtctatcgtactttgacagcatgagtgcagattatggtttgacacctcgggcagagcactatgcctgtgctattgacttgctggcccgctttgggcgattagataaggcatggaaaacagttaaggatatgccaatggagcccaccgcagtagtttgggttgcattactgagtgcctgtagagtacattcaaatgttgaacttgctgaacatgctctgaacaaactggtcgagatgaatgctgaaaatgatggatcttacacgcttatctccaacatatatgccactgcagggcggtggaaggatgtagcgaggatcaggcacttgatgaagaaatcaggaattaagaagaggccaggatgcagctgggtccagggtcaaaagggcacagcatctttctttggctatactactgcacatgtcacacttgatgccagttatccatgggatggcagctgggaggcatctgaccctggctggtaa More
Protein seq		MLLNLPKAVKPIGVRFLSGARAACVGVDVYPSHFASLLKECKSANTVHQIHQQIIASGLLSLPTPLLSVSLPGLPSEPIISPRSLGTGVVASYLACGATDYALLVLERVTPSPAVWWNLLIREHIKQGRLDSAINVSCRMLRAGTRPDHFTLPHVLKACGELPSYRCGSAFHGLICCNGFESNVFICNALVAMYSRCGSLEEASMIFDEITQRGIDDVISWNSIVSAHVKSSNAWTALDLFSKMTLIVHEKPTNERSDIISIVNILPACVPQTKEVHGNAIRNGTFPDVFVGNALIDAYGKCGLMENAVKVFNMMEFKDVVSWNAMVAGYSQSGNFKAAFELFKNIRKENIPLDVVTWTAVIAGYSQRGCSHEALNVFRQMIFSGSLPNCVTIISVLSACASLGAFSQGMEIHAYSLKNCLLTLDNDFGGEDEDLMVYNALIDMYSKCRSFKAAHSIFDDIPLEERNVVTWTVMIGGHAQYGDSNDALKLFVEMISEPYGVAPNAYTISCILMACAHLAAIRIGKQIHAYVLRHHRYDSSAYFVANCFIDMYSKCGDVDTARHVFDSMSQKSAISWTSMMIGYGMHGRGSEALDIFDKMRKAGFVPDDITFLVVLYACSHCGMVDQGLSYFDSMSADYGLTPRAEHYACAIDLLARFGRLDKAWKTVKDMPMEPTAVVWVALLSACRVHSNVELAEHALNKLVEMNAENDGSYTLISNIYATAGRWKDVARIRHLMKKSGIKKRPGCSWVQGQKGTASFFGYTTAHVTLDASYPWDGSWEASDPGW
Function		Pentatricopeptide repeat-containing protein At5g16860 [UniProtKB/Swiss-Prot:Q9LFL5]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLaMu_05g0011100	OsLaMu_05g0011100.01	Chr05	13699131	13705778	-	NAM
CDS seq	atgcttttgaacttgcctaaggcggtaaaaccaattggagtacggttcctttcaggtgcaagggcagcatgcgttggtgtagatgtttatcctagtcactttgcatccctattgaaggaatgcaagtctgcaaatacagttcatcaaattcaccaacagataattgcttctggtcttctttctttgcccacaccattattgtcagtctcactgccaggattgccatccgaaccaattatatctccaagatctctgggtactggtgtcgtagcttcttatcttgcttgtggtgctaccgactatgctctcttggtgttggaacgtgttacaccgtcaccagcagtgtggtggaatctacttatccgagaacacatcaaacaaggccgccttgacagtgcaattaatgtctcttgccgcatgctgcgtgctggaactaggccggaccatttTactctaccacatgtattaaaagcatgtggagagctaccttcataccgttgtggtagtgcattccatggattgatatgctgcaatggctttgagtccaatgtcttcatatgcaatgcgttggtggcaatgtattcccgttgtggttctttggaggaagccagcatgatctttgatgaaataactcagaggggtattgatgatgttatctcatggaactctattgtttcagcccatgttaaaagtagtaatgcttggactgcattggatctgttttcaaagatgacattgattgtccatgagaagcctacaaatgaaaggtcagacatcattagcattgtcaacatactccctgcatgtgtacctcaaactaaagaagtccatggtaatgctattcgtaatggcacatttccagatgtttttgttggtaatgccctgattgatgcttacggtaagtgtggtttgatggaaaatgcggtaaaggttttcaacatgatggaattcaaagatgtggtttcttggaacgcaatggtggctgggtactcccaaagtggcaactttaaggcagcctttgagcttttcaagaacatacgcaaggaaaatatcccattagatgtggtaacatggactgctgtaattgcaggctattctcagaggggatgcagccatgaagcactcaatgtattccgtcaaatgatattttctgggtccttgccaaattgtgtcacaatcatctctgtgttgtctgcatgcgcttctttgggagcattttctcagggtatggaaattcatgcctactccctaaagaactgtcttctaaccttggataatgatttTggtggtgaggatgaggatcttatggtgtacaacgcgctaatagatatgtactcaaagtgcagaagcttcaaagctgcacactccatatttgatgatatacctctagaggaacgcaatgttgtcacctggactgtcatgatcggggggcatgcacaatatggggactcaaatgatgccctcaagcttttcgtggagatgatttcggaaccatatggagtagccccaaatgcttatacaatttcgtgcattttgatggcctgtgcacatttggcagccatacgtataggtaagcagattcatgcttatgtgcttcgtcatcaccgatatgactcatctgcatactttgtggcgaactgcttcattgatatgtactcaaagtgtggggatgttgatacagctaggcatgtattcgatagcatgtctcaaaagagtgctatttcttggacatcaatgatgatagggtatggaatgcacggtcgtggtagtgaggccctggacatatttgacaagatgcggaaagcaggctttgttcctgacgatataaccttcctggttgttctttatgcttgtagtcattgtggaatggttgatcaaggtctatcgtactttgacagcatgagtgcagattatggtttgacacctcgggcagagcactatgcctgtgctattgacttgctggcccgctttgggcgattagataaggcatggaaaacagttaaggatatgccaatggagcccaccgcagtagtttgggttgcattactgagtgcctgtagagtacattcaaatgttgaacttgctgaacatgctctgaacaaactggtcgagatgaatgctgaaaatgatggatcttacacgcttatctccaacatatatgccactgcagggcggtggaaggatgtagcgaggatcaggcacttgatgaagaaatcaggaattaagaagaggccaggatgcagctgggtccagggtcaaaagggcacagcatctttctttggctatactactgcacatgtcacacttgatgccagttatccatgggatggcagctgggaggcatctgaccctggctggtaa More
Protein seq	MLLNLPKAVKPIGVRFLSGARAACVGVDVYPSHFASLLKECKSANTVHQIHQQIIASGLLSLPTPLLSVSLPGLPSEPIISPRSLGTGVVASYLACGATDYALLVLERVTPSPAVWWNLLIREHIKQGRLDSAINVSCRMLRAGTRPDHFTLPHVLKACGELPSYRCGSAFHGLICCNGFESNVFICNALVAMYSRCGSLEEASMIFDEITQRGIDDVISWNSIVSAHVKSSNAWTALDLFSKMTLIVHEKPTNERSDIISIVNILPACVPQTKEVHGNAIRNGTFPDVFVGNALIDAYGKCGLMENAVKVFNMMEFKDVVSWNAMVAGYSQSGNFKAAFELFKNIRKENIPLDVVTWTAVIAGYSQRGCSHEALNVFRQMIFSGSLPNCVTIISVLSACASLGAFSQGMEIHAYSLKNCLLTLDNDFGGEDEDLMVYNALIDMYSKCRSFKAAHSIFDDIPLEERNVVTWTVMIGGHAQYGDSNDALKLFVEMISEPYGVAPNAYTISCILMACAHLAAIRIGKQIHAYVLRHHRYDSSAYFVANCFIDMYSKCGDVDTARHVFDSMSQKSAISWTSMMIGYGMHGRGSEALDIFDKMRKAGFVPDDITFLVVLYACSHCGMVDQGLSYFDSMSADYGLTPRAEHYACAIDLLARFGRLDKAWKTVKDMPMEPTAVVWVALLSACRVHSNVELAEHALNKLVEMNAENDGSYTLISNIYATAGRWKDVARIRHLMKKSGIKKRPGCSWVQGQKGTASFFGYTTAHVTLDASYPWDGSWEASDPGW More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.000000	0.0	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_05g0305300	RBH	0.000000	0.000000	0.000000
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os05g23960	RBH	0.000000	0.000000	0.000000
Nipponbare \| IRGSP 1.0 \| RAP-db	Os05g0305300	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_05g0011070	RBH	0.000000	1.616458	0.000000
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_05g0011090	RBH	0.000000	0.000000	0.000000
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_05g0011030	RBH	0.210784	0.0	0.331380
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_05g0011090	RBH	0.000000	0.000000	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_05g0011060	RBH	0.436128	0.000000	2.481136
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_05G0200800	RBH	0.1254215	0.6519585	0.4167085
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_05g0010850	RBH	0.000000	0.000000	0.326480
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_05G0211300	RBH	0.11621	0.45018	0.425345
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_05g0011010	RBH	0.000000	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_05g0010950	RBH	0.000000	0.000000	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_05g0011100	RBH	0.0	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_05g0011100	RBH	0.000000	0.000000	0.0
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_04g0004720	SBH	0.218898	3.194929	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_05G010790	RBH	0.000000	0.000000	0.000000
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_05g0011120	RBH	0.746538	3.551712	0.524713

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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