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
OsLima_01g0039990		OGI:01110460 \| 10/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr01:38736947-38741763		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		C10501
DNA seq		atggcgagccgagctctcactcccatgcagctcattggcacggtcttcgtggcgctcctcgcgacgtgccacgccggcggcatcgccgtgtactggggccagaacgacggcgaggcatcgctggccgagacgtgcgcgtcgggcaactacgagttcgtcatcatcgccttcctccccaagttcggcaagggccagacgccgcgggtggacctcgccagccactgcgaccccgcgtcgggcggctgcaccggccagagcaaggacatccgcgcgtgccagcgccgcggggtgaaggtcctgctctccatcggcggcggcgacggcagctacggcctcgcatcccccggtgacgcccggcaggtggccatgtacctctggaacaacttcctcggcggctcctcctcgtcccgtcccctcggcgacgccgtcctcgacggcatcgacttcgacatcgagctcggcggcgccaagttctgggacgacctcgccaggtacgtaaccaaaaccaaaccatctccggccatcttcctactcaccggccggccatcgtcacactcatcgtgatgaacagggatctgaagagcctggggaggagcggcgggaggagggtggtgctgagcgcggcgccgcagtgcccgttcccggacgagtgggacggcggcgcgatcagcacggggctgttcgacgccgtgtgggtgcagttctacaacaacccggagtgccagttcagcgcggggcggggcgcgttcatggacgcgtggaggaagtgggagtcggtgccggcggggcgactcttcctgggcctcccggcgtccaaggacgccgccggcaccgggttcgtgcccgccggcgagctcaactcccgcgtgctgccgctcatcaggggctcccccaagtacggcggcgtcatgctgtggtccaagtactacgacgatcaaaccggctacagctccgccatcaagagccacgtgtgatcacaattcacgtgttctataccattatacgttccagagcgcgtgtgcaccttacgtaacgtacgcatcactagctagagtgtgtgactgtgctgcgacgtatttgtaatacttactccgtttcataatgtaaattatgttattctagcattttctatatccatataatatagatgtggaaaatgctaaaatgacttacattatgaaacggatatttgagtatatatgtagcacagtgatgtgtaggagcatgtgttgactgctttcggttaccggtcagacgtttagaccgtagcttaccattgcccccagtttaatttcattcgttcgccactgtcgtttatatgaagaatAAaaaaaggtgaccatttgttgcagcttaaattgatgttttttgagagagagattagttgatgttttgagagaacataaatatgcgagcatttcctgcttgaaaataatattcatttctatatgaaaacaggacaataagatatctaagctcttcgaggttgttgattacatctaaatgtctttatttttaattaagtgcttttggaatgcagaattttcaaaacacgtggaccagAaaaaaaaatgtaattccagtaccttggatcctcgagttccatcggttgccctaataaaccgatgccaaagctaaaattcaaatttttaaacttaaatttgattttgattttaagatatttttaacgtaactttttagcattggcttttaatttgttaggaacacatatataaaagttttacttataaactaatttttattccctaataaatcaaaatagcttactagaaatatgagcaactaatgactCccctcaaatcttataaataaaaatataaaaaaatagaaagactgtttggatggagcacatgaaaaacatatgaatcaaaatgaagatttttttttcaggaggttgatcctcatattagaagtctttcgaaaattcttatgatttgagacaatcctagggaactttgaaagaaatttggggtgactattcctttgctcaaaaatttgtaaaaattgtatgttccaaacgagattttaaagttccaaacgagccctaaatcccttcgcccaatcaacaaatcttatattctgtttgtacaatagaagtagaacgtatcaccgaacctccgctggactgtacaatcagccaactgagctgttcagtcgttagtgttgtcatcctttgttgcttatcattatactgcaatattccattgatagaagaactaagagcattatgctttcaaatagaagaactaacagcaaggattttgctgaatatttttttctacacaaaactgatgcctacgatatatactgctattttgagacttccagagtcaaacttttaggctacctgaactgaattccgtctgttacttgaagctctgggaggccattatttccgatctctaaatagtcaagttatttctattttctttgatgaaaaatagctcccccgctttccccaatgagcttgtggcaggtgaaatttgtaaggtgttcacttgagtttatctttatacttgtagcactgcatatatatctcaaattattgattatcagtgcatatgttcagaaacttcggattgtggtagtgactctgctctgcaacgacaatctgctttctgctgaaaacgataagcacgaacttggcaggccaaaaatactatccaaaactaccaatcagctggtcgtcacgtgaatccacattacccggttcatttgattgcatgaatcaaaatgtttttgtctagttggatagagtacgaagaacgaaagcagcaaacgagcccgcactattcgttcggatgattttctattcctctgtccaggagagaacagagtattaattagctcaataggcccatgcgttaaagttgttaatcgtcggattagctcaaatatgtggtcttttccggtagtgcgtgagtagcaagattgcatgacggttgtttgatcgtcaaacagttttgagcttgtccatttcactggctgaactcgctgcaaaatgtccctttctttctctgttcatgctaaatgccattttattaaaaaaatttttgccatactgctgattagttacagagcaatcctaacattacacttcttaatcttgcatctaattttctttagacatcaaaaaaggataatagcatccagtgattccggaaagaatcctttcatccttttgtactgtctacctactggccactctgcaactgccattgttgaacactgcaaacacaatggcatgatggcatcaaccagtcaactcttacggagtgaagcagtttgacaatcacaagaataattggccatcgcatctcgtgattggtactggcgcgtgataagtggaagctgcgctcaaaccgaagaccaaagctcgcggacgtcaacggtcaaccactgccgacactataggccacaatcttgtgcagctgattggccaatatcatattggcaatggcatgcttcgatgattggtcccaagcacccaccacgcattttcttcttatcttgttgctcacttgttctgttcttgcccggtcaacttgcgacggcgagcagacctaacaaatgatgaaatcgcggaacgcacgtcgcagcggcttcactggctcactgctaccagtattcacacctagttgaattcggctataaatacacaagaaccttgcggttgcggagtagaagcaagaattcgatcgagaatcaccatgatgacaagtagaatgttttcggcaatgcagatgctgatcatggtggtggtggcattggccgggctagccgccggagcgcgcgccggcgacatcgcgatctactggggccagaacggcaacgagggaacgctggcgcagacgtgcgcgaccggtaattacaggttcgtcatcgtggccttcctgcctgtgttcggcaagggccagacgccggttctgaacctggccggccactgcgacccggcgtcgaacggctgcaccggcgtgggcgccgacatcaagtcgtgccagagcctcggcatcaaggtcatgttctcgatcggcggcggcgtcggcaactacggcctgtcctcccgcgacgacgccaagcaggtcgcggcgtacctgtggaacaactacctcggcggcacgtcgccgtcgaggccgctcggcgacgccgtcatggacggcatcgacttcgacatcgagagcggcgggggcatgtactgggacgacttggccaggtacctcaaggcgtactcgcggcaggggagcagcaagaagccggtgtacctgacggcggcgccacagtgccccttcccggacgcgtcgctcggcgtcgcgctcagcaccggcctgttcgactacgtgtgggtgcagttctacaacaacccgccgtgccagtacagctcgtccaacggcgtgggcaacctggcgagcgcgtggaagcagtggacgtcgatcccggcggggcgggtgttcctcggcctgccggcggcagcggcggccgccggcagcgggttcgtggagacgagcgacctggtgtcgaaggtgctccccgtggtgaagaagtctcccaagtacggagggatcatgctgtggtcgcggtactatgacgggctcacggggtacagcgacaaggtgaagtccagcgtttgagctagccagggtaagctcgtgtcaggtcggcgttcgcgtagaatcacacgtgccgcgcgttccctgcaagatggagtagtttctacacatttcagaacaaagcaaacatgtacaatcagatggccggcttgtatactcatttagaagcagaaaaaattgtgagaaatt More
CDS seq		atggcgagccgagctctcactcccatgcagctcattggcacggtcttcgtggcgctcctcgcgacgtgccacgccggcggcatcgccgtgtactggggccagaacgacggcgaggcatcgctggccgagacgtgcgcgtcgggcaactacgagttcgtcatcatcgccttcctccccaagttcggcaagggccagacgccgcgggtggacctcgccagccactgcgaccccgcgtcgggcggctgcaccggccagagcaaggacatccgcgcgtgccagcgccgcggggtgaaggtcctgctctccatcggcggcggcgacggcagctacggcctcgcatcccccggtgacgcccggcaggtggccatgtacctctggaacaacttcctcggcggctcctcctcgtcccgtcccctcggcgacgccgtcctcgacggcatcgacttcgacatcgagctcggcggcgccaagttctgggacgacctcgccagggatctgaagagcctggggaggagcggcgggaggagggtggtgctgagcgcggcgccgcagtgcccgttcccggacgagtgggacggcggcgcgatcagcacggggctgttcgacgccgtgtgggtgcagttctacaacaacccggagtgccagttcagcgcggggcggggcgcgttcatggacgcgtggaggaagtgggagtcggtgccggcggggcgactcttcctgggcctcccggcgtccaaggacgccgccggcaccgggttcgtgcccgccggcgagctcaactcccgcgtgctgccgctcatcaggggctcccccaagtacggcggcgtcatgctgtggtccaagtactacgacgatcaaaccggctacagctccgccatcaagagccacatgctgatcatggtggtggtggcattggccgggctagccgccggagcgcgcgccggcgacatcgcgatctactggggccagaacggcaacgagggaacgctggcgcagacgtgcgcgaccggtaattacaggttcgtcatcgtggccttcctgcctgtgttcggcaagggccagacgccggttctgaacctggccggccactgcgacccggcgtcgaacggctgcaccggcgtgggcgccgacatcaagtcgtgccagagcctcggcatcaaggtcatgttctcgatcggcggcggcgtcggcaactacggcctgtcctcccgcgacgacgccaagcaggtcgcggcgtacctgtggaacaactacctcggcggcacgtcgccgtcgaggccgctcggcgacgccgtcatggacggcatcgacttcgacatcgagagcggcgggggcatgtactgggacgacttggccaggtacctcaaggcgtactcgcggcaggggagcagcaagaagccggtgtacctgacggcggcgccacagtgccccttcccggacgcgtcgctcggcgtcgcgctcagcaccggcctgttcgactacgtgtgggtgcagttctacaacaacccgccgtgccagtacagctcgtccaacggcgtgggcaacctggcgagcgcgtggaagcagtggacgtcgatcccggcggggcgggtgttcctcggcctgccggcggcagcggcggccgccggcagcgggttcgtggagacgagcgacctggtgtcgaaggtgctccccgtggtgaagaagtctcccaagtacggagggatcatgctgtggtcgcggtactatgacgggctcacggggtacagcgacaaggtgaagtccagcgtttga More
Protein seq		MASRALTPMQLIGTVFVALLATCHAGGIAVYWGQNDGEASLAETCASGNYEFVIIAFLPKFGKGQTPRVDLASHCDPASGGCTGQSKDIRACQRRGVKVLLSIGGGDGSYGLASPGDARQVAMYLWNNFLGGSSSSRPLGDAVLDGIDFDIELGGAKFWDDLARDLKSLGRSGGRRVVLSAAPQCPFPDEWDGGAISTGLFDAVWVQFYNNPECQFSAGRGAFMDAWRKWESVPAGRLFLGLPASKDAAGTGFVPAGELNSRVLPLIRGSPKYGGVMLWSKYYDDQTGYSSAIKSHMLIMVVVALAGLAAGARAGDIAIYWGQNGNEGTLAQTCATGNYRFVIVAFLPVFGKGQTPVLNLAGHCDPASNGCTGVGADIKSCQSLGIKVMFSIGGGVGNYGLSSRDDAKQVAAYLWNNYLGGTSPSRPLGDAVMDGIDFDIESGGGMYWDDLARYLKAYSRQGSSKKPVYLTAAPQCPFPDASLGVALSTGLFDYVWVQFYNNPPCQYSSSNGVGNLASAWKQWTSIPAGRVFLGLPAAAAAAGSGFVETSDLVSKVLPVVKKSPKYGGIMLWSRYYDGLTGYSDKVKSSV
Function		Acidic endochitinase [UniProtKB/Swiss-Prot:P29060]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_01g0039990	OsLima_01g0039990.01	Chr01	38736947	38741595	+	NAM
CDS seq	atggcgagccgagctctcactcccatgcagctcattggcacggtcttcgtggcgctcctcgcgacgtgccacgccggcggcatcgccgtgtactggggccagaacgacggcgaggcatcgctggccgagacgtgcgcgtcgggcaactacgagttcgtcatcatcgccttcctccccaagttcggcaagggccagacgccgcgggtggacctcgccagccactgcgaccccgcgtcgggcggctgcaccggccagagcaaggacatccgcgcgtgccagcgccgcggggtgaaggtcctgctctccatcggcggcggcgacggcagctacggcctcgcatcccccggtgacgcccggcaggtggccatgtacctctggaacaacttcctcggcggctcctcctcgtcccgtcccctcggcgacgccgtcctcgacggcatcgacttcgacatcgagctcggcggcgccaagttctgggacgacctcgccagggatctgaagagcctggggaggagcggcgggaggagggtggtgctgagcgcggcgccgcagtgcccgttcccggacgagtgggacggcggcgcgatcagcacggggctgttcgacgccgtgtgggtgcagttctacaacaacccggagtgccagttcagcgcggggcggggcgcgttcatggacgcgtggaggaagtgggagtcggtgccggcggggcgactcttcctgggcctcccggcgtccaaggacgccgccggcaccgggttcgtgcccgccggcgagctcaactcccgcgtgctgccgctcatcaggggctcccccaagtacggcggcgtcatgctgtggtccaagtactacgacgatcaaaccggctacagctccgccatcaagagccacatgctgatcatggtggtggtggcattggccgggctagccgccggagcgcgcgccggcgacatcgcgatctactggggccagaacggcaacgagggaacgctggcgcagacgtgcgcgaccggtaattacaggttcgtcatcgtggccttcctgcctgtgttcggcaagggccagacgccggttctgaacctggccggccactgcgacccggcgtcgaacggctgcaccggcgtgggcgccgacatcaagtcgtgccagagcctcggcatcaaggtcatgttctcgatcggcggcggcgtcggcaactacggcctgtcctcccgcgacgacgccaagcaggtcgcggcgtacctgtggaacaactacctcggcggcacgtcgccgtcgaggccgctcggcgacgccgtcatggacggcatcgacttcgacatcgagagcggcgggggcatgtactgggacgacttggccaggtacctcaaggcgtactcgcggcaggggagcagcaagaagccggtgtacctgacggcggcgccacagtgccccttcccggacgcgtcgctcggcgtcgcgctcagcaccggcctgttcgactacgtgtgggtgcagttctacaacaacccgccgtgccagtacagctcgtccaacggcgtgggcaacctggcgagcgcgtggaagcagtggacgtcgatcccggcggggcgggtgttcctcggcctgccggcggcagcggcggccgccggcagcgggttcgtggagacgagcgacctggtgtcgaaggtgctccccgtggtgaagaagtctcccaagtacggagggatcatgctgtggtcgcggtactatgacgggctcacggggtacagcgacaaggtgaagtccagcgtttga More
Protein seq	MASRALTPMQLIGTVFVALLATCHAGGIAVYWGQNDGEASLAETCASGNYEFVIIAFLPKFGKGQTPRVDLASHCDPASGGCTGQSKDIRACQRRGVKVLLSIGGGDGSYGLASPGDARQVAMYLWNNFLGGSSSSRPLGDAVLDGIDFDIELGGAKFWDDLARDLKSLGRSGGRRVVLSAAPQCPFPDEWDGGAISTGLFDAVWVQFYNNPECQFSAGRGAFMDAWRKWESVPAGRLFLGLPASKDAAGTGFVPAGELNSRVLPLIRGSPKYGGVMLWSKYYDDQTGYSSAIKSHMLIMVVVALAGLAAGARAGDIAIYWGQNGNEGTLAQTCATGNYRFVIVAFLPVFGKGQTPVLNLAGHCDPASNGCTGVGADIKSCQSLGIKVMFSIGGGVGNYGLSSRDDAKQVAAYLWNNYLGGTSPSRPLGDAVMDGIDFDIESGGGMYWDDLARYLKAYSRQGSSKKPVYLTAAPQCPFPDASLGVALSTGLFDYVWVQFYNNPPCQYSSSNGVGNLASAWKQWTSIPAGRVFLGLPAAAAAAGSGFVETSDLVSKVLPVVKKSPKYGGIMLWSRYYDGLTGYSDKVKSSV More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_01g0039990	OsLima_01g0039990.02	Chr01	38740648	38741763	+	IsoSeq
CDS seq	agaagcaagaattcgatcgagaatcaccatgatgac
Protein seq	RSKNSIENHHDD

No AS event found.

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.074233	0.0	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0860400	RBH	0.0	0.0	0.0
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os01g64110	RBH	0.437242	0.0	0.285733
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0860400	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0041010	RBH	0.0	5.290593	0.0
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_01g0040560	RBH	0.0	7.754455	1.146925
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0040930	RBH	0.0	35.405018	2.663350
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0040390	RBH	0.250236	1.940165	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0039960	RBH	0.0	18.283033	3.157826
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0612000	RBH	1.660333	21.7410335	2.7585565
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0039630	RBH	0.130048	0.512200	0.165652
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0611600	RBH	5.0654455	8.495277	0.4058205
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_07g0010640	RBH	0.036821	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0039940	RBH	0.082623	12.084152	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0040180	RBH	2.828008	15.160257	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0040140	RBH	0.161689	1.782064	0.403877
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0040020	RBH	0.104023	15.131411	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G040470	RBH	0.076032	1.570040	0.311115
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0040150	RBH	0.423680	37.038948	0.681147

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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