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_01g0006610		OGI:01017550 \| 16/16			LIMA \| Os127564RS1 \| Gramene(+IsoSeq)			Chr01:5141179-5146144		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		tcatctttgttcatcttccatctctgcatatagatcatcgagcattccgaagacatcctcagctccggtgagattcggcggcgcgctcccggcggcgaaggcgaccaccttgttgtccacttcaatccagctctgccccggattcttcctcaatccggcctccttcgtcatcaccctcaccttcttggactcgtcccacatgccacacatggcgtacaggttggtgatcagcatgtggttgccggtgctctggtcctcggattgcagaacattggcaatggtggcctcggccatggctgcatcaccatgaatcctgcaggaattcagcaatgctccccacacgcacaggtcaggtctcaccggcatcgtctcgacgagctccgacgcgtcccggagcaagccggcgcggccgaggaggtagaccatgcatgtgtagtgctccatggatggggagatcttgtgcgctctcaccatgcgatcgaacaggcggcggCcctccgtgacacgcccggcgtggccgcacgccgacaggacggcgacgaaggtgacgccgtcgggctcaaccgtagctccggccatgtcggtgaacagagcgagggcttcgtcgcacaggccgtgcatgccgtagccggccagcatcgagttccatgagatcaggtccctcgtcttcattccgtcgaacaccttccgtgcgccggagaccttcccgcacttcgcgtacatgttgatgagcccattctcgaccagcgagtgcctatctagctcggctttcatggcgtggccatggagctctcgacccagccgtaacgccagtaggtcgacgcaagcggagaggacggtcgccatggtcaccacgttcggcgagagccattgctgctgcattcgccggaacagctccagtgcgcggtcagtgtcgccggacgacgcgaacccgccgatgaccgcgctccagctgaccacattgggcgcgaccgtgccgccgatctgctccatctgggcgagcacgtccaacgcctcgtcgcacagcccagccgcggcgtagctggtgatcagggtgttccatgtcacggtgttcttcgccgtcgcgtccctgaaagctttcttggcgtcgtccatctctccgagcttgccgtacatgcagatcaacgagttggtgacgaacaggtagccatgcatgaggcccttcacgacgccgcagccgtgtatcgccttccctttggccaatgcaaggtcgccggcgtaagggcacgccgagagcgccacggccatggactcggcgttcccctcgcagccgctcctttgcatttcaccgaacagctgaaggacatccgcgtgcttcccgctccgcgcgtgcgccgagagcagcgccgtccacgtcacggcgtcgggacgcgtccctgcggcggccatgcgcgcgaacgcgtccctcgccgcgtcggggtcgcagccgctggagtaggcggagatgagcgcgttccagtggaaggtcgtcctccccggcggcattgcgtcgaacacgcggcgtgcgtcggcggcgcggccgagcctggagtaggcggcgaggatctggccagcgacgtcgtgctgcgcgtggaggccgaggtgaagggcgtgggcgtggacggcggaggcgacgcgcggggaggcggcggcgcggagggcgagggggagcgtgtaggagttcggcagcgccggggagagcgcgcgcatgcggcggtagagcgcgagggcgaggtccccgcgggaacggccgaggtgggcgcggaggaggcgattccatgggacggcgctggtggtcggagggtggtgatggtggatcggttggtcgccggcggcggtggagagatggcgcgcgccgcgaggccgatggctgggacgagaggtagagccgcgagcgcgaaggagacagcgcatctgggagtgggtcccacttgccagtaaaagcaaaagttatgaactccggattatattataaatcgattgacTtttttatttatcaaacttttttttaagtttaattaaatttgtaaaaaaatatattaatcaatataaatatatcaaaatatatttaatattaaatttaatgaaactaatttaattttatagatgttgctaattttttctacaaacttgatcaaacatgagaaactttaagaacgaaaaaaaatcaaacgacttctaatataaacggaggaatggatggctgaattgaattcagggcaaaaattagcactgcaatctcgccgttaagtacctttttttttaccctcaaaagttaacaaaacacgtacaattctgggttgcttcacaaattacaacatgaacatacaaagtcagggaggggcacatcaatctggaacacatcagggtgtaggagagaatggaaaccaagggaaaaaaaaacaaggataaggtagatgagttagctgtgaagaaagtttttgtcagctgcatcggtggccgtcttctgaacattcagaactttgagatgatccctgaccagcagaggatgtcatgagtctctgcggagatgtagaatagaaccaagattagcatgaggcatataacttgcattttgcacaaacgatttcacaggcatagtgtactaaagagatgcttcaggatatgcatactatttactggaagtgtagagcgatcatgtccttgagttgctagacctatcataatatggaaaaaggttgagcagaactattctatggaacagccgttcaaaaaatgtacctgacgatcttaacatttctgaaggacagcatcacagtaagaatcaaggtaaccatcgcgaagcaaaggtgctccaaggaatggccgctgatgaagtaccggttcacactgtatacctttctgtcagcaaggccttcaaatcttgcaagaaggtaaaaacctgcaccaagatgccaatcaaacaacagttttcgttcaagcttttttttgtagaaagagtttctgctaacataaccttactacataagatgttaacggttacctgtggcaagaaaccaaaatcttgagtgtgtatattttggaggaaacaagaatagcattgcaggaattgcaatgcaaggagcggaattcaaaactacccataaccgcatatcatcaagaaccctgaaatcatcgagaacagagcaagaggactcattttattatctgatatactgacttcaacaatggaacacgctataggtgctggggcactattacctttcacatgcgctgctcaccagtatgagagataagagtgatagcaaacaagataacccagccctttcatcaactctttcaattaccaatatagacaacattgaagaagctgatatcatcatctgcgttcatagcatccagtgagcattcatatcgaggaaaaggatagatacatattcattaatagcattggttatacacgataacatgatagtcagattggctgcctagcacagtagtatggaaactcagacacatccttttttttctctttttgcctatggttaatacttcgatgatattaaggacattcaagtaggtgaactgcaTtttttgaacatgaactacttaatacagttttttctcccaatggactcgaagcataaaatgacaacatatcaaaaaaaattccaagtccagaaaccatggaaaacaccacgaaataagtaaacagtagatagggaaattacagaaagatgagatatttagataccggcaacctgtcccaaattaagcggtcatcatctggtttgaggtgatagtaagccgagccaaatgctgctgctacattcccagcatagaagaggaaccatcccaaggcctcccatctcaagctgcacaattccacagtaaaaacaaaatattaaacaccagatcttacctgctgatctgtttttctgttaaataaggatagcaaaataggaatatctctttaagcatcatgccctcaataccagcctagttgtacaataagcagtatttcaagaaacatgaagatcacacacttgttaaataaaatttcaacatcaaattaaaagattggagtacacgatttggtggaacaccctagctcaaattccattatatacccactctataatatagcaagattacagattattaaagcaattagatgaataaccatgtaatagctacaggcccaggcaaagttatactagcatagcagcaaaaatattatttcactggtcaccaacattacagtccatctttctctcagacagaagcagtttattagagccaggggagttcataaccaccctttcactttgttggtaactgtaaataagttcataaccaggggagtagtaaaatgagcagttatgaaacaattaggcacaaactggcctcctctctctaggttttcgagcataatcagggtaaattgacctcctatataattttgttcaagctcgtggtactcgattctcgaatactttaattacagctcttccctcgctgcaaatcacgaaacaatgtaacttcacgcacttctttataatcctttaggcgagacatttcaccgaacagcagccgagcaagggcaaagggcggagcgcgcacctgatgccgaagcacccactgccacagaggcagaggacgagcccgggcacgcccgccaggaggagcgggtaggcggtgagcacgttgagcgtgttggggacgccgaggaggttgcgcatgtcggcgaagaggtggagcgcgggggagtggcggagccgcggcgtggccaccaggagcagcgccgaggcgaggacggcccccccggcgagcgcgcggcgccggtgctcccggcggagcgccgcggccgcgaggtggccgaggccgaggccgagggcggcgcggccgccgccgccgcggtgggggtggtcggcggcggcgagatgcatgtggccagggggagtgctcagtggagcagaagaatgcggtgaattttttctggtgt More
CDS seq		atgcatctcgccgccgccgaccacccccaccgcggcggcggcggccgcgccgccctcggcctcggcctcggccacctcgcggccgcggcgctccgccgggagcaccggcgccgcgcgctcgccgggggggccgtcctcgcctcggcgctgctcctggtggccacgccgcggctccgccactcccccgcgctccacctcttcgccgacatgcgcaacctcctcggcgtccccaacacgctcaacgtgctcaccgcctacccgctcctcctggcgggcgtgcccgggctcgtcctctgcctctgtggcagtgggtgcttcggcatcagcttgagatgggaggccttgggatggttcctcttctatgctgggaatgtagcagcagcatttggctcggcttactatcacctcaaaccagatgatgaccgcttaatttgggacaggttgccgatgatgatatcagcttcttcaatgttgtctatattggtaattgaaagagttgatgaaagggctgggttatcttgtttgctatcactcttatctctcatactggtgagcagcgcatgtgaaagggttcttgatgatatgcggttatgggtagttttgaattccgctccttgcattgcaattcctgcaatgctattcttgtttcctccaaaatatacacactcaagattttggtttcttgccacaggtttttaccttcttgcaagatttgaaggccttgctgacagaaaggtatacagtgtgaaccggtacttcatcagcggccattccttggagcacctttgcttcgcgatggttaccttgattcttactgtgatgctgtccttcagaaatgttaagatcgtcagccatcggcctcgcggcgcgcgccatctctccaccgccgccggcgaccaaccgatccaccatcaccaccctccgaccaccagcgccgtcccatggaatcgcctcctccgcgcccacctcggccgttcccgcggggacctcgccctcgcgctctaccgccgcatgcgcgcgctctccccggcgctgccgaactcctacacgctccccctcgccctccgcgccgccgcctccccgcgcgtcgcctccgccgtccacgcccacgcccttcacctcggcctccacgcgcagcacgacgtcgctggccagatcctcgccgcctactccaggctcggccgcgccgccgacgcacgccgcgtgttcgacgcaatgccgccggggaggacgaccttccactggaacgcgctcatctccgcctactccagcggctgcgaccccgacgcggcgagggacgcgttcgcgcgcatggccgccgcagggacgcgtcccgacgccgtgacgtggacggcgctgctctcggcgcacgcgcggagcgggaagcacgcggatgtccttcagctgttcggtgaaatgcaaaggagcggctgcgaggggaacgccgagtccatggccgtggcgctctcggcgtgcccttacgccggcgaccttgcattggccaaagggaaggcgatacacggctgcggcgtcgtgaagggcctcatgcatggctacctgttcgtcaccaactcgttgatctgcatgtacggcaagctcggagagatggacgacgccaagaaagctttcagggacgcgacggcgaagaacaccgtgacatggaacaccctgatcaccagctacgccgcggctgggctgtgcgacgaggcgttggacgtgctcgcccagatggagcagatcggcggcacggtcgcgcccaatgtggtcagctggagcgcggtcatcggcgggttcgcgtcgtccggcgacactgaccgcgcactggagctgttccggcgaatgcagcagcaatggctctcgccgaacgtggtgaccatggcgaccgtcctctccgcttgcgtcgacctactggcgttacggctgggtcgagagctccatggccacgccatgaaagccgagctagataggcactcgctggtcgagaatgggctcatcaacatgtacgcgaagtgcgggaaggtctccggcgcacggaaggtgttcgacggaatgaagacgagggacctgatctcatggaactcgatgctggccggctacggcatgcacggcctgtgcgacgaagccctcgctctgttcaccgacatggccggagctacggttgagcccgacggcgtcaccttcgtcgccgtcctgtcggcgtgcggccacgccgggcgtgtcacggaggGccgccgcctgttcgatcgcatggtgagagcgcacaagatctccccatccatggagcactacacatgcatggtctacctcctcggccgcgccggcttgctccgggacgcgtcggagctcgtcgagacgatgccggtgagacctgacctgtgcgtgtggggagcattgctgaattcctgcaggattcatggtgatgcagccatggccgaggccaccattgccaatgttctgcaatccgaggaccagagcaccggcaaccacatgctgatcaccaacctgtacgccatgtgtggcatgtgggacgagtccaagaaggtgagggtgatgacgaaggaggccggattgaggaagaatccggggcagagctggattgaagtggacaacaaggtggtcgccttcgccgccgggagcgcgccgccgaatctcaccggagctgaggatgtcttcggaatgctcgatgatctatatgcagagatggaagatgaacaaagatga More
Protein seq		MHLAAADHPHRGGGGRAALGLGLGHLAAAALRREHRRRALAGGAVLASALLLVATPRLRHSPALHLFADMRNLLGVPNTLNVLTAYPLLLAGVPGLVLCLCGSGCFGISLRWEALGWFLFYAGNVAAAFGSAYYHLKPDDDRLIWDRLPMMISASSMLSILVIERVDERAGLSCLLSLLSLILVSSACERVLDDMRLWVVLNSAPCIAIPAMLFLFPPKYTHSRFWFLATGFYLLARFEGLADRKVYSVNRYFISGHSLEHLCFAMVTLILTVMLSFRNVKIVSHRPRGARHLSTAAGDQPIHHHHPPTTSAVPWNRLLRAHLGRSRGDLALALYRRMRALSPALPNSYTLPLALRAAASPRVASAVHAHALHLGLHAQHDVAGQILAAYSRLGRAADARRVFDAMPPGRTTFHWNALISAYSSGCDPDAARDAFARMAAAGTRPDAVTWTALLSAHARSGKHADVLQLFGEMQRSGCEGNAESMAVALSACPYAGDLALAKGKAIHGCGVVKGLMHGYLFVTNSLICMYGKLGEMDDAKKAFRDATAKNTVTWNTLITSYAAAGLCDEALDVLAQMEQIGGTVAPNVVSWSAVIGGFASSGDTDRALELFRRMQQQWLSPNVVTMATVLSACVDLLALRLGRELHGHAMKAELDRHSLVENGLINMYAKCGKVSGARKVFDGMKTRDLISWNSMLAGYGMHGLCDEALALFTDMAGATVEPDGVTFVAVLSACGHAGRVTEGRRLFDRMVRAHKISPSMEHYTCMVYLLGRAGLLRDASELVETMPVRPDLCVWGALLNSCRIHGDAAMAEATIANVLQSEDQSTGNHMLITNLYAMCGMWDESKKVRVMTKEAGLRKNPGQSWIEVDNKVVAFAAGSAPPNLTGAEDVFGMLDDLYAEMEDEQR
Function		Putative pentatricopeptide repeat-containing protein At1g17630 [UniProtKB/Swiss-Prot:Q9LNP2]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsLima_01g0006610	OsLima_01g0006610.01	Chr01	5141179	5146144	-	NAM
CDS seq	atgcatctcgccgccgccgaccacccccaccgcggcggcggcggccgcgccgccctcggcctcggcctcggccacctcgcggccgcggcgctccgccgggagcaccggcgccgcgcgctcgccgggggggccgtcctcgcctcggcgctgctcctggtggccacgccgcggctccgccactcccccgcgctccacctcttcgccgacatgcgcaacctcctcggcgtccccaacacgctcaacgtgctcaccgcctacccgctcctcctggcgggcgtgcccgggctcgtcctctgcctctgtggcagtgggtgcttcggcatcagcttgagatgggaggccttgggatggttcctcttctatgctgggaatgtagcagcagcatttggctcggcttactatcacctcaaaccagatgatgaccgcttaatttgggacaggttgccgatgatgatatcagcttcttcaatgttgtctatattggtaattgaaagagttgatgaaagggctgggttatcttgtttgctatcactcttatctctcatactggtgagcagcgcatgtgaaagggttcttgatgatatgcggttatgggtagttttgaattccgctccttgcattgcaattcctgcaatgctattcttgtttcctccaaaatatacacactcaagattttggtttcttgccacaggtttttaccttcttgcaagatttgaaggccttgctgacagaaaggtatacagtgtgaaccggtacttcatcagcggccattccttggagcacctttgcttcgcgatggttaccttgattcttactgtgatgctgtccttcagaaatgttaagatcgtcagccatcggcctcgcggcgcgcgccatctctccaccgccgccggcgaccaaccgatccaccatcaccaccctccgaccaccagcgccgtcccatggaatcgcctcctccgcgcccacctcggccgttcccgcggggacctcgccctcgcgctctaccgccgcatgcgcgcgctctccccggcgctgccgaactcctacacgctccccctcgccctccgcgccgccgcctccccgcgcgtcgcctccgccgtccacgcccacgcccttcacctcggcctccacgcgcagcacgacgtcgctggccagatcctcgccgcctactccaggctcggccgcgccgccgacgcacgccgcgtgttcgacgcaatgccgccggggaggacgaccttccactggaacgcgctcatctccgcctactccagcggctgcgaccccgacgcggcgagggacgcgttcgcgcgcatggccgccgcagggacgcgtcccgacgccgtgacgtggacggcgctgctctcggcgcacgcgcggagcgggaagcacgcggatgtccttcagctgttcggtgaaatgcaaaggagcggctgcgaggggaacgccgagtccatggccgtggcgctctcggcgtgcccttacgccggcgaccttgcattggccaaagggaaggcgatacacggctgcggcgtcgtgaagggcctcatgcatggctacctgttcgtcaccaactcgttgatctgcatgtacggcaagctcggagagatggacgacgccaagaaagctttcagggacgcgacggcgaagaacaccgtgacatggaacaccctgatcaccagctacgccgcggctgggctgtgcgacgaggcgttggacgtgctcgcccagatggagcagatcggcggcacggtcgcgcccaatgtggtcagctggagcgcggtcatcggcgggttcgcgtcgtccggcgacactgaccgcgcactggagctgttccggcgaatgcagcagcaatggctctcgccgaacgtggtgaccatggcgaccgtcctctccgcttgcgtcgacctactggcgttacggctgggtcgagagctccatggccacgccatgaaagccgagctagataggcactcgctggtcgagaatgggctcatcaacatgtacgcgaagtgcgggaaggtctccggcgcacggaaggtgttcgacggaatgaagacgagggacctgatctcatggaactcgatgctggccggctacggcatgcacggcctgtgcgacgaagccctcgctctgttcaccgacatggccggagctacggttgagcccgacggcgtcaccttcgtcgccgtcctgtcggcgtgcggccacgccgggcgtgtcacggaggGccgccgcctgttcgatcgcatggtgagagcgcacaagatctccccatccatggagcactacacatgcatggtctacctcctcggccgcgccggcttgctccgggacgcgtcggagctcgtcgagacgatgccggtgagacctgacctgtgcgtgtggggagcattgctgaattcctgcaggattcatggtgatgcagccatggccgaggccaccattgccaatgttctgcaatccgaggaccagagcaccggcaaccacatgctgatcaccaacctgtacgccatgtgtggcatgtgggacgagtccaagaaggtgagggtgatgacgaaggaggccggattgaggaagaatccggggcagagctggattgaagtggacaacaaggtggtcgccttcgccgccgggagcgcgccgccgaatctcaccggagctgaggatgtcttcggaatgctcgatgatctatatgcagagatggaagatgaacaaagatga More
Protein seq	MHLAAADHPHRGGGGRAALGLGLGHLAAAALRREHRRRALAGGAVLASALLLVATPRLRHSPALHLFADMRNLLGVPNTLNVLTAYPLLLAGVPGLVLCLCGSGCFGISLRWEALGWFLFYAGNVAAAFGSAYYHLKPDDDRLIWDRLPMMISASSMLSILVIERVDERAGLSCLLSLLSLILVSSACERVLDDMRLWVVLNSAPCIAIPAMLFLFPPKYTHSRFWFLATGFYLLARFEGLADRKVYSVNRYFISGHSLEHLCFAMVTLILTVMLSFRNVKIVSHRPRGARHLSTAAGDQPIHHHHPPTTSAVPWNRLLRAHLGRSRGDLALALYRRMRALSPALPNSYTLPLALRAAASPRVASAVHAHALHLGLHAQHDVAGQILAAYSRLGRAADARRVFDAMPPGRTTFHWNALISAYSSGCDPDAARDAFARMAAAGTRPDAVTWTALLSAHARSGKHADVLQLFGEMQRSGCEGNAESMAVALSACPYAGDLALAKGKAIHGCGVVKGLMHGYLFVTNSLICMYGKLGEMDDAKKAFRDATAKNTVTWNTLITSYAAAGLCDEALDVLAQMEQIGGTVAPNVVSWSAVIGGFASSGDTDRALELFRRMQQQWLSPNVVTMATVLSACVDLLALRLGRELHGHAMKAELDRHSLVENGLINMYAKCGKVSGARKVFDGMKTRDLISWNSMLAGYGMHGLCDEALALFTDMAGATVEPDGVTFVAVLSACGHAGRVTEGRRLFDRMVRAHKISPSMEHYTCMVYLLGRAGLLRDASELVETMPVRPDLCVWGALLNSCRIHGDAAMAEATIANVLQSEDQSTGNHMLITNLYAMCGMWDESKKVRVMTKEAGLRKNPGQSWIEVDNKVVAFAAGSAPPNLTGAEDVFGMLDDLYAEMEDEQR More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.081233	0.0	None

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0197500	RBH	0.236151	0.000000	0.000000
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os01g10090	RBH	0.090157	0.196957	0.0
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0197450	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0007200	RBH	0.000000	0.000000	0.552042
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_01g0006850	RBH	0.116457	0.0	2.400092
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0007160	RBH	0.000000	1.597690	0.516892
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0006700	RBH	0.000000	0.020815	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0006830	RBH	0.000000	0.000000	2.331209
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0087300	RBH	0.521045	1.030346	2.602306
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0006800	RBH	0.071849	0.057759	0.137548
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0088400	RBH	0	0	0
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_05g0007030	RBH	0.0	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0006790	RBH	0.193650	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0006830	RBH	1.125751	0.000000	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0006820	RBH	0.099127	0.085966	0.152648
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0006750	RBH	0.036884	0.499338	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G006820	RBH	0.000000	0.000000	1.161064
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0006680	RBH	0.784220	0.000000	1.998016

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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