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
LOC_Os01g39970		OGI:01070220 \| 14/16			Nipponbare \| IRGSP 1.0 \| MSU			Chr01:22538988-22542228		Homologues MicroCollinearity RGI-JBrowse RGAP Ricevarmap2
Gene Symbol		RLCK39, OsRLCK39
DNA seq		GGGGAGGGAGGAGGAGGCCATTGCAGAGTTTGAGAGGAAGGTTGGAGGCAAGGAAGAGAGACAGAGGAGAAGGAAGAGCAGGAGGGGAGGGAAAAGGAAAACCCTTTCTCTCTCTCTCTCTCAGCCTCTCTCTCCCTCTCTCTTCTTCTCCTTCCTTGCACCACCGTCCTACTCACCGTCGCATCATCCACTGATCCGGCCGGCGATATCACCTCCATCCATCCATCACATTACGGTCGGCGTCGGCGGCGGCGACGACGAAGGCGGGTGAGATCTCACCGGAGAAGTGCAGGCGGGCAGGATGCAAGGAGGAGGGCCACTCAGCCCCGACGAGCACCGGGCCACCTCGCCGCCGGGGATAATGCACCACCAGCCGGCGATGACGATCGTCGTCGCCGTGGACCGTGACCGGAACAGCCAGCTCGCCGTGAAGTGGGTCGTCGACCACCTCCTCACCGGCGCCTCCAACATCATCCTCCTCCACATCGCCGTCCACCCCCCTGCCGCCAACCGTACGTCGATCGCCGGATCAGCCATTGCCATGCGTCTCTCTGCTGCAACTGCAAGAGATCGTAAAACTGATGTGCATTTTTTGTTTTTTTTTTTGGTGACGTAGATGGATTCGCCATGGCCGAGGCGACGCATGGCGCGTTGGAGGCCGAGATGAGGGAGATCTTTGTCCCCTTCAGAGGATTCTGCACCAGGAATGGGGTAATCAAATATTTAGTTTCAGATCAACACAAGAAATTAATTCTTTCAGATCAAAGACATGAACAAAAAAAAATACTTAATTACGAGAACGCATTTTGTTTTCCATTGTTGATCGATCAGGTGCATGTATCGGAGTTGGTACTGGAAGAGGCAGACGTGTCAAAGGCCTTAATAGAGTTCATCACCGTGAACAAGATCCAGAGCATCGCGCTCGGCGCATCCAACAGAAATGCATTCACCAAGTAAATCAATCAAAGATCAATAATTAGTTTCGTTTTGATTTTGATCCGATTTCGATCCAATTTTAAGGTGTTGTTCTTGGTGGTGATGGTGGTGCTGCATTGTTTGATGGTCAGGAAATTCAAGAACGCCGACGTGCCGTCCAGCCTGATGAAGGGCGCGCCGGACTACTGCAACATCTACGTGGTGGCGAAGGGCAAGTCGGTGAACGTGAGGCTCGCCAAGTGCGGCGTCGATGGCGGTTGCGGCGGTGGCGGTGGCTACGAGGGCGACTCATCGATCAGGAGCCTGTACACGAGGAGGTGCTCGAGGGGGAAGCTGCCGCCGGCGACGCCGTCGCCGGACTCGTCGAGGCGGTCGGTGGACAGTCGCACCCTGCCGGAGCTCACCACGCGGCCGCCGTTCCGCGAGCGCTCGCTCCCGTCCTCGTCGTCCAAGCCCGTCGTGCTGTCCAGCAGGGCGGCGCCCGACTGCGGCGGCGGCGGCGTCGACGGGTCGTACCGCTCCACGAGGCGGTCCGTGTCGAACGAGTCCTTCGTGGGCGACCTCGACTTCGGCCAGAGCTCGCGCTTCTCCTCCATGGACTTCTGCGACAGCCTCGACATGTCGTCGCTCTCCGCCAGCCCACGGGAGAGCAGCTCGCCTCTCTCCGCCGTGCGTTCTTGGACCACTTCGACTGCGACGCCATTGCTGCGACGCCATTGCTGACGTGGGTGTGTGTGCAGCCGCAGCGCGAGGTGGAGGTGGAGATGCGGCGGCTGAGGCTGGAGCTGAAGCAGACGATGGACATGTACAACGCGGCGTGCCGGGAGGCGATCAACGCGAAGCAGCGGACCAAGGAGCTGCAGCTGCTGAAGCTGGAGGAGGCGCGGCGGCTGGAGGAGGCGCGGCACGCGGAGGAGGCGGCGCTGGCGATGGCGGAGATGGAGAAGACCAAGTGCCGCGCGGCCATGGAGGCGGCCGAGGCGGCGCAGCGACTGGCCGACCTGGAGGCCCAGCGGCGTCGCAACGCCGAGGTGCGCGCCCGCCGCGAGGCCGACGAGAAGGTCCGCGCCCTGGACGCCATCTCCAGCCACGACTTCCGCTACCGCCGCTACAACATCGACGACATCGAGCTCGCCACCGAGCGCTTCTCCGACGAGCTCAAGATCGGCGAGGGCGGCTACGGCCCCGTCTACCGCGCCTCCCTCGACCACACCCCGGTGGCCATCAAGGTGCTCCGCCCCGACGCGCAGCAGGGCCGGAAGCAGTTCCAGCAGGAGGTGGAGGTGCTCAGCTGCATCCGCCACCCAAACATGGTGCTCCTCCTCGGCGCCTGCCCGGACTACGGCTGCCTCGTCTACGAGTACATGGACAACGGCAGCCTCGAGGACCGCCTGTTCCGCCGCGGCGGCACGCCGCCGATCCCGTGGAGCCAGCGGTTCAGGATCTCGGCGGAGATCGCCACCGCGCTGCTGTTCCTCCACCAGACCAAGCCGGAGCCGCTGGTGCACCGCGACCTGAAGCCGGCCAACATCCTGCTCGACCGCAACTACGTCAGCAAGATCAGCGACGTCGGGCTGGCGCGCCTCGTGCCGCCGGCGGTGGCGGACAGCGTGACGCAGTACCGGCTGACGGCGACGGCGGGGACCTTCTGCTACATCGACCCGGAGTACCAGCAGACGGGGAAGCTGGGCGTCAAGTCCGACATCTACTCCCTCGGCGTGCTGCTGCTGCAGGTGCTCACCGCGCGGCCGCCCATGGGCCTCACCCACCACGTCGAGAAGGCCATCGACGCCGGCACCTTCGCCCAGATGCTCGACGTCACCGTCAAGGACTGGCCCGTCGACGACGCCATCGGCTTCGCCAAGCTCGCCCTCAAGTGCACCGAAATGCGCCGGAGGGACCGCCCGGACCTCGCCACCGTCATCCTGCCGGAGCTCAACCGCCTCAGGAACCTCGGACACGCCTACGAGGCGCGCATGAGCGCCGCCGCCGCCGACGCCGCCGCGCACGCCCAGGACAACGTCGGCTCGCCGACGGTGGTGGGCGCGTCGTGGAGAACGGCGGAGAGCTAAGCTAGCGGGAGGCCGTGTCAGTTATTTTAGAGTCACAGGAGAGGGTGGAGTTCACACGGTACATTTACGGTCTTTTTTTGTCGGTGTAAATCCTTAAATACCTTGGTGTTTGTACAGTTGACAAAAAAAATTAACATGTTCTGCGGTGGTTGGCTCAAAATTTTGAGGTGTCCGAATGATTCTTTTTTCCTGGTTATACAGCAGAAAGATTAAAAAAAAATTACGGTAATGAC More
CDS seq		ATGCAAGGAGGAGGGCCACTCAGCCCCGACGAGCACCGGGCCACCTCGCCGCCGGGGATAATGCACCACCAGCCGGCGATGACGATCGTCGTCGCCGTGGACCGTGACCGGAACAGCCAGCTCGCCGTGAAGTGGGTCGTCGACCACCTCCTCACCGGCGCCTCCAACATCATCCTCCTCCACATCGCCGTCCACCCCCCTGCCGCCAACCATGGATTCGCCATGGCCGAGGCGACGCATGGCGCGTTGGAGGCCGAGATGAGGGAGATCTTTGTCCCCTTCAGAGGATTCTGCACCAGGAATGGGGTGCATGTATCGGAGTTGGTACTGGAAGAGGCAGACGTGTCAAAGGCCTTAATAGAGTTCATCACCGTGAACAAGATCCAGAGCATCGCGCTCGGCGCATCCAACAGAAATGCATTCACCAAGAAATTCAAGAACGCCGACGTGCCGTCCAGCCTGATGAAGGGCGCGCCGGACTACTGCAACATCTACGTGGTGGCGAAGGGCAAGTCGGTGAACGTGAGGCTCGCCAAGTGCGGCGTCGATGGCGGTTGCGGCGGTGGCGGTGGCTACGAGGGCGACTCATCGATCAGGAGCCTGTACACGAGGAGGTGCTCGAGGGGGAAGCTGCCGCCGGCGACGCCGTCGCCGGACTCGTCGAGGCGGTCGGTGGACAGTCGCACCCTGCCGGAGCTCACCACGCGGCCGCCGTTCCGCGAGCGCTCGCTCCCGTCCTCGTCGTCCAAGCCCGTCGTGCTGTCCAGCAGGGCGGCGCCCGACTGCGGCGGCGGCGGCGTCGACGGGTCGTACCGCTCCACGAGGCGGTCCGTGTCGAACGAGTCCTTCGTGGGCGACCTCGACTTCGGCCAGAGCTCGCGCTTCTCCTCCATGGACTTCTGCGACAGCCTCGACATGTCGTCGCTCTCCGCCAGCCCACGGGAGAGCAGCTCGCCTCTCTCCGCCCCGCAGCGCGAGGTGGAGGTGGAGATGCGGCGGCTGAGGCTGGAGCTGAAGCAGACGATGGACATGTACAACGCGGCGTGCCGGGAGGCGATCAACGCGAAGCAGCGGACCAAGGAGCTGCAGCTGCTGAAGCTGGAGGAGGCGCGGCGGCTGGAGGAGGCGCGGCACGCGGAGGAGGCGGCGCTGGCGATGGCGGAGATGGAGAAGACCAAGTGCCGCGCGGCCATGGAGGCGGCCGAGGCGGCGCAGCGACTGGCCGACCTGGAGGCCCAGCGGCGTCGCAACGCCGAGGTGCGCGCCCGCCGCGAGGCCGACGAGAAGGTCCGCGCCCTGGACGCCATCTCCAGCCACGACTTCCGCTACCGCCGCTACAACATCGACGACATCGAGCTCGCCACCGAGCGCTTCTCCGACGAGCTCAAGATCGGCGAGGGCGGCTACGGCCCCGTCTACCGCGCCTCCCTCGACCACACCCCGGTGGCCATCAAGGTGCTCCGCCCCGACGCGCAGCAGGGCCGGAAGCAGTTCCAGCAGGAGGTGGAGGTGCTCAGCTGCATCCGCCACCCAAACATGGTGCTCCTCCTCGGCGCCTGCCCGGACTACGGCTGCCTCGTCTACGAGTACATGGACAACGGCAGCCTCGAGGACCGCCTGTTCCGCCGCGGCGGCACGCCGCCGATCCCGTGGAGCCAGCGGTTCAGGATCTCGGCGGAGATCGCCACCGCGCTGCTGTTCCTCCACCAGACCAAGCCGGAGCCGCTGGTGCACCGCGACCTGAAGCCGGCCAACATCCTGCTCGACCGCAACTACGTCAGCAAGATCAGCGACGTCGGGCTGGCGCGCCTCGTGCCGCCGGCGGTGGCGGACAGCGTGACGCAGTACCGGCTGACGGCGACGGCGGGGACCTTCTGCTACATCGACCCGGAGTACCAGCAGACGGGGAAGCTGGGCGTCAAGTCCGACATCTACTCCCTCGGCGTGCTGCTGCTGCAGGTGCTCACCGCGCGGCCGCCCATGGGCCTCACCCACCACGTCGAGAAGGCCATCGACGCCGGCACCTTCGCCCAGATGCTCGACGTCACCGTCAAGGACTGGCCCGTCGACGACGCCATCGGCTTCGCCAAGCTCGCCCTCAAGTGCACCGAAATGCGCCGGAGGGACCGCCCGGACCTCGCCACCGTCATCCTGCCGGAGCTCAACCGCCTCAGGAACCTCGGACACGCCTACGAGGCGCGCATGAGCGCCGCCGCCGCCGACGCCGCCGCGCACGCCCAGGACAACGTCGGCTCGCCGACGGTGGTGGGCGCGTCGTGGAGAACGGCGGAGAGCTAA More
Protein seq		MQGGGPLSPDEHRATSPPGIMHHQPAMTIVVAVDRDRNSQLAVKWVVDHLLTGASNIILLHIAVHPPAANHGFAMAEATHGALEAEMREIFVPFRGFCTRNGVHVSELVLEEADVSKALIEFITVNKIQSIALGASNRNAFTKKFKNADVPSSLMKGAPDYCNIYVVAKGKSVNVRLAKCGVDGGCGGGGGYEGDSSIRSLYTRRCSRGKLPPATPSPDSSRRSVDSRTLPELTTRPPFRERSLPSSSSKPVVLSSRAAPDCGGGGVDGSYRSTRRSVSNESFVGDLDFGQSSRFSSMDFCDSLDMSSLSASPRESSSPLSAPQREVEVEMRRLRLELKQTMDMYNAACREAINAKQRTKELQLLKLEEARRLEEARHAEEAALAMAEMEKTKCRAAMEAAEAAQRLADLEAQRRRNAEVRARREADEKVRALDAISSHDFRYRRYNIDDIELATERFSDELKIGEGGYGPVYRASLDHTPVAIKVLRPDAQQGRKQFQQEVEVLSCIRHPNMVLLLGACPDYGCLVYEYMDNGSLEDRLFRRGGTPPIPWSQRFRISAEIATALLFLHQTKPEPLVHRDLKPANILLDRNYVSKISDVGLARLVPPAVADSVTQYRLTATAGTFCYIDPEYQQTGKLGVKSDIYSLGVLLLQVLTARPPMGLTHHVEKAIDAGTFAQMLDVTVKDWPVDDAIGFAKLALKCTEMRRRDRPDLATVILPELNRLRNLGHAYEARMSAAAADAAAHAQDNVGSPTVVGASWRTAES
Function		U-box domain-containing protein 35 [UniProtKB/Swiss-Prot:Q9SW11]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
LOC_Os01g39970	LOC_Os01g39970.1	Chr01	22538988	22542228	+	MSU_osa1r7
CDS seq	ATGCAAGGAGGAGGGCCACTCAGCCCCGACGAGCACCGGGCCACCTCGCCGCCGGGGATAATGCACCACCAGCCGGCGATGACGATCGTCGTCGCCGTGGACCGTGACCGGAACAGCCAGCTCGCCGTGAAGTGGGTCGTCGACCACCTCCTCACCGGCGCCTCCAACATCATCCTCCTCCACATCGCCGTCCACCCCCCTGCCGCCAACCATGGATTCGCCATGGCCGAGGCGACGCATGGCGCGTTGGAGGCCGAGATGAGGGAGATCTTTGTCCCCTTCAGAGGATTCTGCACCAGGAATGGGGTGCATGTATCGGAGTTGGTACTGGAAGAGGCAGACGTGTCAAAGGCCTTAATAGAGTTCATCACCGTGAACAAGATCCAGAGCATCGCGCTCGGCGCATCCAACAGAAATGCATTCACCAAGAAATTCAAGAACGCCGACGTGCCGTCCAGCCTGATGAAGGGCGCGCCGGACTACTGCAACATCTACGTGGTGGCGAAGGGCAAGTCGGTGAACGTGAGGCTCGCCAAGTGCGGCGTCGATGGCGGTTGCGGCGGTGGCGGTGGCTACGAGGGCGACTCATCGATCAGGAGCCTGTACACGAGGAGGTGCTCGAGGGGGAAGCTGCCGCCGGCGACGCCGTCGCCGGACTCGTCGAGGCGGTCGGTGGACAGTCGCACCCTGCCGGAGCTCACCACGCGGCCGCCGTTCCGCGAGCGCTCGCTCCCGTCCTCGTCGTCCAAGCCCGTCGTGCTGTCCAGCAGGGCGGCGCCCGACTGCGGCGGCGGCGGCGTCGACGGGTCGTACCGCTCCACGAGGCGGTCCGTGTCGAACGAGTCCTTCGTGGGCGACCTCGACTTCGGCCAGAGCTCGCGCTTCTCCTCCATGGACTTCTGCGACAGCCTCGACATGTCGTCGCTCTCCGCCAGCCCACGGGAGAGCAGCTCGCCTCTCTCCGCCCCGCAGCGCGAGGTGGAGGTGGAGATGCGGCGGCTGAGGCTGGAGCTGAAGCAGACGATGGACATGTACAACGCGGCGTGCCGGGAGGCGATCAACGCGAAGCAGCGGACCAAGGAGCTGCAGCTGCTGAAGCTGGAGGAGGCGCGGCGGCTGGAGGAGGCGCGGCACGCGGAGGAGGCGGCGCTGGCGATGGCGGAGATGGAGAAGACCAAGTGCCGCGCGGCCATGGAGGCGGCCGAGGCGGCGCAGCGACTGGCCGACCTGGAGGCCCAGCGGCGTCGCAACGCCGAGGTGCGCGCCCGCCGCGAGGCCGACGAGAAGGTCCGCGCCCTGGACGCCATCTCCAGCCACGACTTCCGCTACCGCCGCTACAACATCGACGACATCGAGCTCGCCACCGAGCGCTTCTCCGACGAGCTCAAGATCGGCGAGGGCGGCTACGGCCCCGTCTACCGCGCCTCCCTCGACCACACCCCGGTGGCCATCAAGGTGCTCCGCCCCGACGCGCAGCAGGGCCGGAAGCAGTTCCAGCAGGAGGTGGAGGTGCTCAGCTGCATCCGCCACCCAAACATGGTGCTCCTCCTCGGCGCCTGCCCGGACTACGGCTGCCTCGTCTACGAGTACATGGACAACGGCAGCCTCGAGGACCGCCTGTTCCGCCGCGGCGGCACGCCGCCGATCCCGTGGAGCCAGCGGTTCAGGATCTCGGCGGAGATCGCCACCGCGCTGCTGTTCCTCCACCAGACCAAGCCGGAGCCGCTGGTGCACCGCGACCTGAAGCCGGCCAACATCCTGCTCGACCGCAACTACGTCAGCAAGATCAGCGACGTCGGGCTGGCGCGCCTCGTGCCGCCGGCGGTGGCGGACAGCGTGACGCAGTACCGGCTGACGGCGACGGCGGGGACCTTCTGCTACATCGACCCGGAGTACCAGCAGACGGGGAAGCTGGGCGTCAAGTCCGACATCTACTCCCTCGGCGTGCTGCTGCTGCAGGTGCTCACCGCGCGGCCGCCCATGGGCCTCACCCACCACGTCGAGAAGGCCATCGACGCCGGCACCTTCGCCCAGATGCTCGACGTCACCGTCAAGGACTGGCCCGTCGACGACGCCATCGGCTTCGCCAAGCTCGCCCTCAAGTGCACCGAAATGCGCCGGAGGGACCGCCCGGACCTCGCCACCGTCATCCTGCCGGAGCTCAACCGCCTCAGGAACCTCGGACACGCCTACGAGGCGCGCATGAGCGCCGCCGCCGCCGACGCCGCCGCGCACGCCCAGGACAACGTCGGCTCGCCGACGGTGGTGGGCGCGTCGTGGAGAACGGCGGAGAGCTAA More
Protein seq	MQGGGPLSPDEHRATSPPGIMHHQPAMTIVVAVDRDRNSQLAVKWVVDHLLTGASNIILLHIAVHPPAANHGFAMAEATHGALEAEMREIFVPFRGFCTRNGVHVSELVLEEADVSKALIEFITVNKIQSIALGASNRNAFTKKFKNADVPSSLMKGAPDYCNIYVVAKGKSVNVRLAKCGVDGGCGGGGGYEGDSSIRSLYTRRCSRGKLPPATPSPDSSRRSVDSRTLPELTTRPPFRERSLPSSSSKPVVLSSRAAPDCGGGGVDGSYRSTRRSVSNESFVGDLDFGQSSRFSSMDFCDSLDMSSLSASPRESSSPLSAPQREVEVEMRRLRLELKQTMDMYNAACREAINAKQRTKELQLLKLEEARRLEEARHAEEAALAMAEMEKTKCRAAMEAAEAAQRLADLEAQRRRNAEVRARREADEKVRALDAISSHDFRYRRYNIDDIELATERFSDELKIGEGGYGPVYRASLDHTPVAIKVLRPDAQQGRKQFQQEVEVLSCIRHPNMVLLLGACPDYGCLVYEYMDNGSLEDRLFRRGGTPPIPWSQRFRISAEIATALLFLHQTKPEPLVHRDLKPANILLDRNYVSKISDVGLARLVPPAVADSVTQYRLTATAGTFCYIDPEYQQTGKLGVKSDIYSLGVLLLQVLTARPPMGLTHHVEKAIDAGTFAQMLDVTVKDWPVDDAIGFAKLALKCTEMRRRDRPDLATVILPELNRLRNLGHAYEARMSAAAADAAAHAQDNVGSPTVVGASWRTAES More

Event Type

Chromosome

Start

End

Strand

Alternative mRNAs

Total mRNAs

Source

Expression

	Leaf	Root	Panicle
FPKM	0.174897	0.000000	10.534961

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0581400	RBH	0.259728	0.000000	41.099422
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os12g24550	RBH	0.000000	0.200630	0.200099
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0581400	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0022900	RBH	0.0	0.0	13.611523
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	OsKeNa_01g0022500	RBH	0.000000	0.0	31.008999
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0022830	RBH	0.0	0.0	46.750305
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0022220	RBH	0.000000	0.0	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0021950	RBH	0.000000	0.0	26.383673
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0377000	RBH	13.521719	2.0389015	3.6997935
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0021900	RBH	2.067067	0.083541	15.664396
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0707900	SBH	1.339769	2.7295165	0.9291545
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_01g0021870	SBH	0.782381	0.0	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0021810	RBH	0.000000	0.0	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0022080	RBH	0.000000	0.0	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0022150	RBH	0.000000	0.0	4.596161
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0021930	RBH	0.000000	0.0	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G022240	RBH	0.000000	0.0	9.392284
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0021930	RBH	0.0	0.0	76.316483

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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