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
OsKeNa_01g0003460		OGI:01009140 \| 16/16			KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)			Chr01:2714687-2718972		Homologues MicroCollinearity RGI-JBrowse
Gene Symbol		-
DNA seq		acccgtccgcatcccaaattcccagcaccagcagcgcccgccgccgccgccgccgtcgccgtgccgagctctcctcctccgccagatccgcactagcggctcggttattctctccggcacgagagacgagggttccccggcgagcgagcgagggccggcgatggcggagccggagcagccggagttcgcgcgcgagcggcacgtgctgtttctggaggctatggcgtcggagctccccgcggactacgcctcgcaggaggtcaaccacctcaccctcgcctacttcgccgtcgccggcctatctctccttcgtgagctcgacagtgtaagatccccgctctccgcctgatctgccctagcggttatcctctcgatccgtttcctgaattacgcgtaaattcgtttttttttagttatttgttgaactctagtctagactagatgtgcccgtgtgcaaagcttggatctttactttaccttgtgtggtcgctttgcttgcatttagtggaagcaaagttgcatctgtaggaataaaatcaatcagcagatttggtgcacttatggtaccatgaagtattttgaaacctcaaggatggctattggtagtatattcagagataaattagttgctgtatccataatgggagttgcaattgatctttattgtgacaaacacagggatccaaagtttgtggatagcagaatgccaagtgtggaagggtcttttcaattatttttttttttggaattcctgtaaagaacaactactagctgcaaggtttaagcactttagcccataagtggtcactgaccagtaaccagtctactcaaagcagttagagattattgcggttaggcaatttgcatctgtccggcaactagatcacaatatcacataactacattcgctttcgatttctagccaaactaagaggaaaggggcccatgtgatgtttctgtagcaacgaattggtccacgtcccttaattcggtctaaattccattcgtctttgtcttgtccatgggcagttgccttaatgctctgcacagttaggagccgcctagttggttatgatttaagttcatcatacttgatgccttgctcatgtaaacaacaaaaacatgatagcctcctgatatctccattctcaaattactagtaacttctaaaaaaacttatagcctcatgcaaatatttttttaccagtcttatcatgaaaattgtacctgtatgtattatgtattaaaacaagtaaccatgcctggttgctagctgaaatatttattgtgggaatttaagttcactttgtgccttgactgagttgactcttcaggaagaagtaatatactgagttgactgagtagtaatttgatgagttgtgtacttgtttgcccttttatactttctttaggttaacaaggatcaaatagccaaatggattttgtcttttcaagtacatcctaagacagacaatgaattagataatggtgagttttcctcagtacttatgtaataaagctctcaagatagctaattcatatttttcagatgcaatatattcattatatgacaatttatatgtttttaggacaattttatggattctgtggctctagaacaactcagtttccctcaactaacatgaaggtagatgtggctaattctcaagtcaacccttttttttttcacacatatcaatttgtcatttaatttttacattctgacagtttgaaatatgaattcatgcccttcctcaggacccttgccacaatggtagtcatcttgcaagcacttattctgcccttgctatcctgaagattgtaggttatgatttagcaaacattgataacaaggttcttttgtcctcaatgagaaacctccaacagccagatggaaggtatgcattttagttttggtctccatgctaattattcttgtaattatcctccaaaaatatctatgcatttacatctgctacctgtgtttagttttaactgtaccaccaaaagagtttcagccaactcacattctgtcttaagatttcataataccccatagttggcccacctccttgattattttttgtatgtgttgattgctacctttccatttgcatatgttttctctgcatgaatttagtcatgccatgtcgttcgacaaacttgatattggtaaatacctcctttctggtatatctctgtattgttggtcagtcttcaagcttgttcaatcagaatgttaattaatgtgctgtgatcctaactgcatgcatgtgatagaggtgtttgtgcatgtgcaatgcaatcttgcttgcctgtgagcatttcattgatttcactaagatggcttccatggttccattctgcaaacaactaaactccacgcaccgcttaaatgcattatcttattggccaacttgagaagcattttttttttagcttcatgcctactcatattggtgcggaaacagacctacgctttgtatactgtgcaggtgggttgcactgtcatttatatttagtatgctttcaattttatctttgtttgaaataacttgacacacttgtgttgtcttctcagctgcaatctgctcgatgctaaaagattggacaggaatggacaaggaaaaggccaagcaatacattcttagttgccaggttggcttacaacaattcctgatgcacttggttttgagacaccagtgttttgcaccatgctatttaaaatccttaattcttgtttctaccacatgcagtcatacgatggtggctttggcttggttcctggttcagaatctcatggtacagcttcttttaacctttgatgtgcttcttgtcctactgagtttgtcatttcatgtggcagttttcttcagagtttcagaatgcaataattcagctaaatttttgttttatttttttggagtcggttatgggtactcattgtttgtctttgtgttagtgagtcaggtggagggacattctgtgctgttgcagctttgtgcctgatgggtttcattcaagttgatttggcatcaaatttacaagaaccatcatcaattgatgtacgcttgctcctggagtggtgtcttcaggttaaattctgctcaaccatatatatctgctattaccatcaaaatctgccctttgatgtgatttataggactaacatatatttccaaaactggacagacactatatgcagtacaccaacccgttttaaatgtttctaatttagtagatatatgcatcaaccattcaattttcatttattcatgatggagaagtgcagcttgctcaatgacaccacaccatccagttgtttttaaaatctcccttatgtagagtaaaaaaaatgtgaatcataaacggatttagttagaaatgattaataaggactaggacgactttactagtagggaatcttaactgttttcactattatcatatagagacaagcggcagacggaggttttcaaggaagaaggaacaaatccagtgacacatgctatgcattttggtaaatacaccattcagagttatatatactaattgcctgacaatcaaatagcaaacttgggtaatctgtcttgctgccaatcaacactctgcaggattggaggtgtcctaaagatcatcggtgcataccgcttcattgatcatggtgctttgcgaagttttttgctctattgccaatcacctgtaatgacttcctctctaatcagcttaatttctcacattgatcaagttgcatctttactgatcatgtatgcccttgtttaccattgcaacagtatggaggttttacaaagtttttgtacgatcaattcccggatatctaccattcttactatggacttgccgctctttccttgctggaagaggaagggctggagccactctgcaccgaactggggatcctctctgctgcattgtagcttggaattgattgttcatcttctgtattcagtcaagttatggtgttctttaaagtccattcttgtaatctaatacaacatacagctgaaaagaatgcaagtaatctatagagttcgtttgtttgtttgggtaggcaggtcatgcaacattgtcttggataatatgattgtgaagtacagaggagcattctgtaaaggctatttcattttcagttagtcgaactaactgatattctgatagacagttgagttggctgagcagttctatcacttggaaagctattgaaaacaactcatgtaacagctgaacaaaattatcatctttattctgtttcttgatgtgcttcc More
CDS seq		atggcggagccggagcagccggagttcgcgcgcgagcggcacgtgctgtttctggaggctatggcgtcggagctccccgcggactacgcctcgcaggaggtcaaccacctcaccctcgcctacttcgccgtcgccggcctatctctccttcgtgagctcgacagtgttaacaaggatcaaatagccaaatggattttgtcttttcaagtacatcctaagacagacaatgaattagataatggacaattttatggattctgtggctctagaacaactcagtttccctcaactaacatgaaggacccttgccacaatggtagtcatcttgcaagcacttattctgcccttgctatcctgaagattgtaggttatgatttagcaaacattgataacaaggttcttttgtcctcaatgagaaacctccaacagccagatggaagtcatgccatgtcgttcgacaaacttgatattggtaaatacctcctttctggtatatctctgtattgttgcttcatgcctactcatattggtgcggaaacagacctacgctttgtatactgtgcagctgcaatctgctcgatgctaaaagattggacaggaatggacaaggaaaaggccaagcaatacattcttagttgccagtcatacgatggtggctttggcttggttcctggttcagaatctcatggtggagggacattctgtgctgttgcagctttgtgcctgatgggtttcattcaagttgatttggcatcaaatttacaagaaccatcatcaattgatgtacgcttgctcctggagtggtgtcttcagagacaagcggcagacggaggttttcaaggaagaaggaacaaatccagtgacacatgctatgcattttggattggaggtgtcctaaagatcatcggtgcataccgcttcattgatcatggtgctttgcgaagttttttgctctattgccaatcaccttatggaggttttacaaagtttttgtacgatcaattcccggatatctaccattcttactatggacttgccgctctttccttgctggaagaggaagggctggagccactctgcaccgaactggggatcctctctgctgcattgtag More
Protein seq		MAEPEQPEFARERHVLFLEAMASELPADYASQEVNHLTLAYFAVAGLSLLRELDSVNKDQIAKWILSFQVHPKTDNELDNGQFYGFCGSRTTQFPSTNMKDPCHNGSHLASTYSALAILKIVGYDLANIDNKVLLSSMRNLQQPDGSHAMSFDKLDIGKYLLSGISLYCCFMPTHIGAETDLRFVYCAAAICSMLKDWTGMDKEKAKQYILSCQSYDGGFGLVPGSESHGGGTFCAVAALCLMGFIQVDLASNLQEPSSIDVRLLLEWCLQRQAADGGFQGRRNKSSDTCYAFWIGGVLKIIGAYRFIDHGALRSFLLYCQSPYGGFTKFLYDQFPDIYHSYYGLAALSLLEEEGLEPLCTELGILSAAL
Function		Geranylgeranyl transferase type-1 subunit beta [UniProtKB/Swiss-Prot:O80642]

Transcripts

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsKeNa_01g0003460	OsKeNa_01g0003460.03	Chr01	2714735	2718861	+	NAM
CDS seq	atggcggagccggagcagccggagttcgcgcgcgagcggcacgtgctgtttctggaggctatggcgtcggagctccccgcggactacgcctcgcaggaggtcaaccacctcaccctcgcctacttcgccgtcgccggcctatctctccttcgtgagctcgacagtgttaacaaggatcaaatagccaaatggattttgtcttttcaagtacatcctaagacagacaatgaattagataatggacaattttatggattctgtggctctagaacaactcagtttccctcaactaacatgaaggacccttgccacaatggtagtcatcttgcaagcacttattctgcccttgctatcctgaagattgtaggttatgatttagcaaacattgataacaaggttcttttgtcctcaatgagaaacctccaacagccagatggaaggtatgcattttag More
Protein seq	MAEPEQPEFARERHVLFLEAMASELPADYASQEVNHLTLAYFAVAGLSLLRELDSVNKDQIAKWILSFQVHPKTDNELDNGQFYGFCGSRTTQFPSTNMKDPCHNGSHLASTYSALAILKIVGYDLANIDNKVLLSSMRNLQQPDGRYAF

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsKeNa_01g0003460	OsKeNa_01g0003460.02	Chr01	2714735	2718861	+	NAM
CDS seq	atggcggagccggagcagccggagttcgcgcgcgagcggcacgtgctgtttctggaggctatggcgtcggagctccccgcggactacgcctcgcaggaggtcaaccacctcaccctcgcctacttcgccgtcgccggcctatctctccttcgtgagctcgacagtgttaacaaggatcaaatagccaaatggattttgtcttttcaagtacatcctaagacagacaatgaattagataatggacaattttatggattctgtggctctagaacaactcagtttccctcaactaacatgaaggacccttgccacaatggtagtcatcttgcaagcacttattctgcccttgctatcctgaagattgtaggttatgatttagcaaacattgataacaaggttcttttgtcctcaatgagaaacctccaacagccagatggaagtcatgccatgtcgttcgacaaacttgatattggtaaatacctcctttctggtatatctctgtattgttgcttcatgcctactcatattggtgcggaaacagacctacgctttgtatactgtgcagctgcaatctgctcgatgctaaaagattggacaggaatggacaaggaaaaggccaagcaatacattcttagttgccagtcatacgatggtggctttggcttggttcctggttcagaatctcatggtggagggacattctgtgctgttgcagctttgtgcctgatgggtttcattcaagttgatttggcatcaaatttacaagaaccatcatcaattgatgtacgcttgctcctggagtggtgtcttcagagacaagcggcagacggaggttttcaaggaagaaggaacaaatccagtgacacatgctatgcattttggattggaggtgtcctaaagatcatcggtgcataccgcttcattgatcatggtgctttgcgaagttttttgctctattgccaatcaccttatggaggttttacaaagtttttgtacgatcaattcccggatatctaccattcttactatggacttgccgctctttccttgctggaagaggaagggctggagccactctgcaccgaactggggatcctctctgctgcattgtag More
Protein seq	MAEPEQPEFARERHVLFLEAMASELPADYASQEVNHLTLAYFAVAGLSLLRELDSVNKDQIAKWILSFQVHPKTDNELDNGQFYGFCGSRTTQFPSTNMKDPCHNGSHLASTYSALAILKIVGYDLANIDNKVLLSSMRNLQQPDGSHAMSFDKLDIGKYLLSGISLYCCFMPTHIGAETDLRFVYCAAAICSMLKDWTGMDKEKAKQYILSCQSYDGGFGLVPGSESHGGGTFCAVAALCLMGFIQVDLASNLQEPSSIDVRLLLEWCLQRQAADGGFQGRRNKSSDTCYAFWIGGVLKIIGAYRFIDHGALRSFLLYCQSPYGGFTKFLYDQFPDIYHSYYGLAALSLLEEEGLEPLCTELGILSAAL More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsKeNa_01g0003460	OsKeNa_01g0003460.01	Chr01	2714691	2718861	+	NAM
CDS seq	atggcggagccggagcagccggagttcgcgcgcgagcggcacgtgctgtttctggaggctatggcgtcggagctccccgcggactacgcctcgcaggaggtcaaccacctcaccctcgcctacttcgccgtcgccggcctatctctccttcgtgagctcgacagtgttaacaaggatcaaatagccaaatggattttgtcttttcaagtacatcctaagacagacaatgaattagataatggacaattttatggattctgtggctctagaacaactcagtttccctcaactaacatgaaggacccttgccacaatggtagtcatcttgcaagcacttattctgcccttgctatcctgaagattgtaggttatgatttagcaaacattgataacaaggttcttttgtcctcaatgagaaacctccaacagccagatggaagcttcatgcctactcatattggtgcggaaacagacctacgctttgtatactgtgcagctgcaatctgctcgatgctaaaagattggacaggaatggacaaggaaaaggccaagcaatacattcttagttgccagtcatacgatggtggctttggcttggttcctggttcagaatctcatggtggagggacattctgtgctgttgcagctttgtgcctgatgggtttcattcaagttgatttggcatcaaatttacaagaaccatcatcaattgatgtacgcttgctcctggagtggtgtcttcagagacaagcggcagacggaggttttcaaggaagaaggaacaaatccagtgacacatgctatgcattttggattggaggtgtcctaaagatcatcggtgcataccgcttcattgatcatggtgctttgcgaagttttttgctctattgccaatcaccttatggaggttttacaaagtttttgtacgatcaattcccggatatctaccattcttactatggacttgccgctctttccttgctggaagaggaagggctggagccactctgcaccgaactggggatcctctctgctgcattgtag More
Protein seq	MAEPEQPEFARERHVLFLEAMASELPADYASQEVNHLTLAYFAVAGLSLLRELDSVNKDQIAKWILSFQVHPKTDNELDNGQFYGFCGSRTTQFPSTNMKDPCHNGSHLASTYSALAILKIVGYDLANIDNKVLLSSMRNLQQPDGSFMPTHIGAETDLRFVYCAAAICSMLKDWTGMDKEKAKQYILSCQSYDGGFGLVPGSESHGGGTFCAVAALCLMGFIQVDLASNLQEPSSIDVRLLLEWCLQRQAADGGFQGRRNKSSDTCYAFWIGGVLKIIGAYRFIDHGALRSFLLYCQSPYGGFTKFLYDQFPDIYHSYYGLAALSLLEEEGLEPLCTELGILSAAL More

Gene	Transcript	Chromosome	Start	End	Strand	Source
OsKeNa_01g0003460	OsKeNa_01g0003460.04	Chr01	2714687	2718972	+	IsoSeq
CDS seq	ccgtccgcatcccaaattcccagcaccagcagcgcccgccgccgccgccgccgtcgccgtgccgagctctcctcctccgccagatccgcactagcggctcggttattctctccggcacgagagacgagggttccccggcgagcgagcgagggccggcgatggcggagccggagcagccggagttcgcgcgcgagcggcacgtgctgtttctggaggctatggcgtcggagctccccgcggactacgcctcgcaggaggtcaaccacctcaccctcgcctacttcgccgtcgccggcctatctctccttcgtgagctcgacagtgttaacaaggatc More
Protein seq	PSASQIPSTSSARRRRRRRRAELSSSARSALAARLFSPARETRVPRRASEGRRWRSRSSRSSRASGTCCFWRLWRRSSPRTTPRRRSTTSPSPTSPSPAYLSFVSSTVLTRI

Event Type	Chromosome	Start	End	Strand	Alternative mRNAs	Total mRNAs	Source
A3	Chr01	2717488	2717657	+	OsKeNa_01g0003460.04	OsKeNa_01g0003460.01,OsKeNa_01g0003460.04,OsKeNa_01g0003460.02,OsKeNa_01g0003460.03	All
RI	Chr01	2716445	2717181	+	OsKeNa_01g0003460.04	OsKeNa_01g0003460.01,OsKeNa_01g0003460.04	All
RI	Chr01	2716445	2717344	+	OsKeNa_01g0003460.03	OsKeNa_01g0003460.03,OsKeNa_01g0003460.04	All
SE	Chr01	2716584	2717126	+	OsKeNa_01g0003460.02	OsKeNa_01g0003460.02,OsKeNa_01g0003460.01	All

Expression

	Leaf	Root	Panicle
FPKM	0.294431	1.535562	0.965141

Homologues

Genome & Annotation	Homologs	Type	Expression(FPKM)
Genome & Annotation	Homologs	Type	Leaf	Root	Panicle
Nipponbare \| IRGSP 1.0 \| Gramene(+IsoSeq)	OsNip_01g0150100	RBH	1.321704	0.460248	2.773793
Nipponbare \| IRGSP 1.0 \| MSU	LOC_Os01g05680	RBH	0.166192	0.524606	0.411050
Nipponbare \| IRGSP 1.0 \| RAP-db	Os01g0150100	RBH	None	None	None
Azucena \| AzucenaRS1 \| Gramene(+IsoSeq)	OsAzu_01g0003630	RBH	0.122565	1.692992	3.954034
KETAN NANGKA \| Os128077RS1 \| Gramene(+IsoSeq)	NA	NA	NA	NA	NA
CHAO MEO \| Os132278RS1 \| Gramene(+IsoSeq)	OsCMeo_01g0003610	SBH	1.347394	23.056200	12.605496
ARC 10497 \| Os117425RS1 \| Gramene(+IsoSeq)	OsARC_01g0003290	SBH	0.045135	1.180108	None
PR 106 \| Os127742RS1 \| Gramene(+IsoSeq)	OsPr106_01g0003510	RBH	3.617102	22.207834	10.573362
Minghui 63 \| MH63RS3 \| HZAU	OsMH63_01G0046700	SBH	9.59436	7.9674395	9.0453085
IR 64 \| OsIR64RS1 \| Gramene(+IsoSeq)	OsIR64_01g0003420	RBH	0.095892	0.424919	0.866245
Zhenshan 97 \| ZS97RS3 \| HZAU	OsZS97_01G0048100	RBH	5.8668715	10.345772	22.733634
LIMA \| Os127564RS1 \| Gramene(+IsoSeq)	OsLima_01g0003240	RBH	0.177765	0.000000	None
KHAO YAI GUANG \| Os127518RS1 \| Gramene(+IsoSeq)	OsKYG_01g0003350	RBH	0.153574	2.889673	None
GOBOL SAIL \| Os132424RS1 \| Gramene(+IsoSeq)	OsGoSa_01g0031990	SBH	1.267882	3.387155	None
LIU XU \| Os125827RS1 \| Gramene(+IsoSeq)	OsLiXu_01g0003530	RBH	0.306714	0.058413	0.113796
LARHA MUGAD \| Os125619RS1 \| Gramene(+IsoSeq)	OsLaMu_01g0003390	RBH	0.192026	0.896729	None
N22 \| OsN22RS2 \| Gramene(+IsoSeq)	OsN22_01G003570	RBH	0.280848	3.428406	2.858830
NATEL BORO \| Os127652RS1 \| Gramene(+IsoSeq)	OsNaBo_01g0003420	RBH	0.109494	21.563763	8.029791

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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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