RetrogeneDB ID:

retro_oniv_18

Retrocopy
location
Organism:Indian wild rice (Oryza nivara)
Coordinates:6:13144300..13146298(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ONIVA06G15870
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ONIVA04G20520
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_oniv_18
ATGGTGGCCGCCGGCGAGGCAGGTCAGCACCACGAGTCCGGCGGCGCGGAGTGGAGGGTGACGGTGGCGGAGGCGCCGGA
GGCGGAGGTGGAGCATGAGAACGCGAAAGGCGCGCGGCGGGGGTGCTGCTGCGCCCCGGCGGCGGCGGCGTGGGTGCTGT
GGTGGCTGGCCGCGCCGTGGAAGTGGGTGGCCAGGTTCGGGAGGACGGCGTGGAAGGTCGGCGCCGACGACCCGAGGAGG
GTGGTGCACGGGTTCAAGGTGGCGCTGGCGCTTACCTTGTGCTCCGCCTTCTACTACGTCCGCCCGCTCTACGTCTTCAC
CGGCCAAACCGCCATGTGGGCCGTCCTCACCGTCGTCGTCGTCTTCGAGTACACCGTCGGCGGCTGCATGTACAAGGGGC
TGAACAGGGCGATGGCGACGGTGGCCGGCGGCGCGCTGGCGCTCGGCGTGCACTGGGTCGCCGACAAGTCCGGTGACGAC
GCGGAGCCGTTCGTCCTCACCGCCTCGCTCTTCGTGCTGGCCGCGGCGGCGTCCTTCTCCCGCTTCATCCCCACGCTCAA
GGCGCGGTTCGACTACGGCGTCACCATCTTCATCCTCACCTACAGCCTCGTCGCCGTGTCGGGGTACCGCGTCGACACGC
TGGTCACCATGGCGCAGCAGCGCCTCATCACCATCGCCATCGGAGCGTTCATCTGCTTCGCCGTCTGCACGCTCGTCTTC
CCGGTCTGGGCCGGGCAGGAGCTGCACGTCCTCGTCGCGCGCAACATGGACAAGCTCGCCGCCGCCATCGAGGCCTGCGT
CGACGACTACTTCTCCTCCGCCGAGCACGCTGGCGGTGGCGGCGACGCCGCCACGGCGCTGTCGGAGAAGGCGCGCGGGT
ACAGGGCTGTGCTTAACGCCAAGGCGTCGGAGGACTCGCTGGCGAACCTGGCGAGGTGGGAGCCCGGCCATGGCAAGTTC
GGCTTCCGCCACCCGTACGGCCAGTACCAGAATGTCGGCGCCGCCATGCGCTGCTGCGCCTACTGCATCGACGCCCTCGC
GGCCTGCGTCGGCGCGGGCGGGCAGGCGCCGGCGCACGTCAAGAGGCACCTCGCCGGCGCCTGCGTCGCCCTGAGCCAGC
ACTGCGCCGCCGTGCTCCGCGAGGCGTCGGGCTCCGTCACGTCCATGACGCGGTCCGGCCGCCTCGCCCTCGTCGTCGGG
GACATGAACGCCGCCGCCCAAGACCTGAGGAACGAGCTGAGATGCCTCGCCGAGATACTGGACGACGACGAAGAAGAAGA
AGCCGCGTCATCAGAGGCAGAGCAGCACGAGCACAACACCGCGCCGCCGCCGCTCATCGAGGCGCTGCCGCTCTTCACCG
CCGCCTCTCTCCTGCTTGAGATATCCACTAGAGCGGAGGGGGTCGTCGCCGCCGTGGACGCCCTGGGCACCACGGCGAAG
TTCAAGAAAGCCGACCACGCCGAGCCACCAGCAACCACAACGCTCGACGCCGAGGCGGCCATGCCCGTATCCAACTCCAA
CGCCATCGCCGCAGACGAGGCGCACGGCAATGCCACCGCCGGCGAGCATGACAAGAAGGAGACGGCGGAGCAGACGACGA
CGACGAGCGCGAGCACCGTGGGGCAGCAGCAAGAGGCGCGGGACCAGGTGGGGCAGCTGGTGAAGCTGCTGATGCGGAGG
CGGAGCACCAAGAAGTGGGCGCGCGGCGAGCCCAAGGTGGGCCCGTGCCCGAGGCCGCCGCTGGACTTCCCGCCGGTCCA
CGCGCCCAGCCCGAGGAGCCGGTCCACGGAGCTCGCCGGCCACCCGCCGGTGGTGCCCAGCCCGAGGCACCGGTCCATGG
ACCTGGCGAGCCACGGGCTCGCGCTGCCGAGCTCGAGACACCGGTCCATGGACCTCGCAAGCCATGGGCCCGTGCTGCCG
AGCCCAAGGAACAGGTCCATGGACTTCACGGCCCACGCGCCGAGCCCGAGAAACCGATCCATTCTTGGGATGGCTTGA

ORF - retro_oniv_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.03 %
Parental protein coverage: 71.76 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalWKIGADDPRRAVHGVKVGLALALVSVFYYTRPLYDGVGGAAMWAVMTVVVVFEFTVGGCVYKGFNRATAT
WK.GADDPRR.VHG.KV.LAL.L.S.FYY.RPLY...G..AMWAV.TVVVVFE.TVGGC.YKG.NRA.AT
RetrocopyWKVGADDPRRVVHGFKVALALTLCSAFYYVRPLYVFTGQTAMWAVLTVVVVFEYTVGGCMYKGLNRAMAT
ParentalVSAGVVALGVHWIASKSGDKLEPVVRSGSVFLLAAAATFSRFIPTVKARFDYGVTIFILTYSLVAVSGYR
V..G..ALGVHW.A.KSGD..EP.V...S.F.LAAAA.FSRFIPT.KARFDYGVTIFILTYSLVAVSGYR
RetrocopyVAGGALALGVHWVADKSGDDAEPFVLTASLFVLAAAASFSRFIPTLKARFDYGVTIFILTYSLVAVSGYR
ParentalVDALVAMAQQRVSTIAIGIFICLAVCVLICPVWAGQELHRLTARNMDKLAGAVEACVEGYFVAGEEVAAG
VD.LV.MAQQR..TIAIG.FIC.AVC.L..PVWAGQELH.L.ARNMDKLA.A.EACV..YF...E....G
RetrocopyVDTLVTMAQQRLITIAIGAFICFAVCTLVFPVWAGQELHVLVARNMDKLAAAIEACVDDYFSSAEHAGGG
ParentalPEYKRRPAAAAAAEGYKCVLNSKASEDAQANLARWEPAHGRFGFRHPYAQYKAVGAAMRHCAYCVEALSG
.......A....A.GY..VLN.KASED..ANLARWEP.HG.FGFRHPY.QY..VGAAMR.CAYC..AL..
RetrocopyGD--AATALSEKARGYRAVLNAKASEDSLANLARWEPGHGKFGFRHPYGQYQNVGAAMRCCAYCIDALAA
ParentalCIRSAEAQSPEGVKRHLAGASTRVATRCAAVLREASSSVAAMTTPSRGLDFAVADMNTAVQELQSEVREL
C...A..Q.P..VKRHLAGA.......CAAVLREAS.SV..MT...R.L...V.DMN.A.Q.L..E.R.L
RetrocopyCV-GAGGQAPAHVKRHLAGACVALSQHCAAVLREASGSVTSMTRSGR-LALVVGDMNAAAQDLRNELRCL
ParentalPSKLAAAAGEPAAAQQ
...L.....E.AA...
RetrocopyAEILDDDEEEEAASSE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Oryza nivara was not studied using RNA-Seq expression data.
Oryza nivara was not studied using ChIP-Seq data.
Oryza nivara was not studied using EST data.
Oryza nivara was not studied using FANTOM5 data.
retro_oniv_18 was not experimentally validated.

Retrocopy orthology:
Oryza nivara does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Oryza sativa indicaBGIOSGA0145311 retrocopy
Oryza glumaepatula OGLUM04G220001 retrocopy
Oryza meridionalis OMERI04G184901 retrocopy
Oryza nivara ONIVA04G20520 1 retrocopy
retro_oniv_18 ,
Oryza punctata OPUNC04G197201 retrocopy
Oryza glaberrima ORGLA04G01902001 retrocopy
Oryza sativa japonicaOS04G05672001 retrocopy



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