RetrogeneDB ID:

retro_oniv_7

Retrocopy
location
Organism:Indian wild rice (Oryza nivara)
Coordinates:11:19000380..19002510(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ONIVA11G17660
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ONIVA03G32120
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_oniv_7
ATGCCGGCGCCGCTGGTGCCGTATAGGGAGGAAGAGCTCCGGAACCTGAGAGGCGACGACAATCCGGGCCCGTACAAGGA
CCATGACCGTGTCTACCGCTACGACGTCTACAACGACCTCGGCGAGCCAGACAGTGGCAACCCGCGCCCCGTGCTGGGTG
GCTCCGACGAGCAACCTTACCCTCGCCGCTGCCGCACCGGCCGGAGGCGGACCAACACCGACCCCGACTCCGAGAGCCGC
AACGTCGGCTTCCCCCTAACCAACCATTTCTACGTGCCCCGCGACGAGGTGTTCAACGACCGCAAGAAGGCCTACTTCGA
CACCAACAACCTCAAGCTCTATATCATGCAAAAGTACGCCACCTTTCTCTTGCACGCCGACCAGCAGACCCCCTTCGAGT
TCGACAGCTTCGCCGACGTGCTAAGCCTCTACGACGAGGGCTCCATCAACCTGCCCGGATGGCTCAACACTTTCCTCCAA
CCATTGCTCGGCATAATCCCCTTCAAGTTGCTCCAGCAAGTCCTCACCCCCGACAGCGAGTTCATCCTCAAGTTCCCCAT
GCCGGCGGTCATCAGGGAGGACAAGACGGCATGGCAAACAGACGAAGAGTTTGCGCGCGAGATGCTCGCCGGCACCAACC
CGGTCGTCATCCGCCGGCTCGGGGAAACCGAGTTCCCGCCCAAGAGCAAGCTAGACACAAGCAAGTATCACAACCAGAAC
AGCAGGATCACAGCGGCACACGTCGAGAAGTGCCTCGAGGTCGAGGGCCTCACCGTCGAGCAGGCGCTAGCCGACGGCCG
CCTCTTCATCCTCGACCACCACGACCACTTCATGCCGTACCTGCTCGATGCCAACCATCAACCAGACACTTTCGTCTACG
CGACGAGGACACTGCTCTTCCACCGCAACGATGGCACTCTCCAGCCTGCAGCAATCGAGCTCAGCCTACCTCGCTTTGAG
GCCGGCAGCACACTCATCTCGTCCGTCGGCGAGGTCTACACGCCGGCGTCAGACGGCGTGGAGGGCCACATCTGGCAGCT
TGCCAAGGCCTACGTCACCGTCAATGACTACTCGTGGCACCAGCTCGTCAGCCACTGGCTCAACACGCACGCGGTGATGG
AGCCGTTCGCCATTGCCACGCACCGGCAGCTCAGCGTGGCGCACCCTATCCACAAGCTCCTCCACCCGCACTATCGTGAC
AACTTGTTTATCAACGCCCTCGGCCGCCAGAGTCTGATCAACGCCGGTGGTAGCTCCGAGAACACCGTCTTCCTCGGCAA
GTATGGGCTCTCCATGACATCGGAGGTGTACAGGAACTGGAACTTCACCGAGCAGGCGCTCCCGGAGGACCTCATCAAGA
GGGGCATCGCCAAGCGCCGCTCCAATGGCGAGCTGGAGCTGCTGATCAAGGACTACCCGTACGCCGTCGATGGGCTCGCC
ATCTGGTCGGCAATCGAGACTTGGGTCCGCGACTATTGTGCCATCTACTACGCGGACGATGCCGCGGTCCAGGGCGACGC
CGAGCTGCAGTCGTGGTGGAAAGATGTGCGCGAGGAAGGACACGGAGACCTCAAGGACCACAAATGGTGGCCGGAGATGA
AGACGGTGGCCGAGCTTGTCCAGTCATGCGCCACCATCATCTGGATCGCCTCGGCGCTGCACGCGGCCGTCAACTTCGGC
CAGTACATGTACGCCGGCTACGTCCCGAACCGGCCGTCGGTGAGTCGGCGGCCGATGCCGAAGCCGGGCACCGACTTGTA
CAGGGAGCTGGAGCTCCACCCGGAGAAGGAATTCCTTCTCACCATCACTAAGCAGGACCTGTCCATAGCTGGCATTGCCC
TCGTCGAGCTCCTATCTAGCCATTCCGATGACGAGGTCTACCTCGGGCAGCGCGACTCGCCGAACTGGACGTCCGACCTG
GATGCCATGAACGCGTTCGACCGCTTCCGTGAACGGCTCTTGGAGGTGGAGAAGAACATCGTGGCCAAGAACGACAAGGG
CAGTGGATTCAAGAACAGGACAGGGCCGGTCAACATCCCCTACAATTTGCTCTTCCCTTATGCCTCCGGCGACGCGGAGG
CCAACACCGGGGTCACCGGCAAGGGCATCCCCAACAGCGCCTCCATCTGA

ORF - retro_oniv_7 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.03 %
Parental protein coverage: 54.27 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLEELRKSFPVQLIKDLLPVGGSYLLKFPKPDIIKENEVAWRTDEEFAREILAGLNPMVIRRL--TEFPPK
L..L....P..L....L.......LKFP.P..I.E...AW.TDEEFARE.LAG.NP.VIRRL..TEFPPK
RetrocopyLQPLLGIIPFKLLQQVLTPDSEFILKFPMPAVIREDKTAWQTDEEFAREMLAGTNPVVIRRLGETEFPPK
ParentalSTLDPSKYGDQTSTITPAHIEKNLE--GLSVQQALDSNRLYILDHHDHFMPFLIDINSLDGIFTYATRTL
S.LD.SKY..Q.S.IT.AH.EK.LE..GL.V.QAL...RL.ILDHHDHFMP.L.D.N.....F.YATRTL
RetrocopySKLDTSKYHNQNSRITAAHVEKCLEVEGLTVEQALADGRLFILDHHDHFMPYLLDANHQPDTFVYATRTL
ParentalLFLRDDDTLKPLAIELSLPHIEGNLTTAKS--KVHTPASSGIESWVWQLAKAYVAVNDSGWHQLISHWLN
LF.R.D.TL.P.AIELSLP..E...T...S...V.TPAS.G.E...WQLAKAYV.VND..WHQL.SHWLN
RetrocopyLFHRNDGTLQPAAIELSLPRFEAGSTLISSVGEVYTPASDGVEGHIWQLAKAYVTVNDYSWHQLVSHWLN
ParentalTHAVMEPFVIATNRQLSVTHPVYKLLQPHYRDTMTINALARQTLINGGGIFEQTVFPGKHALAMSSAVYK
THAVMEPF.IAT.RQLSV.HP..KLL.PHYRD...INAL.RQ.LIN.GG..E.TVF.GK..L.M.S.VY.
RetrocopyTHAVMEPFAIATHRQLSVAHPIHKLLHPHYRDNLFINALGRQSLINAGGSSENTVFLGKYGLSMTSEVYR
ParentalNWNFTEQGLPDDLIKRGIAIKDPSSPSKVKLLIKDYPYATDGLAIWQAIEQWVTEYCAIYYPNDGVLQGD
NWNFTEQ.LP.DLIKRGIA.....S.....LLIKDYPYA.DGLAIW.AIE.WV..YCAIYY..D...QGD
RetrocopyNWNFTEQALPEDLIKRGIAKR--RSNGELELLIKDYPYAVDGLAIWSAIETWVRDYCAIYYADDAAVQGD
ParentalVELQAWWKEVREVGHGDLKDADWWPKMQSLPELTKACTTIIWIASALHAAVNFGQYPYAGYLPNRPTISR
.ELQ.WWK.VRE.GHGDLKD..WWP.M....EL...C.TIIWIASALHAAVNFGQY.YAGY.PNRP..SR
RetrocopyAELQSWWKDVREEGHGDLKDHKWWPEMKTVAELVQSCATIIWIASALHAAVNFGQYMYAGYVPNRPSVSR
ParentalRPMPEPGSKEYTELDENPEKFFIRTITSQFQTILGVSLIEILSKHSADEIYLGQRDTPEWTSDPKALEAF
RPMP.PG...Y.EL...PEK.F..TIT.Q...I.G..L.E.LS.HS.DE.YLGQRD.P.WTSD..A..AF
RetrocopyRPMPKPGTDLYRELELHPEKEFLLTITKQDLSIAGIALVELLSSHSDDEVYLGQRDSPNWTSDLDAMNAF
ParentalKRFSRQLVEIESKVLNMN-KDPLLKNRVGPANFPYTLMFPNTSDNKGAAEGITARGIPNSISI
.RF...L.E.E......N.K....KNR.GP.N.PY.L.FP..S....A..G.T..GIPNS.SI
RetrocopyDRFRERLLEVEKNIVAKNDKGSGFKNRTGPVNIPYNLLFPYASGDAEANTGVTGKGIPNSASI

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_7 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Oryza nivara ONIVA03G32120 1 retrocopy
retro_oniv_7 ,



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