RetrogeneDB ID:

retro_ocun_10

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:2:116117550..116118621(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000003634
Aliases:PCBP1, hnRNP E1
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000022490
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_10
ATGGATGCCGGTGTGACTGAAAGCGGACTAAATGTGACTCTCACCATTCGGCTTCTTATGCACGGAAAGGAAGTAGGAAG
CATCATTGGGAAGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATT
GTCCGGAGCGAATCATCACTCTGACCGGCCCCACTAATGCCATCTTCAAGGCATTCGCTATGATCATCGACAAGCTGGAG
GAAGATATCAACAGCTCCATGACCAACAGCACGGCGGCCAGCCGGCCCCCGGTGACCCTGCGGCTGGTGGTGCCGGCCAC
CCAGTGCGGCTCCCTGATCGGGAAAGGCGGGTGTAAGATCAAAGAGATCCGCGAGAGCACGGGGGCCCAGGTCCAGGTGG
CGGGGGATATGCTGCCCAACTCGACCGAGCGGGCCATCACCATCGCGGGCGTGCCGCAGTCTGTCACCGAGTGTGTCAAG
CAGATCTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGGAGAGTCATGACCATTCCGTACCAGCCCATGCC
GGCCAGCTCTCCGGTCATCTGCGCGGGCGGCCAAGATCGCTGCAGCGACGCTGCGGGCTACCCCCACGCCACCCATGACC
TGGAGGGACCACCTCTAGATGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTCGATCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACCGGATTCGCCGGAATTGACTCCAGCTCTCCAGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCATCTACTCAAACCACCCATGAACTCACCATTCCAAATAACTTAATTGGCTGCA
TAATCGGGCGCCAAGGCGCCAACATTAATGAGATCCGCCAGATGTCGGGGGCCCAGATCAAAATTGCCAACCCAGTGGAA
GGCTCTTCTGGTAGGCAGGTTACTATCACTGGCTCTGCTGCCAGTATTAGTCTGGCCCAGTATCTAATCAATGCCAGGCT
TTCCTCTGAGAAGGGCATGGGGTGCAGCTAG

ORF - retro_ocun_10 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.18 %
Parental protein coverage: 98.34 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
RetrocopyMDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK
ParentalAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
RetrocopyAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
ParentalSTERAITIAGIPQSIIECVKQICVVMLETLSQSPP-KGVTIPYRPKPSSSPVIFAGGQQTPVCCSPDSQP
STERAITIAG.PQS..ECVKQIC.VMLETLSQSP.....TIPY.P.P.SSPVI.AGGQ.....CS.D...
RetrocopySTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDR---CS-DAAG
ParentalQKHCWHELEQTPTRAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGNTGFSGIESSSPEVKGYWAGLDA
..H..H.LE..P..AY.IQGQ..I...DL.KL.Q.A.QQSHF.M.HG.TGF.GI.SSSPEVKGYWA.LDA
RetrocopyYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWASLDA
ParentalSAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINV
S.QTT.HELTIPN.LIGCIIGRQGA.INEIRQMSGAQIKIANPVEGS..RQVTITGSAASISLAQYLIN.
RetrocopySTQTT-HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA
ParentalSRRSNQ
...S..
RetrocopyRLSSEK

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 178 .64 RPM 82 .67 RPM
SRP017611_kidney 241 .33 RPM 104 .60 RPM
SRP017611_liver 105 .21 RPM 61 .66 RPM
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_10 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_10 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_10 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_175
Sus scrofa retro_sscr_61
Equus caballus retro_ecab_67
Pongo abelii retro_pabe_92

Parental genes homology:
Parental genes homology involve 26 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000207571 retrocopy
Canis familiaris ENSCAFG000000068211 retrocopy
Callithrix jacchus ENSCJAG000000185902 retrocopies
Cavia porcellus ENSCPOG000000009672 retrocopies
Dasypus novemcinctus ENSDNOG000000086886 retrocopies
Equus caballus ENSECAG000000223891 retrocopy
Erinaceus europaeus ENSEEUG000000010772 retrocopies
Echinops telfairi ENSETEG000000147413 retrocopies
Homo sapiens ENSG000001971112 retrocopies
Gorilla gorilla ENSGGOG000000126132 retrocopies
Macropus eugenii ENSMEUG000000018877 retrocopies
Microcebus murinus ENSMICG000000116512 retrocopies
Myotis lucifugus ENSMLUG000000099713 retrocopies
Macaca mulatta ENSMMUG000000066082 retrocopies
Mus musculus ENSMUSG000000568511 retrocopy
Nomascus leucogenys ENSNLEG000000176931 retrocopy
Oryctolagus cuniculus ENSOCUG000000026961 retrocopy
Oryctolagus cuniculus ENSOCUG00000022490 3 retrocopies
retro_ocun_10 , retro_ocun_1622, retro_ocun_898,
Ochotona princeps ENSOPRG000000046805 retrocopies
Pongo abelii ENSPPYG000000045812 retrocopies
Pan troglodytes ENSPTRG000000050181 retrocopy
Pteropus vampyrus ENSPVAG000000122843 retrocopies
Rattus norvegicus ENSRNOG000000368522 retrocopies
Sus scrofa ENSSSCG000000002741 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000036352 retrocopies
Vicugna pacos ENSVPAG000000004061 retrocopy



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