RetrogeneDB ID:

retro_ogar_1258

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873540.1:14265653..14266383(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000030105
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PCNA
Ensembl ID:ENSOGAG00000033161
Aliases:None
Description:proliferating cell nuclear antigen [Source:HGNC Symbol;Acc:8729]


Retrocopy-Parental alignment summary:






>retro_ogar_1258
ATGTTCGAGGCGCGTCTAGTCCAGAGCTCTATCCTGAAAAATGTGTTGGAGGCACTGAAGGACCTAATCAACGAGGCCTA
CTGGAAAATCATCAGCTTGAACGGCGTGAACCTGCAGAGCTTGGGATTCATCCCACGTCTGGTTGGTGCAGCTCACCCTG
CGCTCCAAGGGCTTGGACAACATACCGCTGAGACTGAAACCTGGCTATGGGCGTGAACCTCACCAGCATGTCCAAAATAC
TAAAATGTGCTGGCAATGAAGGTATCATTACACTAAGGGCTGAAGATCACACGGGCGCCTTGGCAGTAGTGTTTGAAGGA
CCAAATCAGGAGAAAGTTTCAGACTATGACATGAAATTAATGGATTTGGATGTTGAACAACTTGGAATCCCAGAACAATA
CAGCTGTGTAGTAAAGATGCCTTCTGGTGAATTTGCACCTATATGCCGAGATCTCAGTCACACTGGAGAAGCTGTTGTAA
TTTCCTGTGCAAAAGATGGAGTGAAATTTTCTGCAAGTGGAGAACTTGGGAATGGAAACATTAAGTTGTCACAGACAAGT
AACGTGAATAGAGAGAAGGAAGCTGTTACTATAGGGATGAATAAGCCAGTTCAGTTCACTTTTGCACTGAGGTACCTGAA
CTTCACAAAAGCCACTCCACTCTCTTCTACGTAACACTCAGTATGTCTGCAGATGTACCCCGTGTCGTAAAATTCCTGAT
TTGGGACATT

ORF - retro_ogar_1258 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.47 %
Parental protein coverage: 93.49 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMFEARLVQGSILKKVLEALKDLINEACWDISS-SGVNLQSM-DSSHVSLVQLTLRSEGFD-TYRCDRNLA
MFEARLVQ.SILK.VLEALKDLINEA.W.I.S..GVNLQS..DSSHV.LVQLTLRS.G.D.TYR.D.NLA
RetrocopyMFEARLVQSSILKNVLEALKDLINEAYWKIISLNGVNLQSL>DSSHVWLVQLTLRSKGLD>TYR*D*NLA
ParentalMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVV
MGVNLTSMSKILKCAGNE.IITLRAED....LA.VFE.PNQEKVSDY.MKLMDLDVEQLGIPEQ.YSCVV
RetrocopyMGVNLTSMSKILKCAGNEGIITLRAEDHTGALAVVFEGPNQEKVSDYDMKLMDLDVEQLGIPEQ-YSCVV
ParentalKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTF
KMPSGEFA.ICRDLSH.G.AVVISCAKDGVKFSASGELGNGNIKLSQTSNV..E.EAVTI.MN.PVQ.TF
RetrocopyKMPSGEFAPICRDLSHTGEAVVISCAKDGVKFSASGELGNGNIKLSQTSNVNREKEAVTIGMNKPVQFTF
ParentalALRYLNFFTKATPLSST-VTLSMSADVPLVVEYKIADM
ALRYLN.FTKATPLSST.VTLSMSADVP.VV...I.D.
RetrocopyALRYLN-FTKATPLSST<VTLSMSADVPRVVKFLIWDI

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






Otolemur garnettii was not studied using RNA-Seq expression data.
Otolemur garnettii was not studied using ChIP-Seq data.
Otolemur garnettii was not studied using EST data.
Otolemur garnettii was not studied using FANTOM5 data.
retro_ogar_1258 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 24 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000090891 retrocopy
Canis familiaris ENSCAFG000000060302 retrocopies
Callithrix jacchus ENSCJAG000000212783 retrocopies
Cavia porcellus ENSCPOG000000092421 retrocopy
Erinaceus europaeus ENSEEUG000000030691 retrocopy
Echinops telfairi ENSETEG000000065773 retrocopies
Felis catus ENSFCAG000000090682 retrocopies
Homo sapiens ENSG000001326463 retrocopies
Gorilla gorilla ENSGGOG000000016952 retrocopies
Myotis lucifugus ENSMLUG000000016931 retrocopy
Macaca mulatta ENSMMUG000000132593 retrocopies
Monodelphis domestica ENSMODG000000116491 retrocopy
Mustela putorius furoENSMPUG000000061952 retrocopies
Mus musculus ENSMUSG000000273421 retrocopy
Nomascus leucogenys ENSNLEG000000077262 retrocopies
Otolemur garnettii ENSOGAG00000033161 2 retrocopies
retro_ogar_1258 , retro_ogar_2960,
Procavia capensis ENSPCAG000000105001 retrocopy
Pongo abelii ENSPPYG000000107953 retrocopies
Pan troglodytes ENSPTRG000000132223 retrocopies
Pteropus vampyrus ENSPVAG000000028651 retrocopy
Rattus norvegicus ENSRNOG000000212641 retrocopy
Sorex araneus ENSSARG000000040701 retrocopy
Sus scrofa ENSSSCG000000306421 retrocopy
Tursiops truncatus ENSTTRG000000153682 retrocopies



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