RetrogeneDB ID:

retro_pcap_345

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_44707:15993..16866(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPCAG00000007411
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BECN1
Ensembl ID:ENSPCAG00000014049
Aliases:None
Description:beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]


Retrocopy-Parental alignment summary:






>retro_pcap_345
GAGACATCCGACATCTTCACCCTGCTGGGGAAGGTGTGCTCCATGCGAACGCTCAGCAGCATCCAGGAGACCTTCCTGGA
GGCATTCAACATCCTTTCTGGCGAGAAAGAAATGGATCACCCTTTGTGTGAGGAGTGCACTGACAGCCTCTTAGAGCTGC
TAGACATGCAACTCACCCGCACAGAATCTGAGTGTCAGATGTACAAACTCTGCTTGGAGACCAGGGAGCTGACAACATGT
CAGGAGGAGTTGGAGGTGCTGCAGAGAGAGCTGGAGAGCCTGGAGCTGGAGGAGGCGAGACTGGTCCAGGAGCTGGCTGG
TGTGGAGAAGGTCTGGAAACAGGCTGCAGGAGATCTCCAGGCCGCCCAGGCAGAGGCTGAGACACTAGAGCAGCAGGAGA
AACAGTCCTGGAGGGACTACAGCGTCTTGGAGCAGCAACAACTGGAGCTCTTGGATGAACTGAGGAGCTTGGAGAACCGG
CTGCAGGGCGCCCGGATCCAGCTGGGCCAACTGACCGACGCCAGCATCTTCCGCATGGCGTTTCACATCTGGCATGAGGG
CCCCGTCGGCGTCATCAACAACTTCAAGTTGGGCTGCCTTCCCACTGTCCCCGTGAGCTGGAGTGAGATCAGTGCTGCCT
GGGGGCAGACGGCTCTGCTGCTCTTTGTTCTGTCCAAGAAAATAGGACTGCAATTTCAGAGGTATAGACTTGTCCCCTTG
GGAAGCCATTCCTATCTGAAGCCTCTGACGGATGACTCGGCAGGGCTGCCATTGTTCTGTTTCCAGAAGCAGACTGTTTT
CTTGGATAAGTTTGACCATGCGATGGTGGCTTTCCTGGACTGTTTGCAGCAATTAAAGGAAAAGGTTGAGAAA

ORF - retro_pcap_345 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.92 %
Parental protein coverage: 75. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQN
E....FTL.G.......M..LS.........F.I.SG....DHPLCEECTD.LL..LD.QL..TE.ECQ.
RetrocopyETSDIFTLLGKVC---SMRTLSSIQETFLEAFNILSGEKEMDHPLCEECTDSLLELLDMQLTRTESECQM
ParentalYKRCLEILEQMN-EDDSEQLQMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDHEEAQYQ
YK.CLE..E........E.LQ.EL..L.LEE.RL.QEL..VEK..K..A..L...QAEAE.L...E.Q..
RetrocopyYKLCLETRELTTCQEELEVLQRELESLELEEARLVQELAGVEKVWKQAAGDLQAAQAEAETLEQQEKQSW
ParentalREYSEFKRQQLELDDELKSVENQMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
R.YS....QQLEL.DEL.S.EN....A..QL..L.....F...FHIWH.G..G.INNF.LG.LP.VPV.W
RetrocopyRDYSVLEQQQLELLDELRSLENRLQGARIQLGQLTDASIFRMAFHIWHEGPVGVINNFKLGCLPTVPVSW
ParentalNEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMV
.EI.AAWGQT.LLL..L..K.GL.FQRYRLVP.G.HSYL..LTD.S..LPL.C......F.D.KFDHAMV
RetrocopySEISAAWGQTALLLFVLSKKIGLQFQRYRLVPLGSHSYLKPLTDDSAGLPLFCFQKQTVFLD-KFDHAMV
ParentalAFLDCVQQFKEEVEK
AFLDC.QQ.KE.VEK
RetrocopyAFLDCLQQLKEKVEK

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






Procavia capensis was not studied using RNA-Seq expression data.
Procavia capensis was not studied using ChIP-Seq data.
Procavia capensis was not studied using EST data.
Procavia capensis was not studied using FANTOM5 data.
retro_pcap_345 was not experimentally validated.

Retrocopy orthology:
Procavia capensis 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 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068671 retrocopy
Bos taurus ENSBTAG000000199141 retrocopy
Dipodomys ordii ENSDORG000000009561 retrocopy
Felis catus ENSFCAG000000131361 retrocopy
Homo sapiens ENSG000001265811 retrocopy
Macropus eugenii ENSMEUG000000117001 retrocopy
Macaca mulatta ENSMMUG000000299711 retrocopy
Monodelphis domestica ENSMODG000000150641 retrocopy
Mus musculus ENSMUSG000000350861 retrocopy
Nomascus leucogenys ENSNLEG000000118401 retrocopy
Oryctolagus cuniculus ENSOCUG000000159643 retrocopies
Procavia capensis ENSPCAG00000014049 1 retrocopy
retro_pcap_345 ,
Pan troglodytes ENSPTRG000000228191 retrocopy
Sorex araneus ENSSARG000000003671 retrocopy
Sus scrofa ENSSSCG000000173861 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000126121 retrocopy
Tursiops truncatus ENSTTRG000000117161 retrocopy



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