RetrogeneDB ID:

retro_pcap_188

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_14364:11580..11864(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL26L1
Ensembl ID:ENSPCAG00000002246
Aliases:None
Description:ribosomal protein L26-like 1 [Source:HGNC Symbol;Acc:17050]


Retrocopy-Parental alignment summary:






>retro_pcap_188
ATGCAGTCCACACCCATCTGAAAGGATGATGATGTTCAGTTTGTGTGAGGATGCTACAATTTCAGCAAATTGGTGAAGTA
GGCCAGGTATACAGGAAGAAATATGTCTCTTACACTGAATGGGTTCAAGGGGATAAAGCTGATGGCAGAACTGTCCCTGT
GGGCATTCACCACAGCAAGGTGATTATCACTAGACTAAAACTAGACAAGGACCTCAAAAAGATCATGGAACATAAAGCCA
GGTCTCGCCTAAGAAAAAGGGCAAGTAAAAGGAAGAAACAGTTG

ORF - retro_pcap_188 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.89 %
Parental protein coverage: 66.21 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVRSMPIRKDDEVQVVRGHY-KGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLD
..S.PI.KDD.VQ.V.G.Y...QQIG.V.QVYRKKYV.Y.E.VQ..KA.G.TV.VGIH.SKV.ITRLKLD
RetrocopyMQSTPI*KDDDVQFV*GCY<QFQQIGEVGQVYRKKYVSYTEWVQGDKADGRTVPVGIHHSKVIITRLKLD
ParentalKDRKKILERKAKSRQVGKEKGKYKEEL
KD.KKI.E.KA.SR...K...K.K..L
RetrocopyKDLKKIMEHKARSR-LRKRASKRKKQL

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_188 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 12 parental genes, and 85 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG0000000228935 retrocopies
Felis catus ENSFCAG000000269491 retrocopy
Homo sapiens ENSG000000372412 retrocopies
Latimeria chalumnae ENSLACG000000075992 retrocopies
Microcebus murinus ENSMICG0000001131210 retrocopies
Macaca mulatta ENSMMUG000000030701 retrocopy
Oryctolagus cuniculus ENSOCUG000000061724 retrocopies
Procavia capensis ENSPCAG00000002246 10 retrocopies
Pteropus vampyrus ENSPVAG000000032538 retrocopies
Sus scrofa ENSSSCG000000169893 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000268761 retrocopy
Tursiops truncatus ENSTTRG000000106248 retrocopies



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