RetrogeneDB ID:

retro_pcap_249

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_211535:1098..1606(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTP4A1
Ensembl ID:ENSPCAG00000001271
Aliases:None
Description:protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]


Retrocopy-Parental alignment summary:






>retro_pcap_249
GTGAACTGCCCAGCTCCTGTGGAAGTCACATATAAGAGCATGTGATTTCTTACTACCCACTATTCAACTAATGTGAACTT
AAACAAAGTCACAGAGAAGTGTAAGAAAAACAGAGTTACCACAAAAGTAACAGTAGGTGAAGCAACTTACGACGCTGCTT
TTGTGAAAAAAGAAGGCATCCACATTCTTGATGGGCCTTTTGATGATGGTGCACCACCACTCACCCGAATTGTTGATGCC
TGGTAAGTCTTGTAAAACTTAAGTTCTGTGAAGAACCTGCTTGTTGTATTGCTGTTCATTGTGTTGCAGGTCTTGGGAGA
GCTTCAGGGCTTGGTGTTCTAGCATTAATTGAAGGTGGAATGAAATATGATGATGCAATATGGTTCATAAGACAAAAGTG
GAGTGGACCTTTTAATAGCAAGAAATTTTAAATTTGGGGAAATATCATCCTAAAATGTAGCTGAGCTTCGAAGTGTCCAA
CGGTCATAGAAACAACTGTTGCATTCAA

ORF - retro_pcap_249 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.77 %
Parental protein coverage: 98.83 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVNCPAPAAVQCNSTRFLTNHYSTNMNLNKFIE-LKKYGVTTIVRVCEATYDTALVEKEGIHVLDWPFDDG
VNCPAP..V...S..FLT.HYSTN.NLNK..E..KK..VTT.V.V.EATYD.A.V.KEGIH.LD.PFDDG
RetrocopyVNCPAPVEVTYKSM*FLTTHYSTNVNLNKVTEKCKKNRVTTKVTVGEATYDAAFVKKEGIHILDGPFDDG
ParentalAPPSNQIVDDW-LSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFN
APP...IVD.W..SLVK.KF.EEP.CCIAVHCVAGLGRA..L..LALIEGGMKY.DA..FIRQK..G.FN
RetrocopyAPPLTRIVDAW<VSLVKLKFCEEPACCIAVHCVAGLGRASGLGVLALIEGGMKYDDAIWFIRQKWSGPFN
ParentalSK-QLLYLEKYRPKMRLRFKESNGHRNNCCIQ
SK...L.L.KY.PKM.L.F..SNGHRNNCCIQ
RetrocopySK<EILNLGKYHPKM*LSFEVSNGHRNNCCIQ

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_249 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 58 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000185074 retrocopies
Echinops telfairi ENSETEG000000081836 retrocopies
Latimeria chalumnae ENSLACG000000071831 retrocopy
Myotis lucifugus ENSMLUG000000011621 retrocopy
Macaca mulatta ENSMMUG000000027771 retrocopy
Monodelphis domestica ENSMODG000000187015 retrocopies
Oryctolagus cuniculus ENSOCUG000000063114 retrocopies
Procavia capensis ENSPCAG00000001271 8 retrocopies
Rattus norvegicus ENSRNOG000000117714 retrocopies
Rattus norvegicus ENSRNOG000000463704 retrocopies
Tupaia belangeri ENSTBEG0000000995614 retrocopies
Tursiops truncatus ENSTTRG000000041296 retrocopies



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