RetrogeneDB ID:

retro_vpac_496

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:scaffold_251504:65..377(-)
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:ENSVPAG00000004277
Aliases:None
Description:protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]


Retrocopy-Parental alignment summary:






>retro_vpac_496
GAACTTAAGAAAAATGGAGTTACCACCATAGTAAGAGTGTGTGAAACAACTTACAACATGGCCATTTTAGAGAAAGAAGG
CCTCCAGGTTCTGGACTGGCCTGTAGATGATGGTGCACCACCATCCAGCCAGATTGTTGATAAGTGGTTAAAACCTGTGA
AAAAGAAATTTTATGAAGACCTTGGTTCTTGTATAGCGGTCCACTGTGCTGCAGATCTTGGGAGAACTCCAGTACTGGTT
GCCTTTGCATTAATCGAAAGTGAAATGAAGTATGAAGATGTAGTGTAATTCATAAGACAAAAGCGACGTGGA

ORF - retro_vpac_496 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75. %
Parental protein coverage: 75.36 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREDPGCCIAVHCV
ELKK.GVTTIVRVCE.TY.....EKEG..VLDWP.DDGAPPS.QIVD.WL..VK.KF.ED.G.CIAVHC.
RetrocopyELKKNGVTTIVRVCETTYNMAILEKEGLQVLDWPVDDGAPPSSQIVDKWLKPVKKKFYEDLGSCIAVHCA
ParentalAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRG
A.LGR.PVLVA.ALIE..MKYED.V.FIRQKRRG
RetrocopyADLGRTPVLVAFALIESEMKYEDVV*FIRQKRRG

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






Vicugna pacos was not studied using RNA-Seq expression data.
Vicugna pacos was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_vpac_496 retrocopy.
Vicugna pacos was not studied using FANTOM5 data.
retro_vpac_496 was not experimentally validated.

Retrocopy orthology:
Vicugna pacos 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 81 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000024903 retrocopies
Cavia porcellus ENSCPOG000000257595 retrocopies
Dasypus novemcinctus ENSDNOG000000185074 retrocopies
Equus caballus ENSECAG000000224836 retrocopies
Echinops telfairi ENSETEG000000081836 retrocopies
Latimeria chalumnae ENSLACG000000071831 retrocopy
Loxodonta africana ENSLAFG000000065728 retrocopies
Myotis lucifugus ENSMLUG000000011621 retrocopy
Macaca mulatta ENSMMUG000000027771 retrocopy
Mustela putorius furoENSMPUG000000031181 retrocopy
Oryctolagus cuniculus ENSOCUG000000063114 retrocopies
Ochotona princeps ENSOPRG000000049384 retrocopies
Rattus norvegicus ENSRNOG000000117714 retrocopies
Rattus norvegicus ENSRNOG000000463704 retrocopies
Tupaia belangeri ENSTBEG0000000995614 retrocopies
Tursiops truncatus ENSTTRG000000041296 retrocopies
Vicugna pacos ENSVPAG00000004277 9 retrocopies



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