RetrogeneDB ID:

retro_opri_511

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_146551:570..895(-)
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:ENSOPRG00000004938
Aliases:None
Description:protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]


Retrocopy-Parental alignment summary:






>retro_opri_511
CTTGATTGACCTTCTGATGATGGTGCACCTCCATCCAACCAGATTGTTAATGACTGGTTAAGTCTTGTAAAAATAAAGGT
TAGTGAAGAACCCAGTTGTTGTATTGCTGTTTGTGGTGTTGACGGCCTTAGAAGAGCTCCAGTGCTTGTCGTGTCAGCAT
TAATTTGAAGGTGGAATGAAATACTTAGGTGTAGTACAATCCATAAGACAAAAGTGATGTGGAGCTTTTAACAGAAAACA
ACTTTTTTATTTGGAAAAATACCATCCTAAGATGCAGTTGAACTTCAGATATTCCAGTGGTCATAGAAATAACCATTGCA
TTAAA

ORF - retro_opri_511 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.39 %
Parental protein coverage: 78.26 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALI-EGGMKYEDAVQFIR
LD.P.DDGAPPSNQIV.DWLSLVKIK..EEP.CCIAV..V.GL.RAPVLV..ALI.EGGMKY...VQ.IR
RetrocopyLD*PSDDGAPPSNQIVNDWLSLVKIKVSEEPSCCIAVCGVDGLRRAPVLVVSALI>EGGMKYLGVVQSIR
ParentalQKRRGAFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCIQ
QK..GAFN.KQL.YLEKY.PKM.L.F..S.GHRNN.CI.
RetrocopyQK*CGAFNRKQLFYLEKYHPKMQLNFRYSSGHRNNHCIK

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






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_511 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps 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 ENSOPRG00000004938 4 retrocopies
Rattus norvegicus ENSRNOG000000117714 retrocopies
Rattus norvegicus ENSRNOG000000463704 retrocopies
Tupaia belangeri ENSTBEG0000000995614 retrocopies
Tursiops truncatus ENSTTRG000000041296 retrocopies
Vicugna pacos ENSVPAG000000042779 retrocopies



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