RetrogeneDB ID:

retro_opri_184

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_334:1073522..1073893(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOPRG00000010239
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP6V1E1
Ensembl ID:ENSOPRG00000004591
Aliases:None
Description:ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E1 [Source:HGNC Symbol;Acc:857]


Retrocopy-Parental alignment summary:






>retro_opri_184
GAATTGCTCAATGATGCCAAGCTAGGACTTGGCAGGCTGGTGGAGGACCCAGAGGTTTACCAGGAGCTTCTGGACAAGCT
GGTGCTGCAGGCCCTGCTCCGCCTCCTGGAGCCCACGGTGATTGTGCGCTGCAGGCCCCAGGATGTCCTGCTGGTGGAGG
CTGCGGTGCAGAGAGCCATTCCCGAGTACGTGCTAGCCTCCCGGAAACCCGTGCAGGTTCGGCTTGATGCGGAGGCCCCA
CCTGGCTGCCAATGCAGCTGGAGGCGTGGAGGTGTATAGTAGTGATCAGAGAATCAAGGTTCTAATACCCTGGAAAGTCG
GTTGGACCTGTCAGCTCAGCAGAGATGCCAGAAATTCGAAGGGCCTTGTTT

ORF - retro_opri_184 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.63 %
Parental protein coverage: 57.67 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPMYKIATKKD
.LLN.AK..L...V.D...YQ.LLD.LVLQ.L..LLEP..IVRCR.QD..LV.AAVQ.AIP.Y..A..K.
RetrocopyELLNDAKLGLGRLVEDPEVYQELLDKLVLQALLRLLEPTVIVRCRPQDVLLVEAAVQRAIPEYVLASRKP
ParentalVDVQIDQEA-YLPEDIAGGVEIYNGDRKIKV-SNTLESRLDLIAQQM-MPEVRGALF
V.V..D.EA..L....AGGVE.Y..D..IKV.SNTLESRLDL.AQQ..MPE.R.ALF
RetrocopyVQVRLDAEA>HLAANAAGGVEVYSSDQRIKV<SNTLESRLDLSAQQR<MPEIRRALF

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_184 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 14 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000174892 retrocopies
Canis familiaris ENSCAFG000000161517 retrocopies
Callithrix jacchus ENSCJAG000000172771 retrocopy
Dasypus novemcinctus ENSDNOG000000145923 retrocopies
Echinops telfairi ENSETEG000000192832 retrocopies
Loxodonta africana ENSLAFG000000038024 retrocopies
Myotis lucifugus ENSMLUG000000148762 retrocopies
Monodelphis domestica ENSMODG000000184524 retrocopies
Mustela putorius furoENSMPUG000000181092 retrocopies
Oryctolagus cuniculus ENSOCUG000000069641 retrocopy
Ochotona princeps ENSOPRG00000004591 2 retrocopies
retro_opri_184 , retro_opri_539,
Procavia capensis ENSPCAG000000160941 retrocopy
Rattus norvegicus ENSRNOG000000119051 retrocopy
Sarcophilus harrisii ENSSHAG000000083002 retrocopies



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