RetrogeneDB ID:

retro_opri_394

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_107199:4171..4513(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PFDN5
Ensembl ID:ENSOPRG00000015638
Aliases:None
Description:prefoldin subunit 5 [Source:HGNC Symbol;Acc:8869]


Retrocopy-Parental alignment summary:






>retro_opri_394
CAGGCCAAGTATGTGGCAGCCAAGGAGTGTCTGCACGTGCTAAGCAAGAGTAATGTGGGGAACGAATCACTCAGCCTGCT
GACAAGTTCTAGGTACCTCCCAGGCAAGCTGCGCCATGTGGAGCATGTGAGAACTGACATGAGAACGGGCTGCTACCTTG
GGAAGACAGCTGATGATGCCAAAGACTTCCTCACAAGGAGGACAGACTTCCTCCCCAAGCAGATGGGGGAAATTCAACCT
GCCCTGCAGGAGAATCATGCCATGAAACAGGCCATCATGATAATGATGAGCTACAAGATCGTGCTGCTGAAAGCTCTGGG
GGAAGCCTATGCCACGGCCAAG

ORF - retro_opri_394 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.91 %
Parental protein coverage: 74.03 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQTKYVEAKDCLNVLYKSNEGQEILVLVSRSMYVPGKLHDVEHVLIDVGTGYYVEKTAEDAKDFFKRKIDF
Q.KYV.AK.CL.VL.KSN.G.E.L.L...S.Y.PGKL..VEHV..D..TG.Y..KTA.DAKDF..R..DF
RetrocopyQAKYVAAKECLHVLSKSNVGNESLSLLTSSRYLPGKLRHVEHVRTDMRTGCYLGKTADDAKDFLTRRTDF
ParentalLTKQMEKIQPALQEKHAMKQAVMEMMSQKIQQLTALGAAQATAK
L.KQM..IQPALQE.HAMKQA.M.MMS.KI..L.ALG.A.ATAK
RetrocopyLPKQMGEIQPALQENHAMKQAIMIMMSYKIVLLKALGEAYATAK

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_394 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 20 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000124022 retrocopies
Canis familiaris ENSCAFG000000070164 retrocopies
Callithrix jacchus ENSCJAG000000184776 retrocopies
Dasypus novemcinctus ENSDNOG000000130021 retrocopy
Echinops telfairi ENSETEG000000021113 retrocopies
Felis catus ENSFCAG000000058714 retrocopies
Homo sapiens ENSG000001233491 retrocopy
Gorilla gorilla ENSGGOG000000263081 retrocopy
Macropus eugenii ENSMEUG000000121101 retrocopy
Macaca mulatta ENSMMUG000000220302 retrocopies
Mustela putorius furoENSMPUG000000060591 retrocopy
Mus musculus ENSMUSG000000012891 retrocopy
Nomascus leucogenys ENSNLEG000000177063 retrocopies
Otolemur garnettii ENSOGAG000000094632 retrocopies
Ochotona princeps ENSOPRG00000015638 1 retrocopy
retro_opri_394 ,
Procavia capensis ENSPCAG000000124132 retrocopies
Pongo abelii ENSPPYG000000045751 retrocopy
Pan troglodytes ENSPTRG000000050101 retrocopy
Sorex araneus ENSSARG000000062211 retrocopy
Tupaia belangeri ENSTBEG000000164364 retrocopies



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