RetrogeneDB ID:

retro_opri_334

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_5331:10441..10660(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:COX5B
Ensembl ID:ENSOPRG00000002030
Aliases:None
Description:cytochrome c oxidase subunit Vb [Source:HGNC Symbol;Acc:2269]


Retrocopy-Parental alignment summary:






>retro_opri_334
GCCCATGCACCCCATGGGGCAGGTGTCATGCACTCCATGGCTTCTGGAGGGGGTGTCCCAACCACTGAGGAGCAGACAAC
AAGGCTAGAGTGGGAGATCATGATGGCCGCATAAAAGTGCTTGGATGCCTACAATATGCTGATCCCAAAACCAGCTTCGG
GCACCAAGGAAGACCCTAATTTAGTCCCATCCATCATCAACATGTGGACAGTGGCCTGC

ORF - retro_opri_334 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.6 %
Parental protein coverage: 79.35 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalARAPHGAAAVRSMASGGGVPTDEEQATGLEREIMMAARKGLDPYNLLPPKAASGTKEDPNLVPSITNKRI
A.APHGA....SMASGGGVPT.EEQ.T.LE.EIMMAA.K.LD.YN.L.PK.ASGTKEDPNLVPSI.N...
RetrocopyAHAPHGAGVMHSMASGGGVPTTEEQTTRLEWEIMMAA*KCLDAYNMLIPKPASGTKEDPNLVPSIINMWT
ParentalVGC
V.C
RetrocopyVAC

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_334 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 29 parental genes, and 113 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000052427 retrocopies
Bos taurus ENSBTAG000000185422 retrocopies
Canis familiaris ENSCAFG000000023878 retrocopies
Callithrix jacchus ENSCJAG000000169116 retrocopies
Dipodomys ordii ENSDORG000000149943 retrocopies
Equus caballus ENSECAG000000079683 retrocopies
Erinaceus europaeus ENSEEUG000000002581 retrocopy
Felis catus ENSFCAG000000017047 retrocopies
Homo sapiens ENSG000001359407 retrocopies
Gorilla gorilla ENSGGOG000000011426 retrocopies
Loxodonta africana ENSLAFG000000093862 retrocopies
Macropus eugenii ENSMEUG000000058552 retrocopies
Myotis lucifugus ENSMLUG000000145121 retrocopy
Mustela putorius furoENSMPUG000000113278 retrocopies
Mus musculus ENSMUSG000000615181 retrocopy
Nomascus leucogenys ENSNLEG000000116685 retrocopies
Oryctolagus cuniculus ENSOCUG000000170852 retrocopies
Otolemur garnettii ENSOGAG000000168403 retrocopies
Ochotona princeps ENSOPRG00000002030 3 retrocopies
retro_opri_1128, retro_opri_334 , retro_opri_568,
Pongo abelii ENSPPYG000000120786 retrocopies
Pan troglodytes ENSPTRG000000122577 retrocopies
Rattus norvegicus ENSRNOG000000166602 retrocopies
Sorex araneus ENSSARG000000112751 retrocopy
Sarcophilus harrisii ENSSHAG000000173583 retrocopies
Sus scrofa ENSSSCG000000081954 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000109803 retrocopies
Tupaia belangeri ENSTBEG000000121304 retrocopies
Tursiops truncatus ENSTTRG000000134905 retrocopies
Vicugna pacos ENSVPAG000000065601 retrocopy



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