RetrogeneDB ID:

retro_opri_991

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_5324:34215..34641(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA3
Ensembl ID:ENSOPRG00000002835
Aliases:None
Description:proteasome (prosome, macropain) subunit, alpha type, 3 [Source:HGNC Symbol;Acc:9532]


Retrocopy-Parental alignment summary:






>retro_opri_991
GCAATTGGGATCAGAGGTAAAGATGGTGCTGCTTTGCGGTAGAAAAATTAGTCTTTTCTAAACTTTATAAAGAAAGATCT
AACAAGTGACTTTTTAATGTTGGTCAGCATGTTGGAATGGCAGTGATGGGGCTGTAGGTGGATGTGCCCTCTGCAGCAGA
TACTGCAAGGAAAGACGCTCCCAACTTGAGAGTGAATGTTGGTGACCACATTCTACCAAACATGCTGCAGACAGAGTGGC
CATGTAGACCCCCGCCTGCCCACTCTCCAGTGTTCCTGGACATTCGGGCTGCAGTTTCAAGCAGGTTCTTGCAGTGGGAA
TGATGGTGTGCAACTCTACAGGCTTGACCTGTGAGCTGTTTCAGATGGTTCTTGGGGCTGTGCCATTGGCAAAGTCAGAT
AAGTTTCATAAACAGAAATAGAAAGA

ORF - retro_opri_991 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.22 %
Parental protein coverage: 59.83 %
Number of stop codons detected: 6
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAIGIRCKDGVV-FGVEKLVLSKLYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGY
AIGIR.KDG...F.VEKLV.SKLY.E.SNK.LFNV..HVGMAV.GL..D..S.AD.AR..A.N.R.N.G.
RetrocopyAIGIRGKDGAA<FAVEKLVFSKLYKERSNK*LFNVGQHVGMAVMGL*VDVPSAADTARKDAPNLRVNVGD
ParentalNI-PLKHLADRVAMYVHAYTLYSAVRPFGCS-FMLGSYSATDGAQLYMIDPSGVSYGYWGCAIGKARQAA
.I...KH.ADRVAM...A..L.S.....GCS.F..GS.S..DG.QLY..D...VS.G.WGCAIGK.R...
RetrocopyHI<STKHAADRVAM*TPACPLSSVPGHSGCS<FQAGSCSGNDGVQLYRLDL*AVSDGSWGCAIGKVR*VS
ParentalKTEIEK
.TEIE.
Retrocopy*TEIER

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_991 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 21 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000152871 retrocopy
Callithrix jacchus ENSCJAG000000187321 retrocopy
Dasypus novemcinctus ENSDNOG0000000407727 retrocopies
Dipodomys ordii ENSDORG000000021671 retrocopy
Homo sapiens ENSG000001005671 retrocopy
Gorilla gorilla ENSGGOG000000158141 retrocopy
Macaca mulatta ENSMMUG000000035092 retrocopies
Monodelphis domestica ENSMODG000000078391 retrocopy
Mustela putorius furoENSMPUG000000061262 retrocopies
Mus musculus ENSMUSG000000600733 retrocopies
Nomascus leucogenys ENSNLEG000000130921 retrocopy
Oryctolagus cuniculus ENSOCUG000000103161 retrocopy
Otolemur garnettii ENSOGAG000000003822 retrocopies
Ochotona princeps ENSOPRG00000002835 2 retrocopies
retro_opri_67, retro_opri_991 ,
Pongo abelii ENSPPYG000000058552 retrocopies
Pan troglodytes ENSPTRG000000063901 retrocopy
Rattus norvegicus ENSRNOG000000078511 retrocopy
Sorex araneus ENSSARG000000026702 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000135391 retrocopy
Tupaia belangeri ENSTBEG000000169101 retrocopy
Tursiops truncatus ENSTTRG000000135261 retrocopy



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