RetrogeneDB ID:

retro_opri_838

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_36243:8655..8907(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2D3
Ensembl ID:ENSOPRG00000011695
Aliases:None
Description:ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476]


Retrocopy-Parental alignment summary:






>retro_opri_838
GAGCTGCTTGAATTGACCCGTGACCCTCCGGCTCAGTGCTCGGCAGGGCCAGTGGCTGACTACCTTTTTCACTGGCAAGC
TACCATCACGGGGCCAGACGACAGCCCCTACCAGGAAGGCGTGTTCTTCCTGAAGATCCAGTTTCCTTCCGATTATCCTT
TCAAGCCACCTAAGGTGGCGTTTACTACTCGAGTTTAGCACCCAAATATTAATCAGAATGGAACCATTTGTCTGGATATA
CTTAAGTCTGAG

ORF - retro_opri_838 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.57 %
Parental protein coverage: 60.43 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNI
EL..L.RDPPAQCSAGPV.D..FHWQATI.GP.DSPYQ.GVFFL.I.FP.DYPFKPPKVAFTTR..HPNI
RetrocopyELLELTRDPPAQCSAGPVADYLFHWQATITGPDDSPYQEGVFFLKIQFPSDYPFKPPKVAFTTRV*HPNI
ParentalNSNGSICLDILRSQ
N.NG.ICLDIL.S.
RetrocopyNQNGTICLDILKSE

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_838 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 16 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Ciona intestinalis ENSCING000000187112 retrocopies
Ciona savignyi ENSCSAVG000000061361 retrocopy
Dasypus novemcinctus ENSDNOG0000000932030 retrocopies
Erinaceus europaeus ENSEEUG000000146583 retrocopies
Echinops telfairi ENSETEG000000012913 retrocopies
Gorilla gorilla ENSGGOG000000013682 retrocopies
Ornithorhynchus anatinus ENSOANG000000054151 retrocopy
Ochotona princeps ENSOPRG000000106152 retrocopies
Ochotona princeps ENSOPRG00000011695 9 retrocopies
Pongo abelii ENSPPYG000000149671 retrocopy
Pteropus vampyrus ENSPVAG000000154381 retrocopy
Rattus norvegicus ENSRNOG000000137419 retrocopies
Sus scrofa ENSSSCG000000243061 retrocopy
Sus scrofa ENSSSCG000000298224 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000134816 retrocopies
Tupaia belangeri ENSTBEG000000002705 retrocopies



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