RetrogeneDB ID:

retro_opri_294

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_4784:26970..27375(+)
Located in intron of:ENSOPRG00000003228
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1B2
Ensembl ID:ENSOPRG00000017163
Aliases:None
Description:eukaryotic translation elongation factor 1 beta 2 [Source:HGNC Symbol;Acc:3208]


Retrocopy-Parental alignment summary:






>retro_opri_294
GTGGGTTTTGGAGATCTGAAGAGTCCTGCCTGCTGACATGTACTCAGCGACTAACCTGTTGGACAAGAGCTACGTTGAGG
GCTATGTGCCAACACAAGCAGAGGTGGCAGTGTCCGAAGCTGCATTCGGCTGCCACCTGCTCACTTGTGTCATGCCCTCC
GCTGGCAGAATCGCGTCATAAAGGACCAGGAGGAGAAGGCCAGCCTGCTAGGAGGGAGAAGCTTTCGGCAAGTAAAGGCC
CCGTGGATGTGGAAGACACTAAAGGAAGTGAAGGTAGAGAATAAAGAGGATGATGACACTGACCTCTTTGGGTCTAATGA
TGAGGAGGGAAGTGAAGAGGCAAAGAAGCGAAGGGAAGAACTTCCACAGGACGAGTCCAAGACAGCCAAAGAGCCTGCGG
CTGTT

ORF - retro_opri_294 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.99 %
Parental protein coverage: 86.16 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGFGDLKSPAGLQVLND-YLADKSYIEGYVPSQADVAVFEAVSS-PPPGDLCHALRWYNHIKSYEKEKAS
.GFGDLKSPA...VL.D..L.DKSY.EGYVP.QA.VAV.EA.....PP..LCHALRW.N.......EKAS
RetrocopyVGFGDLKSPAC*HVLSD>NLLDKSYVEGYVPTQAEVAVSEAAFG<LPPAHLCHALRWQNRVIKDQEEKAS
ParentalLPGVK-KALGKYGPADVEDTTGSGGTD-GKDDDDIDLFGSDDEEESEEAKKLREERLAQYESKKAKKPAL
L.G...K.....GP.DVEDT.GS.G.....DD.D.DLFGS.DEE.SEEAKK.REE.L.Q.ESK.AK.PA.
RetrocopyLLGGR<KLSASKGPVDVEDTKGSEGRE>KEDD-DTDLFGSNDEEGSEEAKKRREE-LPQDESKTAKEPAA
ParentalV
V
RetrocopyV

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_294 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 46 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000296351 retrocopy
Callithrix jacchus ENSCJAG000000058052 retrocopies
Cavia porcellus ENSCPOG000000144964 retrocopies
Gorilla gorilla ENSGGOG000000070022 retrocopies
Macropus eugenii ENSMEUG000000026548 retrocopies
Myotis lucifugus ENSMLUG000000166028 retrocopies
Oryctolagus cuniculus ENSOCUG000000098484 retrocopies
Oreochromis niloticus ENSONIG000000176301 retrocopy
Ochotona princeps ENSOPRG00000017163 3 retrocopies
retro_opri_1192, retro_opri_294 , retro_opri_748,
Oryzias latipes ENSORLG000000185331 retrocopy
Pongo abelii ENSPPYG000000131077 retrocopies
Sarcophilus harrisii ENSSHAG000000178531 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000054373 retrocopies
Xiphophorus maculatus ENSXMAG000000060501 retrocopy



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