RetrogeneDB ID:

retro_opri_178

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_3274:920462..920762(-)
Located in intron of:ENSOPRG00000004145
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOPRG00000001957
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opri_178
ATCTCTGTGAAGAGGATCAAGGGAAGCTGAATAGACTTCCTGCCACCAGTGTTGGTGACACTGTAATGGCCACATTCAAG
AAGGACCAGCCAGAGCTCCGGAAGAACGTACATCCAACAGTGGTACTCCAAACATGGAAGTCATGTTGAATAAAAAGTGG
TGTTTCTTTATTTTGAAGATATTGCTGGGGTCATAGTAAACAATAAAGGTGAGAGGAAAGGTTCCACCATCACTGAGCCT
GTTGCAAAGGAGTGTGCAGACTTGTGGCCCAGGATTGCATCCAACACAGGCAACACTGCA

ORF - retro_opri_178 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.59 %
Parental protein coverage: 71.22 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalISVKGIKG-RLNRLPAAGVGDMVMATVKKGKPELRKKVHPAVVIRQRKSYRRKDGVFLF-EDNAGVIVNN
ISVK.IKG..LNRLPA..VGD.VMAT.KK..PELRK.VHP.VV....KS...K.GV.LF.ED.AGVIVNN
RetrocopyISVKRIKG<KLNRLPATSVGDTVMATFKKDQPELRKNVHPTVVLQTWKSC*IKSGVSLF>EDIAGVIVNN
ParentalKGEMKGSAIAGPVAKECADLWPRI-SNAGSIA
KGE.KGS.I..PVAKECADLWPRI.SN.G..A
RetrocopyKGERKGSTITEPVAKECADLWPRIASNTGNTA

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_178 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 30 parental genes, and 172 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000042686 retrocopies
Bos taurus ENSBTAG000000032295 retrocopies
Canis familiaris ENSCAFG000000289551 retrocopy
Choloepus hoffmanni ENSCHOG000000091539 retrocopies
Callithrix jacchus ENSCJAG000000083119 retrocopies
Cavia porcellus ENSCPOG000000100022 retrocopies
Dipodomys ordii ENSDORG000000013723 retrocopies
Felis catus ENSFCAG0000001450210 retrocopies
Homo sapiens ENSG000001256919 retrocopies
Gorilla gorilla ENSGGOG000000250829 retrocopies
Latimeria chalumnae ENSLACG000000044301 retrocopy
Loxodonta africana ENSLAFG000000284504 retrocopies
Macropus eugenii ENSMEUG000000011882 retrocopies
Myotis lucifugus ENSMLUG000000156739 retrocopies
Macaca mulatta ENSMMUG000000045029 retrocopies
Monodelphis domestica ENSMODG000000126343 retrocopies
Mustela putorius furoENSMPUG000000150752 retrocopies
Mus musculus ENSMUSG0000007141510 retrocopies
Nomascus leucogenys ENSNLEG000000006427 retrocopies
Ornithorhynchus anatinus ENSOANG000000012301 retrocopy
Oryctolagus cuniculus ENSOCUG000000139156 retrocopies
Otolemur garnettii ENSOGAG000000124457 retrocopies
Ochotona princeps ENSOPRG00000001957 10 retrocopies
Pongo abelii ENSPPYG0000000850110 retrocopies
Pan troglodytes ENSPTRG000000090799 retrocopies
Pteropus vampyrus ENSPVAG000000022772 retrocopies
Rattus norvegicus ENSRNOG0000000410710 retrocopies
Sus scrofa ENSSSCG000000215903 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000142792 retrocopies
Vicugna pacos ENSVPAG000000056942 retrocopies



Copyright © RetrogeneDB 2014-2017