RetrogeneDB ID:

retro_opri_43

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_1304:123628..123954(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FTL
Ensembl ID:ENSOPRG00000002492
Aliases:None
Description:ferritin, light polypeptide [Source:HGNC Symbol;Acc:3999]


Retrocopy-Parental alignment summary:






>retro_opri_43
GTGACCTCCCAGATTCATCAGAATTATTCCACTGAGGTGGAGCCAGCCACCAACTGCCTGGTCAGTTTGCACCTGCGGGA
CTCCCACACCTACCTCTCTCTGGGCTACTATTTTGACCACGACGATGTGACTCTGGAGGACATGGGCCACTTCTCCCGCG
AGTTGGTGGGAGGATAAGTGTGAGGGCATTGAGCCTCTTTTGAAGATATGAAACCAACATGGCAGCTGCACCCTCTTCTA
AGATGTGCAGAAGCCATCTCAAGATGAGTGGGGGCAAGACCCAAGATGCCATGGAAGCCACCTTGGGCCTGGAGAACAAC
CTGAAT

ORF - retro_opri_43 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70. %
Parental protein coverage: 56.54 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMTSQIRQNYSTEVEAAVNRLVNLHLQASYTYLSLGYYFDRDDVALEGVGHFFRELA-DEKREGAERLLKM
.TSQI.QNYSTEVE.A.N.LV.LHL..S.TYLSLGYYFD.DDV.LE..GHF.REL....K.EG.E.LLK.
RetrocopyVTSQIHQNYSTEVEPATNCLVSLHLRDSHTYLSLGYYFDHDDVTLEDMGHFSRELV>EDKCEGIEPLLKI
ParentalQNQRGGRALFQDVQKPPQDEW-GKTQDALEAALGLEKNLN
.NQ.G...LF.DVQKP.QDEW.GKTQDA.EA.LGLE.NLN
Retrocopy*NQHGSCTLF*DVQKPSQDEW>GKTQDAMEATLGLENNLN

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_43 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 23 parental genes, and 312 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001458227 retrocopies
Bos taurus ENSBTAG0000001334333 retrocopies
Canis familiaris ENSCAFG000000038611 retrocopy
Callithrix jacchus ENSCJAG0000000025013 retrocopies
Cavia porcellus ENSCPOG000000205581 retrocopy
Dasypus novemcinctus ENSDNOG000000024559 retrocopies
Dasypus novemcinctus ENSDNOG000000041265 retrocopies
Dasypus novemcinctus ENSDNOG0000000557736 retrocopies
Dasypus novemcinctus ENSDNOG000000078482 retrocopies
Dasypus novemcinctus ENSDNOG000000166838 retrocopies
Felis catus ENSFCAG0000000334837 retrocopies
Gorilla gorilla ENSGGOG000000119999 retrocopies
Loxodonta africana ENSLAFG0000003124811 retrocopies
Macaca mulatta ENSMMUG000000039099 retrocopies
Mustela putorius furoENSMPUG0000000330429 retrocopies
Mus musculus ENSMUSG000000507081 retrocopy
Oryctolagus cuniculus ENSOCUG000000000146 retrocopies
Ochotona princeps ENSOPRG00000002492 10 retrocopies
Ochotona princeps ENSOPRG000000107347 retrocopies
Pan troglodytes ENSPTRG0000001126811 retrocopies
Rattus norvegicus ENSRNOG000000208437 retrocopies
Sus scrofa ENSSSCG0000000315333 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000206397 retrocopies



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