RetrogeneDB ID:

retro_opri_229

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_3847:265126..265396(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NUTF2
Ensembl ID:ENSOPRG00000013727
Aliases:None
Description:nuclear transport factor 2 [Source:HGNC Symbol;Acc:13722]


Retrocopy-Parental alignment summary:






>retro_opri_229
ATGGGAGACAAGCCAATTTGGGAGCGGATTGGATCCAGCTTCATTCAACATTACTACCAGTTATTTGATAATGACAGAAC
CCAGCTAGGCGCCATTTACGTTGATGCATCATGCCTTACATGGGAAGGACAGCAGTTCCAAGGGAAAGCTGCCATTGTGG
AGAAGTTATCTAGCCTTCCCTTCCAAAAAATCCAGCACAGCATCACGGCACAGGATCATCAGCCCACGCCAGATAGCTGC
ATCATTAGCATGGTTGTGGGCCAGCTCAAG

ORF - retro_opri_229 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.78 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITA
MGDKPIWE.IGSSFIQHYYQLFDNDRTQLGAIY.DASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITA
RetrocopyMGDKPIWERIGSSFIQHYYQLFDNDRTQLGAIYVDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITA
ParentalQDHQPTPDSCIISMVVGQLK
QDHQPTPDSCIISMVVGQLK
RetrocopyQDHQPTPDSCIISMVVGQLK

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_229 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 27 parental genes, and 116 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000175485 retrocopies
Choloepus hoffmanni ENSCHOG000000030593 retrocopies
Callithrix jacchus ENSCJAG0000001601514 retrocopies
Equus caballus ENSECAG000000215301 retrocopy
Echinops telfairi ENSETEG000000163549 retrocopies
Felis catus ENSFCAG000000081673 retrocopies
Homo sapiens ENSG000001028987 retrocopies
Gorilla gorilla ENSGGOG000000239255 retrocopies
Loxodonta africana ENSLAFG000000310371 retrocopy
Macropus eugenii ENSMEUG0000000987411 retrocopies
Myotis lucifugus ENSMLUG000000251753 retrocopies
Macaca mulatta ENSMMUG000000120386 retrocopies
Monodelphis domestica ENSMODG000000055176 retrocopies
Mustela putorius furoENSMPUG000000067374 retrocopies
Mus musculus ENSMUSG000000084501 retrocopy
Nomascus leucogenys ENSNLEG000000048897 retrocopies
Ochotona princeps ENSOPRG00000013727 4 retrocopies
Procavia capensis ENSPCAG000000153441 retrocopy
Pongo abelii ENSPPYG000000074727 retrocopies
Pan troglodytes ENSPTRG000000082487 retrocopies
Pteropus vampyrus ENSPVAG000000166051 retrocopy
Sorex araneus ENSSARG000000074721 retrocopy
Sarcophilus harrisii ENSSHAG000000061001 retrocopy
Sus scrofa ENSSSCG000000302953 retrocopies
Tupaia belangeri ENSTBEG000000110161 retrocopy
Tarsius syrichta ENSTSYG000000107023 retrocopies
Drosophila melanogaster FBgn00311451 retrocopy



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