RetrogeneDB ID:

retro_opri_120

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2459:84019..84247(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPE
Ensembl ID:ENSOPRG00000015415
Aliases:None
Description:small nuclear ribonucleoprotein polypeptide E [Source:HGNC Symbol;Acc:11161]


Retrocopy-Parental alignment summary:






>retro_opri_120
GCTGTGGCAAACCAGGGCCAGAAAGCACAGGACGTGATGGTTCAGTCCATCCGATACCTGCAAACTTGATCTTGCATTCA
GGTGTGGCTGTATGAACACGTGAACAGGCAGACAGAGGGCTGCAGCACTGGTTTTGATGAATACATCAAGCAACCTGTAC
TAGATAATGCAGAAGAGATTCATTCTAAAACGAAGTAAAGAAAACAACTGGGTGGGATCATGTTAAAA

ORF - retro_opri_120 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.5 %
Parental protein coverage: 85.87 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNL-VLDDAEEIHSKTKS
A...QGQK.Q.VMVQ.I....RYLQ..S.IQVWLYE.VN...EGC..GFDEY....VLD.AEEIHSKTK.
RetrocopyAVANQGQKAQDVMVQSI----RYLQT*SCIQVWLYEHVNRQTEGCSTGFDEYIKQPVLDNAEEIHSKTK*
ParentalRKQLGRIMLK
RKQLG.IMLK
RetrocopyRKQLGGIMLK

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_120 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 9 parental genes, and 95 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000067351 retrocopy
Dasypus novemcinctus ENSDNOG0000000449024 retrocopies
Echinops telfairi ENSETEG0000001401524 retrocopies
Gorilla gorilla ENSGGOG000000007557 retrocopies
Loxodonta africana ENSLAFG000000093493 retrocopies
Myotis lucifugus ENSMLUG000000132448 retrocopies
Ochotona princeps ENSOPRG00000015415 11 retrocopies
Pongo abelii ENSPPYG000000003268 retrocopies
Sorex araneus ENSSARG000000033119 retrocopies



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