RetrogeneDB ID:

retro_opri_1022

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_588:107893..108250(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS20
Ensembl ID:ENSOPRG00000011042
Aliases:None
Description:ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]


Retrocopy-Parental alignment summary:






>retro_opri_1022
ATGGCCTTTAAGGATACCGGCAAGACGCCCGTGGAGCCCGAGGTGGCCATCCATTGCATCAGGATCACGCTGACCAGCCG
CAACGTCAAGTCCCTGGAGAAGGTGTGTGCTGCCTTGATCAGAGGAGCAAAGGAGAAGAATCTGAAAGTGAAAGGACCAG
TTCGGATGCCTACCAAGACTTTGAGAATCACTACCAGAAAAACGCCCTGTGGGGAAGGGTCCAAGACCTGGGACTGCTTC
CAGATGAGGATCCACAAGCGGCTCATCGACCTGCACAGTCCTTCAGAGATTGTGAAGCAGATCACCTCCATCAGCATTGA
GCCGGGAGTGGAGGTGGAGGTCACCATCACAGATGCC

ORF - retro_opri_1022 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPC
MAFKDTGKTPVEPEVAIH.IRITLTSRNVKSLEKVCA.LIRGAKEKNLKVKGPVRMPTKTLRITTRKTPC
RetrocopyMAFKDTGKTPVEPEVAIHCIRITLTSRNVKSLEKVCAALIRGAKEKNLKVKGPVRMPTKTLRITTRKTPC
ParentalGEGSKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA
GEGSKTWD.FQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTI.DA
RetrocopyGEGSKTWDCFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTITDA

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_1022 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 20 parental genes, and 280 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000001914711 retrocopies
Canis familiaris ENSCAFG0000002988420 retrocopies
Callithrix jacchus ENSCJAG000000166314 retrocopies
Dipodomys ordii ENSDORG000000057942 retrocopies
Echinops telfairi ENSETEG000000033943 retrocopies
Felis catus ENSFCAG0000002923322 retrocopies
Homo sapiens ENSG0000000898826 retrocopies
Gorilla gorilla ENSGGOG0000000183721 retrocopies
Macropus eugenii ENSMEUG0000001417121 retrocopies
Monodelphis domestica ENSMODG000000091146 retrocopies
Mustela putorius furoENSMPUG0000001045215 retrocopies
Nomascus leucogenys ENSNLEG0000000121419 retrocopies
Otolemur garnettii ENSOGAG0000000776010 retrocopies
Ochotona princeps ENSOPRG00000011042 11 retrocopies
Procavia capensis ENSPCAG000000043003 retrocopies
Pongo abelii ENSPPYG0000001860030 retrocopies
Pan troglodytes ENSPTRG0000002026427 retrocopies
Rattus norvegicus ENSRNOG000000085557 retrocopies
Sarcophilus harrisii ENSSHAG0000001120010 retrocopies
Sus scrofa ENSSSCG0000000624912 retrocopies



Copyright © RetrogeneDB 2014-2017