RetrogeneDB ID:

retro_opri_253

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_4240:166780..167203(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSOPRG00000012620
Aliases:None
Description:ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]


Retrocopy-Parental alignment summary:






>retro_opri_253
CCCAAAGCTGAAGCCAAAGCGAAGGCTCTGGAGGCCAAGAAGGCGGTGCTGAGCGATGTCCACAGCCACATGTATACCTG
CATGTCACCCACCTTCCAGTGGCCCAAGACTCAGGGCCTGCAGCAGCAGCCCAAACTCCCAGGAAGAACACCCCCAGGAG
GAACAAGCTTGATTGCTACACTATCATCAAGTTCTCCCTGAGCACAGAGTCCGCTATGAAGAAATTAGAAGACAACAACA
CACTTGTGTTCATTGTGATGTCAAGGCCGACTAGCAGCAAATCAAATAAGCCGTGAGGAAGCTCTGTGACACTGATGTGG
CCCAAGTCAATACCCTGATCAGACCTGATGGAAAAAGAAGGCGTATGTGTGACTGGCTCCTGATTACGATTGTCTGGATG
TCGCCAATAAAATTGGGATCATT

ORF - retro_opri_253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.47 %
Parental protein coverage: 97.96 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTQRLRRQPKYP-RKSAPRRNKLDHYAIIKFPL
PKAEAKAKAL.AKKAVL..V..H.......SPTF..PKTQ.L..QPK.P.RK..PRRNKLD.Y.IIKF.L
RetrocopyPKAEAKAKALEAKKAVLSDV--HSHMYTCMSPTFQWPKTQGLQQQPKLP<RKNTPRRNKLDCYTIIKFSL
ParentalTTESAMKKIEDNNTLVFIV-DVKANKHQIKQAVKKLYDIDVAKVNTLIRPDG-EKKAYVRLAPDYDALDV
.TESAMKK.EDNNTLVFIV.DVKA...QIK.AV.KL.D.DVA.VNTLIRPDG..KKAYV.LAPDYD.LDV
RetrocopySTESAMKKLEDNNTLVFIV<DVKAD*QQIK*AVRKLCDTDVAQVNTLIRPDG<KKKAYV*LAPDYDCLDV
ParentalANKIGII
ANKIGII
RetrocopyANKIGII

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_253 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 6 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG0000000097410 retrocopies
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG0000001338716 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Ochotona princeps ENSOPRG00000012620 49 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies



Copyright © RetrogeneDB 2014-2017