RetrogeneDB ID:

retro_opri_1016

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_5809:21422..21746(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBA52
Ensembl ID:ENSOPRG00000004784
Aliases:None
Description:ubiquitin A-52 residue ribosomal protein fusion product 1 [Source:HGNC Symbol;Acc:12458]


Retrocopy-Parental alignment summary:






>retro_opri_1016
GTAGATCCTTGTGAAGACTCTGAAAATGTCAAGGCGAAGACCCAGAACAAAGAGGGCATCCTCCCGGACCAGCAGCATCT
TATCTTTGCCGGCAAGCCTCTGGAGGACGGTGGCACTCTGTGGGACTACAACATCCAGGAAGAGTGCACACTGCACCTGG
TGCTCCACCTGCAGGGCGGCATCATTGAGCAGTCCCTGCGCCAGCTCGCCCAGAAGTTACCACTGTGACAATATGATCTG
CTGCAAGTGCAACGCCCACCTGCACCCCTGCGCCCTCAACTGCCGCTGAGAAAACGCCGCCACACCAACAGCCTGCGCCC
CAAG

ORF - retro_opri_1016 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.82 %
Parental protein coverage: 84.38 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLRQLA
V.P....ENVKAK.Q.KEGI.PDQQ.LIFAGK.LEDG.TL.DYNIQ.E.TLHLVL.L.GGIIE.SLRQLA
RetrocopyVDPCEDSENVKAKTQNKEGILPDQQHLIFAGKPLEDGGTLWDYNIQEECTLHLVLHLQGGIIEQSLRQLA
ParentalQK-YNCDKMICRKCYARLHPRAVNCR-KKKCGHTNNLRPK
QK.Y.CD.MIC.KC.A.LHP.A.NCR...K..HTN.LRPK
RetrocopyQK>YHCDNMICCKCNAHLHPCALNCR<LRKRRHTNSLRPK

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_1016 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 16 parental genes, and 99 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001135610 retrocopies
Bos taurus ENSBTAG000000077373 retrocopies
Callithrix jacchus ENSCJAG0000000747022 retrocopies
Equus caballus ENSECAG000000206608 retrocopies
Felis catus ENSFCAG0000000974514 retrocopies
Homo sapiens ENSG000002219832 retrocopies
Latimeria chalumnae ENSLACG000000081321 retrocopy
Mustela putorius furoENSMPUG000000155278 retrocopies
Mus musculus ENSMUSG000000901373 retrocopies
Ochotona princeps ENSOPRG00000004784 6 retrocopies
Pongo abelii ENSPPYG000000097462 retrocopies
Pan troglodytes ENSPTRG000000392238 retrocopies
Rattus norvegicus ENSRNOG000000199747 retrocopies
Sarcophilus harrisii ENSSHAG000000070753 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000046781 retrocopy
Xiphophorus maculatus ENSXMAG000000039111 retrocopy



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