RetrogeneDB ID:

retro_opri_1107

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_71816:1357..1616(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS13
Ensembl ID:ENSOPRG00000000162
Aliases:None
Description:ribosomal protein S13 [Source:HGNC Symbol;Acc:10386]


Retrocopy-Parental alignment summary:






>retro_opri_1107
ATGGGTCCCATGCACGGTCCCGGGAAGGGCCTGTCCCAGTCGGCTCTGCCCCTATCGCCGCAGCGTCCCCACCTGGCTGA
AGCTGACGTCCGACGACGTGAAGGAGCAGATTTACAAACTGGGCAAAGAAGGGCCTGACGCCCTCCCAGATCGGTGTGAT
CCTGAGGGGACTCCCACGGCGTCGCTCAGCTGCGTTTCGTGACAGGCAATAAGATCTTGGAGGATCCTGAAGGCCAAAGG
CTGGCTCCCCGATCCTCCC

ORF - retro_opri_1107 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.64 %
Parental protein coverage: 56.29 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGRMHAPGKGLSQSAL-PYRRSVPTWLKLTSDDVKEQIYKL-AKKGLTPSQIGVILR-DSHGVAQVRFVT
MG.MH.PGKGLSQSAL.PYRRSVPTWLKLTSDDVKEQIYKL.AKKGLTPSQIGVILR.DSHGVAQ.RFVT
RetrocopyMGPMHGPGKGLSQSAL>PYRRSVPTWLKLTSDDVKEQIYKL>AKKGLTPSQIGVILR>DSHGVAQLRFVT
ParentalGNKIL-RILKSKGLAPDLP
GNKIL.RILK.KG..PD.P
RetrocopyGNKIL>RILKAKGWLPDPP

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_1107 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 35 parental genes, and 161 retrocopies.

Species Parental gene accession Retrocopies number
Caenorhabditis elegans C16A3.91 retrocopy
Ailuropoda melanoleuca ENSAMEG000000028953 retrocopies
Bos taurus ENSBTAG000000403085 retrocopies
Choloepus hoffmanni ENSCHOG000000087214 retrocopies
Callithrix jacchus ENSCJAG000000095641 retrocopy
Cavia porcellus ENSCPOG000000000233 retrocopies
Dipodomys ordii ENSDORG000000025073 retrocopies
Equus caballus ENSECAG0000001492812 retrocopies
Felis catus ENSFCAG000000053702 retrocopies
Homo sapiens ENSG000001107006 retrocopies
Gorilla gorilla ENSGGOG000000074503 retrocopies
Latimeria chalumnae ENSLACG000000171741 retrocopy
Loxodonta africana ENSLAFG000000268813 retrocopies
Macropus eugenii ENSMEUG000000149862 retrocopies
Microcebus murinus ENSMICG000000037168 retrocopies
Myotis lucifugus ENSMLUG000000097513 retrocopies
Macaca mulatta ENSMMUG000000225472 retrocopies
Monodelphis domestica ENSMODG000000070786 retrocopies
Mustela putorius furoENSMPUG000000133161 retrocopy
Mus musculus ENSMUSG0000009086219 retrocopies
Nomascus leucogenys ENSNLEG000000267394 retrocopies
Ornithorhynchus anatinus ENSOANG000000076871 retrocopy
Oryctolagus cuniculus ENSOCUG000000055366 retrocopies
Otolemur garnettii ENSOGAG000000021287 retrocopies
Ochotona princeps ENSOPRG00000000162 5 retrocopies
Pongo abelii ENSPPYG000000034566 retrocopies
Pteropus vampyrus ENSPVAG000000128063 retrocopies
Rattus norvegicus ENSRNOG000000205022 retrocopies
Sarcophilus harrisii ENSSHAG000000040523 retrocopies
Sus scrofa ENSSSCG000000133815 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000089965 retrocopies
Tupaia belangeri ENSTBEG000000077177 retrocopies
Tarsius syrichta ENSTSYG0000001311411 retrocopies
Tursiops truncatus ENSTTRG000000163213 retrocopies
Vicugna pacos ENSVPAG000000014635 retrocopies



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