RetrogeneDB ID:

retro_opri_38

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_1225:101094..101342(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP1
Ensembl ID:ENSOPRG00000001163
Aliases:None
Description:ribosomal protein, large, P1 [Source:HGNC Symbol;Acc:10372]


Retrocopy-Parental alignment summary:






>retro_opri_38
CAGATCAACACCCTTTTTAAGGCAGCCTGCGACAACGTGGAGCCCTTCTGGCCTGGCTTGCTCGGCAAGGTCCTGGCCAA
TATCAAATCAGGAGCCTCATCTGTAACATGGGGTCTGGTGGACCAGCTCCAGTAGCAGGTGCTGCCCCTGCAGGAGGTAC
TGCGCCCACCACCACTGCCGCTCCAGCTAAGAGAGTGCGAGCCAAGAACGAAAAGTCTGGTGACGACATGGGCTTCGGGC
TTTTTGAT

ORF - retro_opri_38 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.42 %
Parental protein coverage: 77.19 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKINALIKAAGVNVEPFWPGLFAKALANVNIG-SLICNVGAGGPAPAAGAAPAGGPAPAAAAAPAEEKKVE
.IN.L.KAA..NVEPFWPGL..K.LAN...G.SLICN.G.GGPAP.AGAAPAGG.AP...AAPA..K.V.
RetrocopyQINTLFKAACDNVEPFWPGLLGKVLANIKSG<SLICNMGSGGPAPVAGAAPAGGTAPTTTAAPA--KRVR
ParentalAKKEESEESDDDMGFGLFD
AK.E.S....DDMGFGLFD
RetrocopyAKNEKS---GDDMGFGLFD

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_38 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 30 parental genes, and 282 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001425120 retrocopies
Bos taurus ENSBTAG000000183204 retrocopies
Choloepus hoffmanni ENSCHOG0000000594410 retrocopies
Callithrix jacchus ENSCJAG0000003291919 retrocopies
Cavia porcellus ENSCPOG000000043216 retrocopies
Dasypus novemcinctus ENSDNOG0000001422426 retrocopies
Equus caballus ENSECAG000000085424 retrocopies
Felis catus ENSFCAG0000003203723 retrocopies
Gorilla gorilla ENSGGOG0000000398013 retrocopies
Latimeria chalumnae ENSLACG000000126301 retrocopy
Loxodonta africana ENSLAFG000000320603 retrocopies
Macropus eugenii ENSMEUG000000152776 retrocopies
Macropus eugenii ENSMEUG000000152822 retrocopies
Myotis lucifugus ENSMLUG0000001054233 retrocopies
Macaca mulatta ENSMMUG000000148887 retrocopies
Monodelphis domestica ENSMODG000000092091 retrocopy
Monodelphis domestica ENSMODG000000092184 retrocopies
Mustela putorius furoENSMPUG0000000020413 retrocopies
Mustela putorius furoENSMPUG000000170962 retrocopies
Mus musculus ENSMUSG000000078926 retrocopies
Oryctolagus cuniculus ENSOCUG000000150878 retrocopies
Ochotona princeps ENSOPRG00000001163 11 retrocopies
Pongo abelii ENSPPYG000000066015 retrocopies
Pan troglodytes ENSPTRG000000072281 retrocopy
Rattus norvegicus ENSRNOG000000119556 retrocopies
Rattus norvegicus ENSRNOG000000138743 retrocopies
Sus scrofa ENSSSCG0000000497016 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000278938 retrocopies
Tarsius syrichta ENSTSYG000000139271 retrocopy
Tursiops truncatus ENSTTRG0000001365620 retrocopies



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