RetrogeneDB ID:

retro_opri_114

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2379:60788..61128(+)
Located in intron of:ENSOPRG00000014110
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS14
Ensembl ID:ENSOPRG00000008422
Aliases:None
Description:ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]


Retrocopy-Parental alignment summary:






>retro_opri_114
CATTTTTTTGAGTCCTTCAATGACACTTTTTTCCATGTCACTGATTTTTCTGGCAAGGAAACCATGTGCCACATGACCAA
TAGGATGAAGGTGACTGCTGACCGAGATGAATCCTCACTATACGCTGCCAGGTTGGCTGCCCAGGATGTTGCCCAGAGGT
GTAAGGAGCTGGGCATTACTGCCCTACACATCAAACTGTGGGCCACAAGAGGAAATAGGACCATCACCCACAGATCCAGA
CCCCAGTGAGCTCTCAGAGCCCTTGCCTGCTCGGGGATGGAACTGAGTGAACTGAGGATGTCACCCCAGCCCCTCTGACA
GCATCCGCAGGAAGGGGGGC

ORF - retro_opri_114 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.41 %
Parental protein coverage: 75.5 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESSPYAAMLAAQDVAQRCKELGITALHLKLRATG
H.F.SFNDTF.HVTD.SGKET.C..T..MKV.ADRDESS.YAA.LAAQDVAQRCKELGITALH.KL.AT.
RetrocopyHFFESFNDTFFHVTDFSGKETMCHMTNRMKVTADRDESSLYAARLAAQDVAQRCKELGITALHIKLWATR
ParentalGNRTKTPGPGAQSALRALARSGMKIGRI-EDVTPI-PSDSTRRKGG
GNRT.T.....Q.ALRALA.SGM......EDVTP..PSDS.RRKGG
RetrocopyGNRTITHRSRPQ*ALRALACSGMELSEL<EDVTPA<PSDSIRRKGG

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_114 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 14 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000046442 retrocopies
Bos taurus ENSBTAG000000085702 retrocopies
Canis familiaris ENSCAFG000000180942 retrocopies
Callithrix jacchus ENSCJAG000000209811 retrocopy
Equus caballus ENSECAG000000243363 retrocopies
Latimeria chalumnae ENSLACG000000161641 retrocopy
Loxodonta africana ENSLAFG000000311952 retrocopies
Myotis lucifugus ENSMLUG000000132794 retrocopies
Macaca mulatta ENSMMUG000000028485 retrocopies
Mustela putorius furoENSMPUG000000137761 retrocopy
Nomascus leucogenys ENSNLEG000000103661 retrocopy
Oryctolagus cuniculus ENSOCUG000000115091 retrocopy
Otolemur garnettii ENSOGAG000000007211 retrocopy
Ochotona princeps ENSOPRG00000008422 17 retrocopies



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