RetrogeneDB ID:

retro_opri_734

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_269:376293..376717(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PHB
Ensembl ID:ENSOPRG00000000868
Aliases:None
Description:prohibitin [Source:HGNC Symbol;Acc:8912]


Retrocopy-Parental alignment summary:






>retro_opri_734
ATGGTGGCGCGCTTTGACGCAGGCGAGCTCATCACGCAGCGAGAACTGGTCTCCAGGCAGGTGAGCGACGACCTCACGAA
GTGGGCAGCCACCTTTGGCCTCATCCTGGATGACGTGTCCTTAATGCAGCTGACCTTCGGGAAGGAGTTCACAGAAGCTG
TGGAGCCAAGCAGGTGGCTCAGCAGGAGGCCAAGCGGGCCAGATTTGTGGTGGAGAAGGCCGAGCAGCAGCAGAAGGCTG
CCATCATTTCTGCCGAAGGTGACTCCAAGGCCACTGAGCTGATTGCCAACTCGCTGGCCTCAGCGGGTGACGGCCTGATT
GAGCTGTGCAAGCTGGAGGCGGGGAGGACATCGCATACCAGCTCTTGCGCTCCCTGAACATCACCTACCTGCCGGCCGGC
CAGTCTGCTCCTGCAGCTGCCCCA

ORF - retro_opri_734 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.81 %
Parental protein coverage: 52.21 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVVARFDAGELITQRELVSRQVSDDLTERAATFGLILDDVSLTHLTFGKEFTEAVE-AKQVAQQEAERARF
.VARFDAGELITQRELVSRQVSDDLT..AATFGLILDDVSL..LTFGKEFTEAVE.AKQVAQQEA.RARF
RetrocopyMVARFDAGELITQRELVSRQVSDDLTKWAATFGLILDDVSLMQLTFGKEFTEAVE<AKQVAQQEAKRARF
ParentalVVEKAEQQKKAAIISAEGDSKAAELIANSLASAGDGLIELRKLEA-AEDIAYQLSRSRNITYLPAGQSVL
VVEKAEQQ.KAAIISAEGDSKA.ELIANSLASAGDGLIEL.KLEA..EDIAYQL.RS.NITYLPAGQS..
RetrocopyVVEKAEQQQKAAIISAEGDSKATELIANSLASAGDGLIELCKLEA<GEDIAYQLLRSLNITYLPAGQSAP
ParentalLQLP
...P
RetrocopyAAAP

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_734 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 18 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000047971 retrocopy
Choloepus hoffmanni ENSCHOG000000075882 retrocopies
Callithrix jacchus ENSCJAG0000000717422 retrocopies
Erinaceus europaeus ENSEEUG000000064813 retrocopies
Homo sapiens ENSG0000016708515 retrocopies
Gorilla gorilla ENSGGOG0000002800212 retrocopies
Macropus eugenii ENSMEUG000000051221 retrocopy
Microcebus murinus ENSMICG000000069669 retrocopies
Myotis lucifugus ENSMLUG000000082032 retrocopies
Macaca mulatta ENSMMUG0000000015613 retrocopies
Monodelphis domestica ENSMODG000000122101 retrocopy
Oryctolagus cuniculus ENSOCUG000000072091 retrocopy
Otolemur garnettii ENSOGAG000000270151 retrocopy
Ochotona princeps ENSOPRG00000000868 2 retrocopies
retro_opri_180, retro_opri_734 ,
Procavia capensis ENSPCAG000000088511 retrocopy
Pan troglodytes ENSPTRG0000000937614 retrocopies
Rattus norvegicus ENSRNOG0000004679918 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000199292 retrocopies



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