RetrogeneDB ID:

retro_opri_654

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_221:239436..239836(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NSA2
Ensembl ID:ENSOPRG00000001867
Aliases:None
Description:NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30728]


Retrocopy-Parental alignment summary:






>retro_opri_654
AAGGGAAAAACAGAAGTATGACAAGTTATTTGAACAGGAAAAAGAAAAAAGAAGGCATGGAAGAGGATGGTTACCAAAGC
CTGCTTTGTTGGAGATGGCTTTACAAGAAAACCACCCAAATAGGAAAGATGCATTAGACCAAGGCAATTACATTTCAAGA
AAAGCCCATGGAACATATCCAGAACTGGAAGACACCTTCTGCCTGCCAATATTAGGTGTAAAACAGAGCCCATCATCCCC
ATTGTATACAACTCTGGGTGTAACTACCAAAGGTACTGCTATTGGGGTGAATGTGAGTAAGTGGGCTTTGTAATACAAGG
AAGCAAGTTATATGGGAGAAATATGTCCAAGTTCTCACAATCCTGAAAATGATGGATACATAAATTTAGTCTTACTTGTT

ORF - retro_opri_654 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.64 %
Parental protein coverage: 51.54 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalQGETEVLKVIRTGKRKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFK-KAHVTHPELKATFCLP
.G.TEV..VI.TGKRKKKAWKRMVTK.CFVGDGFTRKPPK.ER.IRP..L.FK.KAH.T.PEL..TFCLP
RetrocopyKGKTEV*QVI*TGKRKKKAWKRMVTKACFVGDGFTRKPPK*ERCIRPRQLHFK>KAHGTYPELEDTFCLP
ParentalILGVKKNPSSPLYTTLGVITKGTVIEVNVSE-LGLVTQGGK-VIWGKYAQV-TNNPENDGCINAVLLV
ILGVK..PSSPLYTTLGV.TKGT.I.VNVS...G.V.QG.K.VIW.KY.QV...NPENDG.IN.VLLV
RetrocopyILGVKQSPSSPLYTTLGVTTKGTAIGVNVSK<VGFVIQGSK<VIWEKYVQV<SHNPENDGYINLVLLV

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_654 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 24 parental genes, and 176 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000083114 retrocopies
Callithrix jacchus ENSCJAG000000168741 retrocopy
Cavia porcellus ENSCPOG000000066481 retrocopy
Dasypus novemcinctus ENSDNOG000000106151 retrocopy
Echinops telfairi ENSETEG0000000409513 retrocopies
Felis catus ENSFCAG000000119781 retrocopy
Homo sapiens ENSG000001643464 retrocopies
Gorilla gorilla ENSGGOG000000143656 retrocopies
Loxodonta africana ENSLAFG000000099104 retrocopies
Macropus eugenii ENSMEUG000000157983 retrocopies
Microcebus murinus ENSMICG000000007523 retrocopies
Macaca mulatta ENSMMUG000000111966 retrocopies
Monodelphis domestica ENSMODG000000019004 retrocopies
Mustela putorius furoENSMPUG000000057955 retrocopies
Nomascus leucogenys ENSNLEG0000000504610 retrocopies
Oryctolagus cuniculus ENSOCUG000000065366 retrocopies
Ochotona princeps ENSOPRG00000001867 7 retrocopies
Pongo abelii ENSPPYG000000259268 retrocopies
Pan troglodytes ENSPTRG000000169906 retrocopies
Rattus norvegicus ENSRNOG0000001653015 retrocopies
Sorex araneus ENSSARG000000094244 retrocopies
Sarcophilus harrisii ENSSHAG000000176545 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000079593 retrocopies
Tupaia belangeri ENSTBEG0000001297856 retrocopies



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