RetrogeneDB ID: retro_opri_295

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4807:105337..106092(-)
• Located in intron of: ENSOPRG00000006016

Retrocopy information

• Ensembl ID: ENSOPRG00000006043
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000018613
• Aliases: None
• Description: None

Sequence

>retro_opri_295
CCTGCCAACACATCTCTGTTTGTCAGGAACATGGTGGATGACACCAGGTCTGAAGATCTGCGGTGTAAGTTTGGTGGCTA
TGGTCCTATAGTTGATGTGTATGTTCCACTTGATTTCTACACTTGCCGTCCAAGAGGATTTGCTTATGTTCAATTTGAGG
ATGTTCAGGATGCTGAAGATGCTTTATATAATCTGGACAGAAAATGGATTTGCAGTCGCCAGACTGAAAACAGTTTGCAC
TGGGAGACCAGAAGACACCAAATCAAATAAAAGCCAAGCAAGGGAGAAATATGTACAGTTCTTCATCTTACGATGATTAT
GACAAATATAGACCTTCCAGACGCCGAAGTTATGAAACAAGATCAAGAAGTCGGTCTTTTGATTACAACTATAGAAGATC
TTACAGTCCTAGAAACAGTAGACCGACAGAAGGACCTCACCGTAGCAGGAGCCATTCCGACAATGATAGATTCAAACACT
GAAATCGATCTTTTTCAAGATCTAAATCCAATTCAAGATCACGGTCCAAGTCCCAGCCCAAGAAAGAAATGAAGGCTAAA
TCACAGTCTAGGTCTGCATCTCACACCACAAGTAGAGGCACCTCTAAAACAGAGTCCAAAACACATTATAAATCTGGCTC
AAAAGATGAATAGGAATCAAGGAAAAAGGAACCACCTAGATCCAAATCTCAGTCATGATCACAGTCTAGGTCCAAATCTA
GATCAAGGTCTTGGACTAGTCCTAAGTCCAGTGGC

Alignment

ORF - retro_opri_295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 97.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWI
          P.NTSLFVRN..DDTRSEDLR..FG.YGPIVDVYVPLDFYT.RPRGFAYVQFEDV.DAEDAL.NLDRKWI
Retrocopy PANTSLFVRNMVDDTRSEDLRCKFGGYGPIVDVYVPLDFYTCRPRGFAYVQFEDVQDAEDALYNLDRKWI

Parental  CGRQIEI-QFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYRRSYSPR
          C.RQ.E..QFA.GD.KTPNQ.KAK.GRN.YSSS.YDDYD.YR.SR.RSYE.R.SRSRSFDYNYRRSYSPR
Retrocopy CSRQTEN<QFALGDQKTPNQIKAKQGRNMYSSSSYDDYDKYRPSRRRSYETR-SRSRSFDYNYRRSYSPR

Parental  NSRPTGRPRRSRSHSDNDRFKHRNRSFSRSKSNSRSRSKSQPKKEMKAKSRSRSASHTKSRGTSKTDSKT
          NSRPT..P.RSRSHSDNDRFKH.NRSFSRSKSNSRSRSKSQPKKEMKAKS.SRSASHT.SRGTSKT.SKT
Retrocopy NSRPTEGPHRSRSHSDNDRFKH*NRSFSRSKSNSRSRSKSQPKKEMKAKSQSRSASHTTSRGTSKTESKT

Parental  HYKSGSRDEKESRKKEPPRSKSQSRSQSRSRSKSRSRSWTSPKSSG
          HYKSGS.DE.ESRKKEPPRSKSQS.SQ..SRSKSRSRSWTSPKSSG
Retrocopy HYKSGSKDE*ESRKKEPPRSKSQS*SQ--SRSKSRSRSWTSPKSSG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_295 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Loxodonta africana	ENSLAFG00000026905	1 retrocopy	retro_lafr_148,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mus musculus	ENSMUSG00000028676	5 retrocopies	retro_mmus_1081, retro_mmus_1311, retro_mmus_1814, retro_mmus_3480, retro_mmus_982,
Ochotona princeps	ENSOPRG00000018613	3 retrocopies	retro_opri_1067, retro_opri_295 , retro_opri_916,
Pan troglodytes	ENSPTRG00000024234	4 retrocopies	retro_ptro_1295, retro_ptro_1413, retro_ptro_1986, retro_ptro_918,