RetrogeneDB ID: retro_opri_55

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1464:66535..67318(+)
• Located in intron of: ENSOPRG00000004385

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RBM39
• Ensembl ID: ENSOPRG00000002183
• Aliases: None
• Description: RNA binding motif protein 39 [Source:HGNC Symbol;Acc:15923]

Sequence

>retro_opri_55
CCCTTCAGAGAAGACGAGGGGCCTGTGAGAGAGCCTGGGGATATTGTAACTCCTGAGCAAAGAGATGCTTGGGCAATATT
CTGCATGCAGTTGGCAATGAGAATTTGACCACGAGATTGGGAAGAATTCTTTTCTGCAGTAGGAAAGGTTCAAGATGTGA
GGGTGGTTTCTGATAGGAATTCAAGTCATTCCAAGGGAATTGCTTATGTAGAGTTTGTCGATGTGAGCTTATTGCCTCTA
GCAATAGTATTAATTGGCCAGCGAGTTTTAGGAATGCCAGTCATAGTACAGGCTTCACAGGCAGAAAAAACAGAGCTGCA
GCATTGCCAAACAATTTACAAAAGGGGATAGATAGCTGGGCCTGTGAGACTTTATGTGGGCTTGTTCACTTAAACATAAC
AGAAGACATGCTTAGAGGAATCTTTGAACCTTTTGGAAGGATTGAAAGTAGACAGCTCATGCTGGATGGCAAACCAGGCC
ATTGGAAAAGATGTGGGTTTATTACATTATCTGATTTAGAATTTGCCAAAAAGGCTTCAGAACAACTGAATGGATTTGAA
CTAGCAAGAAGGCCATGAAGGTTGGTCATGTTACTGAGTGGACGGATGCTTCCAGTGCTAGCTCATCTTTGGACAGTGAT
GAACTGGAAAGGACTAGAGTTGGCTTGGGAGCAACTAGTCATCTGCAATTAGTGTCAAGACTTGCACAGGGCACAGATTG
GCAGATTCCTCCAGCAGCACGAGCTCTGGGAATGATGGTTCTTTGGCATTCGGTGCTGTGGCA

Alignment

ORF - retro_opri_55 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.18 %
• Parental protein coverage: 56.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PFRKDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYV
          PFR.D..PVREP.D..TPE.RDA...FCMQLA.RI.PRD.EEFFS.VGKV.DVR..SDRNS..SKGIAYV
Retrocopy PFREDEGPVREPGDIVTPEQRDAWAIFCMQLAMRI*PRDWEEFFSAVGKVQDVRVVSDRNSSHSKGIAYV

Parental  EFVDVSSVPLAIGLTGQRVLGVPIIVQASQAE-KNRAAAMANNLQKG-SAGPMRLYVGSLHFNITEDMLR
          EFVDVS..PLAI.L.GQRVLG.P.IVQASQAE.KNRAAA..NNLQKG..........G..H.NITEDMLR
Retrocopy EFVDVSLLPLAIVLIGQRVLGMPVIVQASQAE<KNRAAALPNNLQKGIDSWACETLCGLVHLNITEDMLR

Parental  GIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRP-MKVGHVTERTDASSAS
          GIFEPFGRIES.QLM.D...G..K..GFIT.SD.E.AKKA.EQLNGFELA.RP.MKVGHVTE.TDASSAS
Retrocopy GIFEPFGRIESRQLMLDGKPGHWKRCGFITLSDLEFAKKASEQLNGFELARRP<MKVGHVTEWTDASSAS

Parental  SFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQM-SGSLAFGAVA
          S.LDSDELERT...LG.T..LQL..RLA.GT..QIPPAA..AL.M..GSLAFGAVA
Retrocopy SSLDSDELERTRVGLGATSHLQLVSRLAQGTDWQIPPAA-RALGM<DGSLAFGAVA

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_55 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017535	1 retrocopy	retro_cjac_2199,
Homo sapiens	ENSG00000131051	1 retrocopy	retro_hsap_4679,
Gorilla gorilla	ENSGGOG00000003950	1 retrocopy	retro_ggor_2902,
Myotis lucifugus	ENSMLUG00000003000	1 retrocopy	retro_mluc_1152,
Macaca mulatta	ENSMMUG00000031284	1 retrocopy	retro_mmul_2491,
Mus musculus	ENSMUSG00000027620	3 retrocopies	retro_mmus_1512, retro_mmus_2792, retro_mmus_2793,
Nomascus leucogenys	ENSNLEG00000010350	1 retrocopy	retro_nleu_2170,
Otolemur garnettii	ENSOGAG00000011227	1 retrocopy	retro_ogar_267,
Ochotona princeps	ENSOPRG00000001092	2 retrocopies	retro_opri_126, retro_opri_412,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55 , retro_opri_913,
Pongo abelii	ENSPPYG00000010963	1 retrocopy	retro_pabe_3634,