RetrogeneDB ID: retro_opri_413

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_112372:62..736(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000017105
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OTUD6B
• Ensembl ID: ENSOPRG00000007655
• Aliases: None
• Description: OTU domain containing 6B [Source:HGNC Symbol;Acc:24281]

Sequence

>retro_opri_413
CACCAGCAGGAGATACAGGGATTCGACCAGAGCCCTGCCGGGCCCGCCGATGTCGATACGATCACGGAAGACCTGGCTAA
GATGGATCTGGAGAACCAGCCACCTTTCGTGTCCAGAGCTCAGCGAAGGCGTGAACGAAAGGCGGCCATCGAGCGAGAGC
GACGGGAGAGGATCCGCGTACAGGACAGGGAGCGTACGGCCAGCTATGGTCGTGAAGAGGAAGCGAAGCTGGCCACCATC
CTGCTCGCCAAGAATCTGGAGATGAAGTACATCCCAGCCGACGGCCACTGCATGTACCGCGCTGTGCAGCACCAGCTGCC
AGTATTTGTGACTGTGGCCAGCCTGCGCCGCAGCACTGCAGAATATATGCAACATCATGTTGACGAGTTCCTGCCATTTT
TTAGCAATCCCGACGGCCACACCTGTACCCGCAAAGACTTCCTCAAATACTGCGAGGATATCGACAGATGTGCATCCTGG
GGAACCCAAATCGAACTGCGAGCCCTGTCGCACATCCTGCAGACACCAATCGAGGTGATCCAGGCCGATTCGCCCATCAT
CACTATCGGAGAGGAGTACAACAAGAAGCCTCTCATCCTCGTCTACCTCCGCTACGCCTGCGACATAGGAGACATTACAA
TTCCGTAAGATCTATTGAGGTCAAAGGCACAGAA

Alignment

ORF - retro_opri_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.48 %
• Parental protein coverage: 77.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HKEELEQLKLSAKNK--IDSVADNLSNLVLENQPPRISKAQKRRDRKAALEKEREERIAEAEIENLSGAR
          H..E......S.......D.....L....LENQPP..S.AQ.RR.RKAA.E.ER.ERI.....E......
Retrocopy HQQEIQGFDQSPAGPADVDTITEDLAKMDLENQPPFVSRAQRRRERKAAIERERRERIRVQDRERTASYG

Parental  HIESEKLAQILAARQLEMKQIPSDGHCMYRAIEDQLKAHDCALTVAALRSRAAEYMRSHVDDFLPFLTNP
          ..E..KLA.IL.A..LEMK.IP.DGHCMYRA...QL.......TVA.LR...AEYM..HVD.FLPF..NP
Retrocopy REEEAKLATILLAKNLEMKYIPADGHCMYRAVQHQLPVF---VTVASLRRSTAEYMQHHVDEFLPFFSNP

Parental  NTGHVYSAEEFGKYCEDIVNTASWGGQLELRALSHILQTPIEIIQADSLPIVVGEEYKKNPLILVYMRHA
          ..GH......F.KYCEDI...ASWG.Q.ELRALSHILQTPIE.IQADS..I..GEEY.K.PLILVY.R.A
Retrocopy D-GHTCTRKDFLKYCEDIDRCASWGTQIELRALSHILQTPIEVIQADSPIITIGEEYNKKPLILVYLRYA

Parental  YGLGE-HYNSVTPLVSTTTE
          ...G..HYNSV.......TE
Retrocopy CDIGD<HYNSVRSIEVKGTE

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_413 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 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006971	1 retrocopy	retro_amel_74,
Bos taurus	ENSBTAG00000003481	2 retrocopies	retro_btau_236, retro_btau_969,
Choloepus hoffmanni	ENSCHOG00000004266	2 retrocopies	retro_chof_1969, retro_chof_2069,
Cavia porcellus	ENSCPOG00000013595	1 retrocopy	retro_cpor_103,
Equus caballus	ENSECAG00000018205	1 retrocopy	retro_ecab_44,
Felis catus	ENSFCAG00000029900	1 retrocopy	retro_fcat_124,
Loxodonta africana	ENSLAFG00000011002	1 retrocopy	retro_lafr_16,
Microcebus murinus	ENSMICG00000012278	1 retrocopy	retro_mmur_1222,
Myotis lucifugus	ENSMLUG00000016954	1 retrocopy	retro_mluc_1226,
Macaca mulatta	ENSMMUG00000013396	1 retrocopy	retro_mmul_350,
Monodelphis domestica	ENSMODG00000007551	2 retrocopies	retro_mdom_119, retro_mdom_1326,
Mustela putorius furo	ENSMPUG00000009194	1 retrocopy	retro_mputfur_51,
Mus musculus	ENSMUSG00000040550	1 retrocopy	retro_mmus_2456,
Nomascus leucogenys	ENSNLEG00000002420	1 retrocopy	retro_nleu_2365,
Oryctolagus cuniculus	ENSOCUG00000000218	1 retrocopy	retro_ocun_29,
Otolemur garnettii	ENSOGAG00000011298	1 retrocopy	retro_ogar_228,
Ochotona princeps	ENSOPRG00000007655	1 retrocopy	retro_opri_413 ,
Pan troglodytes	ENSPTRG00000020413	1 retrocopy	retro_ptro_3120,
Sus scrofa	ENSSSCG00000006120	1 retrocopy	retro_sscr_52,
Ictidomys tridecemlineatus	ENSSTOG00000002954	1 retrocopy	retro_itri_9,
Tupaia belangeri	ENSTBEG00000017070	1 retrocopy	retro_tbel_304,
Tursiops truncatus	ENSTTRG00000004345	1 retrocopy	retro_ttru_1207,