RetrogeneDB ID: retro_opri_1178

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_88455:398..1225(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000010838
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSOPRG00000001281
• Aliases: None
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_opri_1178
CTGTTCAGGCTGGACGTGCACTCAGGCCAGATCACACACTGCCCCCTGATGGTGGACAGAGAGCCTCCTCGAGCCGGGAG
CCTGCCTGGCTCTGGCATCCATGCCATTGAGCTGAATCCCTCCAAGACACTTCTGGCCACAGGAGGCAAGAACCCCAATA
GCCTGGCTGTGTACCAGCTGCCCACCATGGACCCTGTGTGCCTGGGTGACATCCAAGGCCACAAAGACTGGATCTTTGCC
ATCGTATGGGTGCGTGACACCATGGTAGTGAGCGGTTCCGTGATGGCACCCTGGCTTTATGGCAGTTGGACTGTGAACTT
TTCCATGATACCATTGATTCTCACAGTAGCAGTGGTATCCCTGTGTATGGCCACATCCGTCCAGTGGATATGGTAGATAT
CTCCACATACAGCCCTCATCCCAGTCACCACCACGTGCGTGCCCTTGCCTTCAGCAGCAGAAACCAGGAACTGGGATCAG
TTTCCCTGGATGGCTACTTCCACCTCTGGAAACCTCAGAGCAACCTGTCCAGGCTGCTCTCCATCAGGATGCCCTACTTT
GGAGGGAATGTGTGCATGACTTACTGCAATGAGCTCTCCCTGTATGCTGTGGGCTCTAGTACCTATGTCTCTTTCCTGAG
TCCATGCCAGCCACAGGACAACTTCTGGGCCCTGCACTGTAGGGAATTTGGCATCAGTGTGTGCTCACTGAGTTACAACC
AGGACATTATCACTTTGGGAACGGTGCATGGCTCCCTGCTCTTCTATGGCATCCGTGCTAAGAAGTTCCTAGAGGACAGC
CCTGAGGTCCGCCAGGACTCTTCTCCA

Alignment

ORF - retro_opri_1178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.35 %
• Parental protein coverage: 60.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFVVDVQTSQITKIPILKDREPG-VMTQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGD
          LF..DV...QIT..P...DREP.......G.GIHAIELNPS.TLLATGG.NPNSLA.Y.LPT.DPVC.GD
Retrocopy LFRLDVHSGQITHCPLMVDREPPRAGSLPGSGIHAIELNPSKTLLATGGKNPNSLAVYQLPTMDPVCLGD

Parental  -DGHKDWIFSIAWISDTMAVSGS-RDGSMGLWEVTDEVLTKSDARHNMSQVPVYSHITHKALKDIPKEDT
          ..GHKDWIF.I.W..DTM.VSGS.RDG...LW....E........H..S..PVY.HI......DI.....
Retrocopy IQGHKDWIFAIVWVRDTMVVSGS<RDGTLALWQLDCELFHDTIDSHSSSGIPVYGHIRPVDMVDISTYSP

Parental  NPDNCKVRALAFNDKNKELGAVSLC-YFHLWA-ENTLSRLLSTKLPYCRENVCLAYGSEWTVYAEGSQAH
          .P....VRALAF...N.ELG.VSL..YFHLW.....LSRLLS...PY...NVC..Y..E...YA.GS...
Retrocopy HPSHHHVRALAFSSRNQELGSVSLDGYFHLWKPQSNLSRLLSIRMPYFGGNVCMTYCNELSLYAVGSSTY

Parental  VSFLDPRQPSYNVKSVCSRERGSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGSKP
          VSFL.P.QP..N......RE.G....S.S....IIT.GT..GSLLFY.IRA..FLE........S.P
Retrocopy VSFLSPCQPQDNFWALHCREFGISVCSLSYNQDIITLGTVHGSLLFYGIRAKKFLEDSPEVRQDSSP

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_1178 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000309	1 retrocopy	retro_amel_73,
Bos taurus	ENSBTAG00000021573	3 retrocopies	retro_btau_1794, retro_btau_1795, retro_btau_1796,
Equus caballus	ENSECAG00000023064	2 retrocopies	retro_ecab_1128, retro_ecab_1129,
Erinaceus europaeus	ENSEEUG00000013279	1 retrocopy	retro_eeur_403,
Microcebus murinus	ENSMICG00000005881	1 retrocopy	retro_mmur_14,
Macaca mulatta	ENSMMUG00000017458	1 retrocopy	retro_mmul_202,
Nomascus leucogenys	ENSNLEG00000004996	1 retrocopy	retro_nleu_6,
Otolemur garnettii	ENSOGAG00000015799	1 retrocopy	retro_ogar_237,
Ochotona princeps	ENSOPRG00000001281	2 retrocopies	retro_opri_1178 , retro_opri_470,
Pongo abelii	ENSPPYG00000019127	1 retrocopy	retro_pabe_64,
Pteropus vampyrus	ENSPVAG00000008654	1 retrocopy	retro_pvam_16,
Sus scrofa	ENSSSCG00000010986	1 retrocopy	retro_sscr_17,
Ictidomys tridecemlineatus	ENSSTOG00000006904	1 retrocopy	retro_itri_168,
Tarsius syrichta	ENSTSYG00000014394	1 retrocopy	retro_tsyr_1965,
Tursiops truncatus	ENSTTRG00000010591	1 retrocopy	retro_ttru_8,