RetrogeneDB ID: retro_ocun_1857

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019423:11273..12239(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEK
• Ensembl ID: ENSOCUG00000003869
• Aliases: None
• Description: DEK oncogene [Source:HGNC Symbol;Acc:2768]

Sequence

>retro_ocun_1857
GAGAGTCTCACGGTGGAAGGCAAGAGGGAAAAGAACAAAGTAGAGAGGTTGACAGTGCAAGTCTCTTCCTTACAAAGGGA
GCCATTTACAGTTGCACAAGGACAGGGGCAGGCACTTTGTGAAACTGAAAGGATGTATTTGTTTCTGAGTAAGAAGAAAG
CAGATAAAATTAGAAATCTACAAAAACTGCTTTACAATAGACCAGACACAGTGTCCTCATTGAAGAAGAATGTGGGTCAG
TTCAGAGGTTTTCCACTTGAAAATGGAAGTATTCAGTATAAAAAGAAGGAAGAAATGTTGAAAAAGTTTAGAAATGCCAT
GTTAAAGAGCATCTGCATGGTTCTTGATTAGGAGAGGTCAGGTGTAAATAGTGAACGAGTGAAGAGGATCTTGAATTTCT
TATTGCATCCAAAGCCTTCTGGCAAACCATTGCCAAATTCTAGAAAGACTTCTAGCAAAGGCAAGAAGAAGGTGCGCAAC
AGCTCTGGAACAACAAGGAAGGCGAAGCAAACCAAATATCCTGAAATTCTGTCAGATGAGTCTAGTAGTGATGATGAAAA
GAAAAACAAGAGTCTTCAGAGGATGAAGGTAAAGAAAGTGAAGAGGAGCCATTGAAAAAGACTTCTAATAGAGAAAAACC
TAAACAGAAAGCTACTGCAAAAGTAAAATGTCTGTAAAAAGTGCTAATGTTAAGAAAGCAGACAGCAGCACTGCCAAGAA
GAATCAAGACAGTTCAAGAAAGAAAGTGAATCTGAGGATAGTTCAGATGATGAACCTTTAAGTAAAAAATTGAAGAAACC
ACCTACCGAAGAAGAGTTAAAGGAAACAGTAAAGAAATTATTGGCCAAATCTAACTTGGAGGAAGTCACAATGAAGCAGA
TTTGTAAAGAGGTATAGGAAAATTATCCTGCTTATGAGTTAACTGAAAGAAAAGATTTCATTAAAACAACCGTTAAAGAA
CTAATT

Alignment

ORF - retro_ocun_1857 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.15 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSLIVEGKREKKKVERLTMQVSSLQREPFTIAQGKGQKLCEIERIHFFLSKKKTDELRNLHKLLYNRPGT
          .SL.VEGKREK.KVERLT.QVSSLQREPFT.AQG.GQ.LCE.ER...FLSKKK.D..RNL.KLLYNRP.T
Retrocopy ESLTVEGKREKNKVERLTVQVSSLQREPFTVAQGQGQALCETERMYLFLSKKKADKIRNLQKLLYNRPDT

Parental  VSSLKKNVGQFSGFPFEKGSIQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPKPS
          VSSLKKNVGQF.GFP.E.GSIQYKKKEEMLKKFRNAMLKSIC.VLD.ERSGVNSE.VKRILNFL.HPKPS
Retrocopy VSSLKKNVGQFRGFPLENGSIQYKKKEEMLKKFRNAMLKSICMVLD*ERSGVNSERVKRILNFLLHPKPS

Parental  GKPLPKSKKTSSKGSKKERNSSGTTRKAKRTKYPEILSDESSSDEDEKKN-KEESSEDEDKESEEEPPKK
          GKPLP.S.KTSSKG.KK.RNSSGTTRKAK.TKYPEILSDE..S..D..K..K.ESSEDE.KESEEEP.KK
Retrocopy GKPLPNSRKTSSKGKKKVRNSSGTTRKAKQTKYPEILSDE--SSSDDEKK<KQESSEDEGKESEEEPLKK

Parental  TSKREKPKQKAVAK-SKKSVKSANVKKADSSTTKKNQNSS-KKESESEDSSDDEPLIKKLKKPPTDEELK
          TS.REKPKQKA.AK.SK.SVKSANVKKADSST.KKNQ.SS.KKESESEDSSDDEPL.KKLKKPPT.EELK
Retrocopy TSNREKPKQKATAK<SKMSVKSANVKKADSSTAKKNQDSS<KKESESEDSSDDEPLSKKLKKPPTEEELK

Parental  ETVKKLLANANLEEVTMKQICKEVYENYPAYDLTERKDFIKTTVKELI
          ETVKKLLA..NLEEVTMKQICKEV.ENYPAY.LTERKDFIKTTVKELI
Retrocopy ETVKKLLAKSNLEEVTMKQICKEV*ENYPAYELTERKDFIKTTVKELI

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.06 RPM	89.35 RPM
SRP017611_kidney	0.00 RPM	90.71 RPM
SRP017611_liver	0.00 RPM	45.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1857 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1857 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1857 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000018188	1 retrocopy	retro_etel_1367,
Loxodonta africana	ENSLAFG00000004470	1 retrocopy	retro_lafr_517,
Macaca mulatta	ENSMMUG00000019763	2 retrocopies	retro_mmul_1266, retro_mmul_2627,
Oryctolagus cuniculus	ENSOCUG00000003869	4 retrocopies	retro_ocun_1583, retro_ocun_1791, retro_ocun_1851, retro_ocun_1857 ,