RetrogeneDB ID: retro_ocun_1583

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018702:5871018..5871597(-)
• Located in intron of: ENSOCUG00000017834

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_1583
AGACTCACTGGTTTCTTAAGGCACCCAAACCTTCTGGCAAACCATTGTTAAAGTCTGATAAGACTTCTAGCAAAGGCAGT
AAGAAGGATTGGGACAGTTCTGGAACAGCAAGGAAAGCAAACAAACCAAATATCCTGAAATTCTGTGATATTAGCCTAAT
AGTGATACAGACAAAAACAAAAACCAGTAAGTCTTCAGAGAATGAAGATAAAGAAAGTGAAGAGGAGCCACCAAAAAAGA
CTTCTAAAAGAGAAAAACCTAAACAGAGGGCTGCAGCTAAAAGTAAAATGTCTCTAAAGTGCTAGTGTTAAGAAAGCAGA
TAGCAGCACCACCAAGAAAAATCAAAACGGTTCCAAGAAATAAAGTAAATCTGAGGACAGTTTGAATGCTGAACCTTTAA
TGTAAAAACTGAAGAAACCACCTACAGATGAAGAGTTAAAGGAAACAGTTAAGAAATTATTGGACAATACTAACTTGGAG
GAAGCCACAATGAAGCAGATTTGTAAAGACATTTAGGAAAATTTTCCTGCTTATGACTTAACTGAAATAAAATATTTCAT
AAAAACTGTTGAAGAACTA

Alignment

ORF - retro_ocun_1583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.5 %
• Parental protein coverage: 52.27 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RILNFLMHP-KPSGKPLPKSKKTSSKGSKKERNSSGTTRKA-KRTKYPEILSDESSSDEDEKKNK-EESS
          R...FL.HP.KPSGKPL.KS.KTSSKGSKK...SSGT.RKA.K.TKYPEIL.....SD.D..KN....S.
Retrocopy RLTGFLRHP<KPSGKPLLKSDKTSSKGSKKDWDSSGTARKA<KQTKYPEIL*Y*PNSDTDKNKNQ>KSSE

Parental  EDEDKESEEEPPKKTSKREKPKQKAVAKSKKSVK-SANVKKADSSTTKKNQNSSKKESESEDSSDDEPLI
          ....KESEEEPPKKTSKREKPKQ.A.AKSK.S.K.....K...S.T.KKNQN.SKK.S.SEDS...EPL.
Retrocopy NED-KESEEEPPKKTSKREKPKQRAAAKSKMSLK>ASVKKADSSTT-KKNQNGSKK*SKSEDSLNAEPLM

Parental  KKLKKPPTDEELKETVKKLLANANLEEVTMKQICKEVYENYPAYDLTERKDFIKTTVKEL
          .KLKKPPTDEELKETVKKLL.N.NLEE.TMKQICK...EN.PAYDLTE.K.FIK.TV.EL
Retrocopy *KLKKPPTDEELKETVKKLLDNTNLEEATMKQICKDI*ENFPAYDLTEIKYFIK-TVEEL

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	0.10 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_1583 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1583 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,