RetrogeneDB ID: retro_cfam_1362

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:10279772..10280732(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000007622
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DEK
• Ensembl ID: ENSCAFG00000010184
• Aliases: None
• Description: DEK oncogene [Source:HGNC Symbol;Acc:2768]

Sequence

>retro_cfam_1362
GGAAGGCAAGAGGGAAAAGAAAAAAGTAGATTGACCATGCAAGTCTCTTCCTTACAGAGAGAGCCATTTACAATTGCACA
AGGAAAGGGGCAGAAACTTTGTGAAATTGAGAGGATACATTTCTTCCTGAGTAAAAAGAAAACAGATGAACTTAGAAATC
TACATAAACTGCTTTACAACAGACCAGGCACAGTGTCCTCATTAAAGAAGAATGTGGGTCAGTTCAGTGGCTTTCCATTT
GAAAAAGGAAGTGCCCAGTATAAAAAGAAGGAAGAAATGTTGAAAAAATTTAGAAATGCCATGTTAAAGAGCATCTGTGA
GGTTCTTGATTTGGAGAGATCGGGTGTAAATAGTGAACTGGTGAAGAGGATCTTGAATTTCTTAATGCATCCAAAGCCTT
CTGGCAAACCATTGCCAAAATCTAAAAAAAGTTCTAGCAAAGGCAACAAAAAGGAACGGAACAGTTCTGGAATGGCAAGG
AAAGCTAAGCGAACCAAATGTCCTGAAATCCTGTCAGATGAATCTAGCAGTGATGAAGATGAAAAGAAAAACAAGGAAGA
GTCTTCAGATGATGAAGATAAAGAAAGTGAAGAGGAGCCCCCAAAAAAGACTTCTAAAAGAGAAAAACCTAAGCAGAAAG
CCACTTCTAAGAGTAAGAAAACTGTCAAGAGTGCTAATGTTAAGAAGGCAGATAGCAGCACCACCAAGAAAAATCAGAAC
AGTTCCAAAAAAGAAAGTGAATCCGAGGATAGTTCAGATGATGAACCTTTAATTAAAAAATTAAAGAAACCTCCTACAGA
TGAAGAGTTAAAGGAAACCGTGAAGAAACTATTGGCTAGTGCCAACTTGGAGGAAGTCACAATGAAGCAGATTTGCAAGG
AGGTATATGAAAATTATCCTGCTTATGATTTAACTGAAAGAAAAGATTTCATAAAAACAACCGTGAAAGAGCTGATTTCT

Alignment

ORF - retro_cfam_1362 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.82 %
• Parental protein coverage: 84.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKREKKKVERLTMQVSSLQREPFTIAQGKGQKLCEIERIHFFLSKKKTDELRNLHKLLYNRPGTEVSSLK
          G..E.K...RLTMQVSSLQREPFTIAQGKGQKLCEIERIHFFLSKKKTDELRNLHKLLYNRPGT.VSSLK
Retrocopy GRQEGKEKSRLTMQVSSLQREPFTIAQGKGQKLCEIERIHFFLSKKKTDELRNLHKLLYNRPGT-VSSLK

Parental  KNVGQFSGFPFEKGSAQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPKPSGKPLP
          KNVGQFSGFPFEKGSAQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPKPSGKPLP
Retrocopy KNVGQFSGFPFEKGSAQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPKPSGKPLP

Parental  KSKKSSSKGNKKERNSSGMARKAKRTKCPEILSDESSSDEDEKKNKEESSDDEDKESEEEPPKKTSKREK
          KSKKSSSKGNKKERNSSGMARKAKRTKCPEILSDESSSDEDEKKNKEESSDDEDKESEEEPPKKTSKREK
Retrocopy KSKKSSSKGNKKERNSSGMARKAKRTKCPEILSDESSSDEDEKKNKEESSDDEDKESEEEPPKKTSKREK

Parental  PKQKATSKSKKTVKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELKETVKKLLA
          PKQKATSKSKKTVKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELKETVKKLLA
Retrocopy PKQKATSKSKKTVKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELKETVKKLLA

Parental  SANLEEVTMKQICKEVYENYPAYDLTERKDFIKTTVKELIS
          SANLEEVTMKQICKEVYENYPAYDLTERKDFIKTTVKELIS
Retrocopy SANLEEVTMKQICKEVYENYPAYDLTERKDFIKTTVKELIS

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
SRP012049_cerebellum	7.27 RPM	26.67 RPM
SRP017611_brain	2.06 RPM	7.54 RPM
SRP017611_kidney	5.55 RPM	17.37 RPM
SRP017611_liver	2.32 RPM	7.32 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1362 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1362 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010184	1 retrocopy	retro_cfam_1362 ,
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,
Otolemur garnettii	ENSOGAG00000007750	1 retrocopy	retro_ogar_3258,
Sus scrofa	ENSSSCG00000001075	1 retrocopy	retro_sscr_203,