RetrogeneDB ID: retro_ogar_3258

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873758.1:743113..743666(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033568
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DEK
• Ensembl ID: ENSOGAG00000007750
• Aliases: None
• Description: DEK oncogene [Source:HGNC Symbol;Acc:2768]

Sequence

>retro_ogar_3258
TGTGAAATTGAGAGGATACATTTTTTTCTGAGTAAGAAGAAAGCAGATGAACTTAGAAATCTACATAAACTACTTTACAA
TAGGTGGGCACGGTGTTCTCATTAAAGAAGAATATGGGTCAATTCAGTGGCTTTCCATTTGAAACAGGAAGTACTCAGTA
TAAAAAGAAAGAAGAAATGTTGAAAAATTTAGAAATGCCATGTTAAAGAGCATCTGTGAGGTTCTTGATTTGGAGAGATT
GAGTGTAAATAGTGAATTAATGAAGAGAATCTTGAATTTCTTAATGCATCCAAAGCCATCTGGCAAACCACTGCCAAAAT
CTAAGAAAAATTCTAGGAAAGGCAGTAAAAAGGAACGGAACATTTCTGGAATGGTAAGAAAGGCGAAGCAAACCAAATGT
CCTGAAATTCTGTCAGATGAATCTAGTAGTGATGAAGATGAAAAGAAAAACAAAGAAGAGTCTTCAGATAATGAAGATAA
AGAGAGTGAAGAGGAGCCACCAAATAAGACATCTAAAAGAGAAAAACCTAAACAGAAAGCTACTTGTAAAAGT

Alignment

ORF - retro_ogar_3258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.37 %
• Parental protein coverage: 50.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CEIERIHFFLSKKKTDELRNLHKLLYNR-PGTVSSLKKNVGQFSGFPFEKGSTQYKKKEEMLK-KFRNAM
          CEIERIHFFLSKKK.DELRNLHKLLYNR..GTV.SLKKN.GQFSGFPFE.GSTQYKKKEEMLK.KFRNAM
Retrocopy CEIERIHFFLSKKKADELRNLHKLLYNR<VGTVFSLKKNMGQFSGFPFETGSTQYKKKEEMLK<KFRNAM

Parental  LKSICEVLDLERSGVNSELVKRILNFLMHPKPSGKPLPKSKKTSSKGSKKERNSSGMARKAKRTKCPEIL
          LKSICEVLDLER..VNSEL.KRILNFLMHPKPSGKPLPKSKK.S.KGSKKERN.SGM.RKAK.TKCPEIL
Retrocopy LKSICEVLDLERLSVNSELMKRILNFLMHPKPSGKPLPKSKKNSRKGSKKERNISGMVRKAKQTKCPEIL

Parental  SDESSSDEDEKKNKEESSDDEDKESEEEPPKKTSKREKPKQKATSKS
          SDESSSDEDEKKNKEESSD.EDKESEEEPP.KTSKREKPKQKAT.KS
Retrocopy SDESSSDEDEKKNKEESSDNEDKESEEEPPNKTSKREKPKQKATCKS

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3258 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 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,