RetrogeneDB ID: retro_etel_1367

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_255491:1865..2432(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000002577
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DEK
• Ensembl ID: ENSETEG00000018188
• Aliases: None
• Description: DEK oncogene [Source:HGNC Symbol;Acc:2768]

Sequence

>retro_etel_1367
TTGACAATGCAAGTGTCCTCCTTACAGAGAGAGCCATTTACAATTGCACAAGGCAAGTGACAGAAACTTTGTGAAATTGA
AAGGATACATTTCTTTTTGAGTAAGAAGAAAACGGATGAACTTAGAAACCTACACAAACTGCTTTACAACAGACCAGGCA
CAGTGTCCTCACTAAAGAAGAATGTGGGTCAGTTCAGTGGCTTTCCGTTTGAAAAAGGAAGTGCCCAATATAAAAAGAAG
GAAGAAATGTTGAAGAAGTTCAGAAATGCCATGTTAAAGAGCATCTGTGAGATTCTGGATTTGGAAAGATCAGGTGTAAA
CAGTGAGCTGGTGAAGCGGATCTGGAATTTCTTAATTCATCCAAAGCCCACTGGCAAGCCATTGTCCAAGTCCAAAAAAT
CTTCCAGCAAAGGCAGCCAACCAGAGCGGAGCAGTTCCGGAATGGCAAGGAAGGGCAAGCGAACCAAATGTCCCGAGATT
TTGTCAGATGAATCTAGTAGTGATGAAGCTGAGAAGAAAACCCAGGAAGAGTCTTCAGATGATGAAGATAAGGAAAGCGA
AGAGGAG

Alignment

ORF - retro_etel_1367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.37 %
• Parental protein coverage: 57.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTTQVSSLQRETFTIAQGKGQTLCEPHRMDFFATKKKTDDLRN----LHKLQRTVCSLKKNLGQFSDFLL
          LT.QVSSLQRE.FTIAQGK.Q.LCE..R..FF..KKKTD.LRN....L.....TV.SLKKN.GQFS.F..
Retrocopy LTMQVSSLQREPFTIAQGK*QKLCEIERIHFFLSKKKTDELRNLHKLLYNRPGTVSSLKKNVGQFSGFPF

Parental  EKGSAQYK-KEE----FRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPKPSGKPLPKSKKSSSKGSK
          EKGSAQYK.KEE....FRNAMLKSICE.LDLERSGVNSELVKRI.NFL.HPKP.GKPL.KSKKSSSKGS.
Retrocopy EKGSAQYKKKEEMLKKFRNAMLKSICEILDLERSGVNSELVKRIWNFLIHPKPTGKPLSKSKKSSSKGSQ

Parental  KERSSSGMARKGKRTKCPEILSDESSSDEDEKKNQEESSDDEDKESEEE
          .ERSSSGMARKGKRTKCPEILSDESSSDE.EKK.QEESSDDEDKESEEE
Retrocopy PERSSSGMARKGKRTKCPEILSDESSSDEAEKKTQEESSDDEDKESEEE

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1367 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 7 parental genes, and 11 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,
Oryctolagus cuniculus	ENSOCUG00000003869	4 retrocopies	retro_ocun_1583, retro_ocun_1791, retro_ocun_1851, retro_ocun_1857,
Otolemur garnettii	ENSOGAG00000007750	1 retrocopy	retro_ogar_3258,
Sus scrofa	ENSSSCG00000001075	1 retrocopy	retro_sscr_203,