RetrogeneDB ID: retro_etel_1133

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_216258:354..614(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000016342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR83OS
• Ensembl ID: ENSETEG00000019481
• Aliases: None
• Description: WD repeat domain 83 opposite strand [Source:HGNC Symbol;Acc:30203]

Sequence

>retro_etel_1133
GTGTTGAGGAACAAGCCTCTGCTGAATGAGTGTAACCTGGCTTTGATTGATCTGATGCCAGACTACATGAACCTACTCGG
CATGTGGGAAATCATGCTCAAGCCATAATGGTATGATTGGGTTGCTGTCTACTGCTCCTTCATCAGCTTCCTTAATTCCC
AGAACTCAGAGGTTCCAAATAAATGTTGAGCAGTTTCATGTTTTCCATCTCAGTCATGGTGATGTCTTATCTGCAGAACC
CTCAACACATGATGCCCCCA

Alignment

ORF - retro_etel_1133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 85.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLRYKPPPSECNPALDDPTPDYMNLLGMIFSMCGLMLKLKWCAWVAVYCSFISFANSRSSE-DTKQMMSS
          VLR.KP...ECN.AL.D..PDYMNLLG....M...MLK..W..WVAVYCSFISF.NS..SE...K.M.SS
Retrocopy VLRNKPLLNECNLALIDLMPDYMNLLG----MWEIMLKP*WYDWVAVYCSFISFLNSQNSE<GSK*MLSS

Parental  FMLSISAVVMSYLQNPQPMTPP
          FM.SIS..VMSYLQNPQ.M.PP
Retrocopy FMFSISVMVMSYLQNPQHMMPP

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_1133 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028908	2 retrocopies	retro_cfam_1489, retro_cfam_1951,
Callithrix jacchus	ENSCJAG00000005285	1 retrocopy	retro_cjac_133,
Echinops telfairi	ENSETEG00000019481	1 retrocopy	retro_etel_1133 ,
Felis catus	ENSFCAG00000000463	1 retrocopy	retro_fcat_1902,
Macropus eugenii	ENSMEUG00000014450	3 retrocopies	retro_meug_1695, retro_meug_1733, retro_meug_2081,
Mus musculus	ENSMUSG00000059355	2 retrocopies	retro_mmus_1327, retro_mmus_2061,
Pteropus vampyrus	ENSPVAG00000013403	1 retrocopy	retro_pvam_1464,
Sus scrofa	ENSSSCG00000013721	1 retrocopy	retro_sscr_488,
Tupaia belangeri	ENSTBEG00000001250	1 retrocopy	retro_tbel_2034,