RetrogeneDB ID: retro_etel_674

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_140522:115..680(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000017476
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSETEG00000018447
• Aliases: None
• Description: translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]

Sequence

>retro_etel_674
GCTGTGAGAGGAAGAGCCCTGGCCTCCAGCTCCCTTTATAATTATGGGGTCAGAGATCTGGCCACGGTTTTCTTCTACAT
GCTGGTGGCGATCATTATTCACGCCACCATTCAGGAGTATGTGCTAGGTAGAATCAACAGGCAAATGCAGTTTCTCAAAA
CGAAACAGAGCAAATTCAATGAATGTGGGCAGCTCGGTGTATTTTATCTTGTCTCATATTTGGGGCGCACTCATTCTAGT
CTCTGAAAACTACGTTTCAGACACGTTTGTCGTGTGAAGGGCTCATCCCCACAGCATGATGACGTTTCAAATGAAGTTCT
TCTACATCTCCCAGTTGGCTTACTGGCTCCATGCTTTTCCGGAACTCTACTTCCAGAGAAACAAAAAGCAAGACCTTCCT
CACCTGATCATCTACTTCTGCCTCCACCTCTTTCACATTGCTGGCGCTTACCTTTTGTACTTGGATCACCTGGGACTGGT
CCTTTTGGCGATGTATTACTTCGTGGAGCTCCTCTCGCACATGGGCGACCTGCTTTATTTGAGTGACGAAAAGTATGAGA
AAGGT

Alignment

ORF - retro_etel_674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.05 %
• Parental protein coverage: 50.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATEEQATESTTHYYYGIKDLATVFFYMLVAVIIHAIIQEYVLDKINRRMHF-SKTKHSKFNESGQLSAFY
          A....A..S...Y.YG..DLATVFFYMLVA.IIHA.IQEYVL..INR.M.F.SK.........G..S...
Retrocopy AVRGRALASSSLYNYGVRDLATVFFYMLVAIIIHATIQEYVLGRINRQMQF>SKRNRANSMNVGS-SVYF

Parental  LFSCIWGTFILISENYITDPTILWRAYPHNRMTFQMKFFYISQLAYWFHAFPELYFQKTKKEDIPRQLVY
          ..S.IWG..IL.SENY..D.....RA.PH..MTFQMKFFYISQLAYW.HAFPELYFQ..KK.D.P....Y
Retrocopy ILSHIWGALILVSENYVSDTFVV*RAHPHSMMTFQMKFFYISQLAYWLHAFPELYFQRNKKQDLPHLIIY

Parental  IGLYLFHIAGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKG
          ..L.LFHIAGAYLL.L.HLGLVLL...YFVE.L.H...L.Y.SDEKY.KG
Retrocopy FCLHLFHIAGAYLLYLDHLGLVLLAMYYFVELLSHMGDLLYLSDEKYEKG

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_674 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 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674 ,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,