RetrogeneDB ID: retro_etel_1985

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_321805:54414..54842(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TSPAN5
• Ensembl ID: ENSETEG00000007405
• Aliases: None
• Description: tetraspanin 5 [Source:HGNC Symbol;Acc:17753]

Sequence

>retro_etel_1985
GAGGGTGTGCTCTCCAACATCTCCTAGGTGAAGGATCTCGGGGGGGTTGGACCCTGATGGCTGTCGGTGGTGGTTGGAGG
CATCATGATGGAGCGGGCTTTGCAGGCTGCATGGGGGTCCTAAGGGGGAACACTTTCCTGCTCAAGATTTTCTCCATGTT
CCTCAGTCTCCGATTCTTCCTGGACATGGCCGCGGGGATCTTGACCTTCGTCTTCAAGGACTGGATTCAAGACCAGCTCA
ACCTCTTCATCATCAACAACATCCAGGCCTAACTGGATGACATCAACCTCCAGAATCTCATTGACTTTGCTCAGGAACAC
TGGTCTTGCTGCAGAGGCCGACTGCCCAATGACTGGAACCTCAAGGTCTACTAAGAGTGCACGGACCTGATTCTGATGCA
GGAGCGCTGCGGGTGCCCTTCTGGATGT

Alignment

ORF - retro_etel_1985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.42 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGVLSNISSITDLGGFDPVWLFLVVGGVMFI-LGFAGCIGALRENTLLLKFFSVFLGIIFFLELTAGVLA
          .GVLSNIS...DLGG..P.WL..VVGG.M....GFAGC.G.LR.NT.LLK.FS.FL...FFL...AG.L.
Retrocopy EGVLSNIS*VKDLGGVGP*WLSVVVGGIMME<AGFAGCMGVLRGNTFLLKIFSMFLSLRFFLDMAAGILT

Parental  FVFKDWIKDQLYFFINNNIRAYRDDIDLQNLIDFTQEYWQCCGAFGADDWNLNIYFNCTDSNASRERCGV
          FVFKDWI.DQL..FI.NNI.A..DDI.LQNLIDF.QE.W.CC......DWNL..Y..CTD.....ERCG.
Retrocopy FVFKDWIQDQLNLFIINNIQA*LDDINLQNLIDFAQEHWSCCRGRLPNDWNLKVY*ECTDLILMQERCGC

Parental  PFSC
          P..C
Retrocopy PSGC

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_1985 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013851	1 retrocopy	retro_amel_742,
Canis familiaris	ENSCAFG00000010287	1 retrocopy	retro_cfam_314,
Choloepus hoffmanni	ENSCHOG00000013549	1 retrocopy	retro_chof_2337,
Dasypus novemcinctus	ENSDNOG00000012685	1 retrocopy	retro_dnov_91,
Echinops telfairi	ENSETEG00000007405	1 retrocopy	retro_etel_1985 ,
Pteropus vampyrus	ENSPVAG00000003024	1 retrocopy	retro_pvam_79,