RetrogeneDB ID: retro_etel_1400

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_259539:0..682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETF1
• Ensembl ID: ENSETEG00000007362
• Aliases: None
• Description: eukaryotic translation termination factor 1 [Source:HGNC Symbol;Acc:3477]

Sequence

>retro_etel_1400
CTTACAGCACTACTTTCGGATGATAGCAAGTTTGAGTTTCATTGTAGTAGATGGTAGTGGTGCGCTTTTTGGCACACTCC
AAGGAAGCACAAGAGAAGTCCTGCACAAATTCACTGTGGATCTTCCAAAGAAACACGGTAGAGGAGGTCAGTCTGCTTTG
CGTTTTGCCCGTTTAAGAATGGAAAAACGACACAATTACGTTCGGAAAGTAGCCGAGACTGCTGTGCAACTGTTTATTTC
TGGGGACAAAGTAAATGTGGCTGGTCTCATTTTAGCTGGATCAGCTGACTTTAAAACTGAACTAAGCCAATCGGATATGT
TTGATCAGAGGTTGCAATCCAAAGTTTTAAAATTAGTTGATATCTCCTATAGTGGTGAAAATGGATTCAACCAAGCTATT
GAATTATCTACTGAAGTCCTCTCCAACGTGAGGTTCATTCAAGAGAAGAAATTAATAGGACGATACTTTGATGAAATCAG
CCAAGACACGGGCAAGTACTGTTTTGGAGTTGAAGATACACTAAAGGCTTTGGAAATGGGAGCTGTAGAGATTCTAATAG
TCTATGAAAATCTGGATATAATGAGATATGTTCTTCATTGCCAAGGCACCGAAGAGGAGAAAATTCTCTATCTAACTGCA
GAACAAGAGAAGGATAAATCTCATTTCACAGATAAAGAGACA

Alignment

ORF - retro_etel_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.49 %
• Parental protein coverage: 52.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTALLSDDSKF-GFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRK
          LTALLSDDSKF..FIV.DGSGALFGTLQG.TREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRK
Retrocopy LTALLSDDSKF>SFIVVDGSGALFGTLQGSTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRK

Parental  VAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEV
          VAETAVQLFISGDKVNVAGL.LAGSADFKTELSQSDMFDQRLQSKVLKLVDISY.GENGFNQAIELSTEV
Retrocopy VAETAVQLFISGDKVNVAGLILAGSADFKTELSQSDMFDQRLQSKVLKLVDISYSGENGFNQAIELSTEV

Parental  LSNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKIL
          LSNV.FIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKIL
Retrocopy LSNVRFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKIL

Parental  YLTPEQEKDKSHFTDKET
          YLT.EQEKDKSHFTDKET
Retrocopy YLTAEQEKDKSHFTDKET

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_1400 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316, retro_cjac_4133,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400 ,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935,