RetrogeneDB ID: retro_etel_1234

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_232601:3385..3900(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000010466
• Aliases: None
• Description: None

Sequence

>retro_etel_1234
ATTGATGAACTCCCAGAAGGAGCTGTGAAGCCTCCGGCAAACAAGTACCCTATCTTCTTTTTTGGCACCCATGAAACTGC
ATTTCTAGGTCCCAAAGACCTATTCCCATATAAGGAATACAAAGACAAGTTTGGAAAGTCAAATAAGCGGAAAGGATTTA
ATGAAGGATTGTGGGAAATTGAAAATAACCCTGGAGTAAAATTTACTGGCTATCAGGCAATTCAACAACAGAGTTCTTCA
GAAACGGAGGGAGAGGGTGGAAATACTGCAGATGCCAGCAGTGAAGAAGAAGGCGGGAGAGTCGAAGAAGATGGAAAAGG
CCAAAGAAAGAATGAAAAAGGCTCCCAACGAAAAAAGCATACGCTTCGAAGAAACCCTCCAAACGGTCCCGGAGATCTGC
AGAAGATGATGACGAGGACCGCAAACAAGAAGAACACAAAAGCCGCTCTGACGGTGGCGGTGCCGGCAACGACACAAGAA
ACACGACTTCAGACTTGCAGAGAACCAGTGAAGGG

Alignment

ORF - retro_etel_1234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDKFGKSNKRKGFNEGLWEIENNPGVKFTG
          IDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDKFGKSNKRKGFNEGLWEIENNPGVKFTG
Retrocopy IDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDKFGKSNKRKGFNEGLWEIENNPGVKFTG

Parental  YQAIQQQSSSETEGEGGNTADASSEEEGGRVDEEGKGKRKNEKAGSKR-KKAYTSKKSSKQSRRSAGDDD
          YQAIQQQSSSETEGEGGNTADASSEEEGGRV.E.GKG.RKNEK.GS.R.KKAY.SKK.SK.SRRSA..DD
Retrocopy YQAIQQQSSSETEGEGGNTADASSEEEGGRVEEDGKGQRKNEK-GSQR<KKAYASKKPSKRSRRSA-EDD

Parental  DKDRKEEEHKSSSDGGDAGNDTRNTASDLQKTSEG
          D.DRK.EEHKS.SDGG.AGNDTRNT.SDLQ.TSEG
Retrocopy DEDRKQEEHKSRSDGGGAGNDTRNTTSDLQRTSEG

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_1234 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000005243	1 retrocopy	retro_etel_1899,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234 ,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292, retro_itri_864,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380,