RetrogeneDB ID: retro_eeur_472

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_318265:2306..2776(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM40L
• Ensembl ID: ENSEEUG00000004808
• Aliases: None
• Description: translocase of outer mitochondrial membrane 40 homolog (yeast)-like [Source:HGNC Symbol;Acc:25756]

Sequence

>retro_eeur_472
ACAGCGGCCGTCACCCTGGGCAACCCAGACGTGCTGGTGGGCTCAGGAATCCTAGTGGCCCACTACCTCCAGAGCATCAC
ACCCTGCCTGGCCCTGGGTGGGGAGCTGGTCAACCACCGGTAGCAGAGGGAAGAGGGCACTGTCATGTCGCTGGCTGGGA
AATACACAATGAACAACTGGTTGGTGACAGTAGCGCTGGGCCAGGCAGGCATGCACACAACATAATATCACAAAGCCAGT
GACCAGCTACAGGTAGGTGTGGAGTTCGAGGCCAGCACCAGGATGCAGAACAAAAGCGTCTCCTTCGGGTACCAGCTGGA
CCTGCCCAAGGCCAACCTCCTCTTCAAAGGCTCCGTGGACAGCAACTGGATCATGGGCGCCATGCTGGAGAAGAAGCTGC
TGCTGCTGCCCCTAACACTGGCCCTGGCGCCTTCCTCAATTACCGAAAGAACAAGTTCCAGTGCGGCTTC

Alignment

ORF - retro_eeur_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.23 %
• Parental protein coverage: 50.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TATLTLGNPDLIGESVIMVAHFLQSLTQRLVLGGELVYHRRPGEEGAILTLAGKYSAGHWVATLNVGSGG
          TA..TLGNPD....S.I.VAH.LQS.T..L.LGGELV.HR...EEG....LAGKY....W..T...G..G
Retrocopy TAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVNHR*QREEGTVMSLAGKYTMNNWLVTVALGQAG

Parental  AHASYYHRANEQVQVGVEFEANTRLQDTTFSFGYHLTLPQANMVFRGLVDSNWCVGAVLEKKMTPLPVTL
          .H...YH.A..Q.QVGVEFEA.TR.Q....SFGY.L.LP.AN..F.G.VDSNW..GA.LEKK...LP.TL
Retrocopy MHTT*YHKASDQLQVGVEFEASTRMQNKSVSFGYQLDLPKANLLFKGSVDSNWIMGAMLEKKLLLLPLTL

Parental  AL-GAFLNHWRNRFHCGF
          AL.GAFLN...N.F.CGF
Retrocopy AL<GAFLNYRKNKFQCGF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	6.77 RPM	11.60 RPM
SRP017611_kidney	10.31 RPM	21.00 RPM
SRP017611_liver	5.95 RPM	5.14 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_472 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000004808	1 retrocopy	retro_eeur_472 ,
Echinops telfairi	ENSETEG00000015755	2 retrocopies	retro_etel_1124, retro_etel_1461,
Gorilla gorilla	ENSGGOG00000005720	2 retrocopies	retro_ggor_1075, retro_ggor_1761,
Otolemur garnettii	ENSOGAG00000013733	1 retrocopy	retro_ogar_2524,
Ictidomys tridecemlineatus	ENSSTOG00000003800	2 retrocopies	retro_itri_301, retro_itri_724,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,