RetrogeneDB ID: retro_eeur_378

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_275419:3223..3495(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000008642
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARFRP1
• Ensembl ID: ENSEEUG00000005894
• Aliases: None
• Description: ADP-ribosylation factor related protein 1 [Source:HGNC Symbol;Acc:662]

Sequence

>retro_eeur_378
GAATCCTAGAGAGCATTTGAGAAGATGGTCACAAGTGAGGCTTTGGTAGGCATCCCCATCCTGGTGCTGGCCAACAAGCA
GGATGTGCAGATGTGCCTCTGTCTCCCCGACATCAAGACTGCCTTCAGTCACTGCACCTCTAAGATCAGTCAGGGGACTG
CCTCAGCCAGGCCTGCTCAGTCCTCAGGGGCCAGGGGGTGCAATGTGGCATAGAGTGGATGGTGAAGTGTGTCTTATTGA
ACATGCACCAGGCACTGCAGCAGAGGGACATC

Alignment

ORF - retro_eeur_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.74 %
• Parental protein coverage: 53.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESKKAFEKMVTSEALDGVPILVLANKQDVQXXXSIPDIKTAFSDCTSKIGR-RDCLTQACSALTGQGVRE
          ES..AFEKMVTSEAL.G.PILVLANKQDVQ.....PDIKTAFS.CTSKI....DCL.QACS.L.GQGV..
Retrocopy ES*RAFEKMVTSEALVGIPILVLANKQDVQMCLCLPDIKTAFSHCTSKISQ<GDCLSQACSVLRGQGVQC

Parental  GIEWMVKCVVRNVHRPPRQRDI
          GIEWMVKCV..N.H....QRDI
Retrocopy GIEWMVKCVLLNMHQALQQRDI

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	0.00 RPM	11.12 RPM
SRP017611_kidney	0.38 RPM	19.69 RPM
SRP017611_liver	0.16 RPM	13.51 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_378 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014423	1 retrocopy	retro_cpor_1198,
Erinaceus europaeus	ENSEEUG00000005894	1 retrocopy	retro_eeur_378 ,