RetrogeneDB ID: retro_eeur_458

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_312892:4773..5013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: URM1
• Ensembl ID: ENSEEUG00000012945
• Aliases: None
• Description: ubiquitin related modifier 1 [Source:HGNC Symbol;Acc:28378]

Sequence

>retro_eeur_458
CCCTTGCCAGTGAAGGTGGAGTTTGAAAGTGGTGAAAAGCTCCTGTTTGACGACATAAAGAAGCATCAGGTCACTTTGCC
TGGGCAGGAGTAGCCCTGGGACTTCTGAAACCTCCTTGTCTGGATCAAAAAGAATTTGCTAAAAGAGCTGCCAGAGTTGT
TCATCCAGGGAGACAGCGTGCGACCAGGAATTCTGGTACTGTTTAATGACTTGGACTGGGAGCTGCTGGGTGAGCTGGAG

Alignment

ORF - retro_eeur_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 79.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLSVEVEFGGGAELLFDGIRKHQVTLPGQEEPWDIRNLLVWIKNNLLKEQPELFIQGDSVRPGILVLVND
          PL.V.VEF..G..LLFD.I.KHQVTLPGQE.PWD..NLLVWIK.NLLKE.PELFIQGDSVRPGILVL.ND
Retrocopy PLPVKVEFESGEKLLFDDIKKHQVTLPGQE*PWDF*NLLVWIKKNLLKELPELFIQGDSVRPGILVLFND

Parental  ADWELLGELD
          .DWELLGEL.
Retrocopy LDWELLGELE

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	9.83 RPM
SRP017611_kidney	0.00 RPM	11.06 RPM
SRP017611_liver	0.00 RPM	4.02 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_458 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025612	2 retrocopies	retro_btau_1694, retro_btau_570,
Erinaceus europaeus	ENSEEUG00000012945	1 retrocopy	retro_eeur_458 ,
Loxodonta africana	ENSLAFG00000002178	1 retrocopy	retro_lafr_542,
Macropus eugenii	ENSMEUG00000014147	1 retrocopy	retro_meug_1161,