RetrogeneDB ID: retro_eeur_44

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2579:14833..15289(+)
• Located in intron of: ENSEEUG00000011406

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC8
• Ensembl ID: ENSEEUG00000011856
• Aliases: None
• Description: ER membrane protein complex subunit 8 [Source:HGNC Symbol;Acc:7864]

Sequence

>retro_eeur_44
CCCCTCTTCCACGGCTCGCTCGCCCTTGCACCCATGCTCGAGGTGGCCCTCACCCTGATTGATTCCTGGTGCAAAGATAA
TAGTTACGTGATTGCTGGTTATTATCAAGCTAATGAACAAGTAAAGGATGCCAGCCCAAACCAGGTGGCCGAAAAGGTTG
CTTCCAGAATCGCTGAGGGCTTCCGTGACACAGCGCTCATCATGGTGGACAACACTAAGTTCACGATGGACTGTGTGGTG
CCTACGATCCGTGTGTACGAGCACCACGAAAACAAATGGCGGTGCCGAGACCCACTCTATGATTACTGTGAAGACTGGCC
AGAGACCCAGGGGATCTCAGCATCTCTCCTGGACTGCCGATCCTGCGAAACACTTGTGGATTTCGGTAACCACCTGGATG
ACATTCGGAATGACTGGACAAATCCAGAGATCAATAAGACTGTTCTGCACCTATGT

Alignment

ORF - retro_eeur_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.76 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLFHGTLALAPMLEVALTLIDSWCKDNSYVIAGYYQANERVKDASPNQVAEKVASRIAEGFSDTALIMVD
          PLFHG.LALAPMLEVALTLIDSWCKDNSYVIAGYYQANE.VKDASPNQVAEKVASRIAEGF.DTALIMVD
Retrocopy PLFHGSLALAPMLEVALTLIDSWCKDNSYVIAGYYQANEQVKDASPNQVAEKVASRIAEGFRDTALIMVD

Parental  NTKFTMDCVVPTIHVYEHHENKWRCRDPHYDYCEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWT
          NTKFTMDCVVPTI.VYEHHENKWRCRDP.YDYCEDWPE.Q.ISASLLD.RS.ETLVDF.NHLDDIRNDWT
Retrocopy NTKFTMDCVVPTIRVYEHHENKWRCRDPLYDYCEDWPETQGISASLLDCRSCETLVDFGNHLDDIRNDWT

Parental  NPEINKAVLHLC
          NPEINK.VLHLC
Retrocopy NPEINKTVLHLC

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	0.32 RPM	10.47 RPM
SRP017611_kidney	0.19 RPM	18.38 RPM
SRP017611_liver	0.00 RPM	10.29 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_44 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019922	1 retrocopy	retro_cfam_2117,
Callithrix jacchus	ENSCJAG00000017312	1 retrocopy	retro_cjac_675,
Erinaceus europaeus	ENSEEUG00000011856	1 retrocopy	retro_eeur_44 ,
Macropus eugenii	ENSMEUG00000009360	5 retrocopies	retro_meug_1050, retro_meug_1386, retro_meug_636, retro_meug_709, retro_meug_97,
Monodelphis domestica	ENSMODG00000004596	1 retrocopy	retro_mdom_163,
Otolemur garnettii	ENSOGAG00000010372	1 retrocopy	retro_ogar_2503,