RetrogeneDB ID: retro_eeur_62

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_3330:6984..7658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPKAPK2
• Ensembl ID: ENSEEUG00000000525
• Aliases: None
• Description: mitogen-activated protein kinase-activated protein kinase 2 [Source:HGNC Symbol;Acc:6887]

Sequence

>retro_eeur_62
GGCACCAACGGGAAAGTTTTGCAGATCTTCAACAGGAGGACTCAGGAGAAATTTGCCCTAAAATGCTTCAGGATTGCCCC
AAGGCCCATCGCGAGGTGGAACTGAATTGGAGGGCTTCCCAGTGTCCACACATTGTGCGGATTGTGGATGTCTATGAGAA
TCTATATGCTAGCAGGAAATGCCTGCTGATTGTCATGGAGTGCTTGGATGGTGGAGAACTCTTTAGCCGAATCCAGGACA
GAGGAGACCAAGCATTCACAGAAAGAGAAGCATCAGAAATCAGGAAGAGTATTGGTGAGGCCATCCAGTATCTGCATTCA
ATCAACATAGCTCATTGGGATGTCAAGCTTGAGAATCTTTTATACACCTCTAAAAGTCCAATGCCATTCTGAAACTCATC
AATTTTTGGCTTTGCCAAGGAAACCACCAGCCACAACTCTTTGACCACTCCTTGCTATACACCATACTATGTGGCTCCAG
AATTGCTGGGCCGGGAGAAGTATGACAAGCCCTGTGACATGTGGTCCTTGGTTGTTATCATATGTATCTTGCTATGTGGG
TATCCCCTTTTCTATTCCAACCATGGCCTTGCCATCTCTCTGGGCACGAAGACTCGTATCAGAATGGGCCACTATGAGTT
TCCCAACCCTGAATGGTCAGAAGTATCCAAAGAA

Alignment

ORF - retro_eeur_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.04 %
• Parental protein coverage: 56.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GINGKVLQIFNKRTQEKFALK-MLQDCPKARREVELHWRASQCPHIVRIVDVYENLYAGRKCLLIVMECL
          G.NGKVLQIFN.RTQEKFALK.MLQDCPKA.REVEL.WRASQCPHIVRIVDVYENLYA.RKCLLIVMECL
Retrocopy GTNGKVLQIFNRRTQEKFALK<MLQDCPKAHREVELNWRASQCPHIVRIVDVYENLYASRKCLLIVMECL

Parental  DGGELFSRIQDRGDQAFTEREASEIMKSIGEAIQYLHSINIAHRDVKPENLLYTSKRP-NAILKLTD-FG
          DGGELFSRIQDRGDQAFTEREASEI.KSIGEAIQYLHSINIAH.DVK.ENLLYTSK.P.NAILKL...FG
Retrocopy DGGELFSRIQDRGDQAFTEREASEIRKSIGEAIQYLHSINIAHWDVKLENLLYTSKSP<NAILKLIN>FG

Parental  FAKETTSHNSLTTPCYTPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRI
          FAKETTSHNSLTTPCYTPYYVAPE.LG.EKYDK.CDMWSL.VI..ILLCGYP.FYSNHGLAIS.G.KTRI
Retrocopy FAKETTSHNSLTTPCYTPYYVAPELLGREKYDKPCDMWSLVVIICILLCGYPLFYSNHGLAISLGTKTRI

Parental  RMGQYEFPNPEWSEVSEE
          RMG.YEFPNPEWSEVS.E
Retrocopy RMGHYEFPNPEWSEVSKE

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	0.48 RPM	9.19 RPM
SRP017611_kidney	2.06 RPM	35.63 RPM
SRP017611_liver	0.80 RPM	13.18 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_62 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
Erinaceus europaeus	ENSEEUG00000000525	1 retrocopy	retro_eeur_62 ,
Myotis lucifugus	ENSMLUG00000001421	1 retrocopy	retro_mluc_978,