RetrogeneDB ID: retro_eeur_31

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_1656:29633..30164(+)
• Located in intron of: ENSEEUG00000014134

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM2
• Ensembl ID: ENSEEUG00000005022
• Aliases: None
• Description: tropomyosin 2 (beta) [Source:HGNC Symbol;Acc:12011]

Sequence

>retro_eeur_31
GCTGAAGCCGACGTCACCTCCCTGAACAGAAGCATCCAGCTGGTTGAGGAGGAGCTGGACCGAGCCCAGGAGCGTCTGGC
CACCGCTCTGCAGAAGCTGGAGGAGGCTGAGAAGGCGGCCGACGAAAGCGAGAGAGGCATGAAGGTCATTGAAAGCCGAG
CCCAGAAGGATGAGGAGAAGATGGAGATCCAGGAGATCCAGCTGAAGGAGGCCAAGCACATCGCTGAGGATGCCGACCGC
AAGTATGAAGAGGTGGCCCGGAAGCTGGTCATCATTGAGAGTGACTTGGAGCGTGCAGAGGAGCGGGCCAAACTCTCAGA
AGGCAAATGCGCCGAGCTTGAAGAAGAATTGAAAACTGTGACCAACAACCTGAAGTCACTGGAGGCTCAGGCCGAGAAGT
ACTCCCAGAAGGAAGACAAGTACGAGGAGGAGATCAAGGTCCTTTCCGACAAGCTGAAGGAGGCAGAGACTCGGGCTGAG
TTTGCAGAGAGATCTGTAACTAAATTGGAGAAAAGCATCGACGACTTGGAA

Alignment

ORF - retro_eeur_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 75.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRAMKDEEKMELQEMQLKE
          AEADV.SLNR.IQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIE.RA.KDEEKME.QE.QLKE
Retrocopy AEADVTSLNRSIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKE

Parental  AKHIAEDSDRKYEEVARKLVILEGELERSEERAEVAESKCGDLEEELKIVTNNLKSLEAKADKYSTKEDK
          AKHIAED.DRKYEEVARKLVI.E..LER.EERA...E.KC..LEEELK.VTNNLKSLEA.A.KYS.KEDK
Retrocopy AKHIAEDADRKYEEVARKLVIIESDLERAEERAKLSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDK

Parental  YEEEVNCWEEKLKEAERRV-VAKRFVAKLEKTIDDRE
          YEEE......KLKEAE.R...A.R.V.KLEK.IDD.E
Retrocopy YEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLE

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	41.58 RPM	5.96 RPM
SRP017611_kidney	52.70 RPM	13.50 RPM
SRP017611_liver	29.74 RPM	0.96 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_31 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009627	2 retrocopies	retro_cjac_1839, retro_cjac_1894,
Erinaceus europaeus	ENSEEUG00000005022	1 retrocopy	retro_eeur_31 ,
Mustela putorius furo	ENSMPUG00000005359	1 retrocopy	retro_mputfur_647,