RetrogeneDB ID: retro_eeur_87

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_5440:5069..5426(-)
• Located in intron of: ENSEEUG00000005157

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000006156
• Aliases: None
• Description: None

Sequence

>retro_eeur_87
CTCGAGAGATGGCTGGGTTTGTGAGGAGGATGCAAATATGGTGCGCAGGGCGAGCGGCAGGTTCCTGTCCTTCAAACAAA
CAATGGTCTAAGTCTAACAGGATTGACGACTATAGCAGCTTACCTGGTCAAGAAAGCCAACAAAGAATAGTTACTTGGGA
ACACTGCAGAGGAAAAGGCAATTGTTCAGCAGTGGCTAGAATATAGGGTAATTCGAGTAGATGGGCCCTGTGGTAAAGAG
GAAGTCCACACTCTCTTGAAGGATCTTAATTCTTACCTTGACGATAAAGTCTACCTTACAGGATATAACTTTACCTTAGA
AGATGTCTTACTGTACTATTGGCTGCACCACTTTATA

Alignment

ORF - retro_eeur_87 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 92.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LERWLGLRGGRKYGAQGERQVPVLQTNNGLSLTGLTTIAAYLVKQANKEYLLGNTAEEKAIVQQWLEYRV
          LERWLGL.GG.KYGAQGERQVPVLQTNNGLSLTGLTTIAAYLVK.ANKE.LLGNTAEEKAIVQQWLEYRV
Retrocopy LERWLGL*GGCKYGAQGERQVPVLQTNNGLSLTGLTTIAAYLVKKANKE*LLGNTAEEKAIVQQWLEYRV

Parental  TRIDGPCGKEEVRILLKDLNSYLEDKVYLTGYNFTLADVLLYYGLHRFI
          .R.DGPCGKEEV..LLKDLNSYL.DKVYLTGYNFTL.DVLLYY.LH.FI
Retrocopy IRVDGPCGKEEVHTLLKDLNSYLDDKVYLTGYNFTLEDVLLYYWLHHFI

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	0.16 RPM	8.06 RPM
SRP017611_kidney	0.19 RPM	9.56 RPM
SRP017611_liver	0.00 RPM	3.22 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_87 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017318	1 retrocopy	retro_amel_636,
Dasypus novemcinctus	ENSDNOG00000019203	1 retrocopy	retro_dnov_1550,
Erinaceus europaeus	ENSEEUG00000006156	1 retrocopy	retro_eeur_87 ,
Felis catus	ENSFCAG00000011622	1 retrocopy	retro_fcat_1075,
Macropus eugenii	ENSMEUG00000008960	1 retrocopy	retro_meug_1883,
Microcebus murinus	ENSMICG00000012636	1 retrocopy	retro_mmur_1404,
Myotis lucifugus	ENSMLUG00000007715	1 retrocopy	retro_mluc_1474,
Mustela putorius furo	ENSMPUG00000000588	1 retrocopy	retro_mputfur_486,
Pteropus vampyrus	ENSPVAG00000012305	2 retrocopies	retro_pvam_1374, retro_pvam_190,
Rattus norvegicus	ENSRNOG00000016390	5 retrocopies	retro_rnor_1682, retro_rnor_2013, retro_rnor_2132, retro_rnor_2133, retro_rnor_785,