RetrogeneDB ID: retro_eeur_265

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_229037:2639..3023(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABHD17A
• Ensembl ID: ENSEEUG00000001302
• Aliases: None
• Description: abhydrolase domain containing 17A [Source:HGNC Symbol;Acc:28756]

Sequence

>retro_eeur_265
CTGGGCCAGATGAGCCGCTTCTACGTGGGCCTGGGCTCCCACTGTGGCTGCAACATCCTCTCCTATGACTACTCGTCCGG
GCTATCGGGCCGGCCCTCTGAGAAGAACCTGTAGGCAGACATTGACGCTGCCGTCTGGCAGGTGCTGCGCACGAGGTACG
GGATCAGCCCCGACAGCGTGGTGCTATATGGCCAGAGCATCCGCACGGTGCCCACCGAGGGCTTGGCGGCCCGAACTGAG
TGAGCTGCGGTGGTGCTGCACTCGCCACTCACGTCGGGCATTCGGGTAGCCTTCCCCGACACCACGAAGACCTACTGCCT
CGACGCCTCCCCCAACATCTAGAAGGTGTCCCGCATCTCATCGCTGGTTTTGCTGATCCACGGC

Alignment

ORF - retro_eeur_265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.54 %
• Parental protein coverage: 65.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGQMSSFYVGLGSRLGCNIFSYDYSGYGASSGRPSEKNLYADIDAA-WQALRTRYGISPDSVVLYGQSIG
          LGQMS.FYVGLGS..GCNI.SYDYS.....SGRPSEKNL.ADIDAA.WQ.LRTRYGISPDSVVLYGQSI.
Retrocopy LGQMSRFYVGLGSHCGCNILSYDYSS--GLSGRPSEKNL*ADIDAAVWQVLRTRYGISPDSVVLYGQSIR

Parental  TVPTVDLAARYECAAVVLHSPLTSGMRVAFPDTKKTYCFDAFPNIEKVSRISSPVLVIHG
          TVPT..LAAR.E.AAVVLHSPLTSG.RVAFPDT.KTYC.DA.PNI.KVSRISS.VL.IHG
Retrocopy TVPTEGLAARTE*AAVVLHSPLTSGIRVAFPDTTKTYCLDASPNI*KVSRISSLVLLIHG

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	5.16 RPM
SRP017611_kidney	0.00 RPM	7.88 RPM
SRP017611_liver	0.00 RPM	8.68 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_265 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001302	1 retrocopy	retro_eeur_265 ,
Erinaceus europaeus	ENSEEUG00000013750	1 retrocopy	retro_eeur_688,
Microcebus murinus	ENSMICG00000013508	1 retrocopy	retro_mmur_48,