RetrogeneDB ID: retro_eeur_164

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_127518:4..571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP25
• Ensembl ID: ENSEEUG00000013388
• Aliases: None
• Description: synaptosomal-associated protein, 25kDa [Source:HGNC Symbol;Acc:11132]

Sequence

>retro_eeur_164
TCTCTGGAAAGTACAAGGAGAACCCTTGGTTTAGCCATTGACGTCTCAGGATGCAGGAATCAAGACTATCACTATGCTTG
AGGAACAAGGAGAACAACTAAACCACATAGAAGAAGACATGGACCAAATAAATAAAGACATGAGAGAGGCAGAGAAGACA
ACAAAAGAACTCAAGTGCTGTGGCCTTTGTGTCTGCCCATGTAATAGGACAAAGAACTTTGAGTCTGGTAAGGCCTATAG
GAGTACATGGGGAGATGGTGGAGACAGCTCTCCGGGCAATGTCGTATCTAAGCAGCCAGGCCGAGTGACAGTCGGTCAAG
GCAAGCAAGGGCGGGAGTAACTGGTGGATAGATAAAACATATTACTAATGATGCCAGAGAAGATGAAATGGAAGAGAGCC
TGACTCAAGTGGGCAGTATCCTAGGGAATCTAAAAAACATGGCCCCGGACACGGGCAATGAGATTGATGTTCAAAATCAA
CAAATCAAACGAATCACAGAAAAGGCCGACACCAACAGCTATCGTATTGACATTGCTAATGCCAGAACACAGAAACTCAT
TGACAGC

Alignment

ORF - retro_eeur_164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.04 %
• Parental protein coverage: 87.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLESTRRMLQLVEE-SKDAGIRTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFCGLCVCPCN
          SLESTRR.L.L....S.DAGI.T..ML.EQGEQL...............EAEK....L.K.CGLCVCPCN
Retrocopy SLESTRRTLGLAID>SQDAGIKTITMLEEQGEQLXXXXXXXXXXXXXXREAEKTTKEL-KCCGLCVCPCN

Parental  KLK---SSDAYKKAW---GNNQDGVVASQP-ARVVDEREQMA---ISGGFIRRVTNDARENEMDENLEQV
          ..K...S..AY...W...G....G.V.S...AR..D.R...A.....GG.I...TNDARE.EM.E.L.QV
Retrocopy RTKNFESGKAYRSTWGDGGDSSPGNVVSKQ<ARPSDSRSRQARAGVTGG*IKHITNDAREDEMEESLTQV

Parental  SGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGS
          ..I.GNL..MA.D.GNEID.QN.QI.RI.EKAD.N..RID.AN.R..K...S
Retrocopy GSILGNLKNMAPDTGNEIDVQNQQIKRITEKADTNSYRIDIANARTQKLIDS

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	0.81 RPM	1014.57 RPM
SRP017611_kidney	1.31 RPM	1.88 RPM
SRP017611_liver	1.29 RPM	0.16 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_164 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	ENSEEUG00000013388	1 retrocopy	retro_eeur_164 ,
Drosophila melanogaster	FBgn0011288	1 retrocopy	retro_dmel_28,