RetrogeneDB ID: retro_eeur_337

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_261733:1737..1989(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL2
• Ensembl ID: ENSEEUG00000011134
• Aliases: None
• Description: GABA(A) receptor-associated protein-like 2 [Source:HGNC Symbol;Acc:13291]

Sequence

>retro_eeur_337
GTGATTGTGGAAAAAGTCTCTGGTTCTCAGATTGTTGATATTGACAAACGGAAGTATCTAGTTCCATCAGACATCACTGT
GGCTCAGTTTATGTGGATCATCAGGTAAAAGATTCAACTTCCTTCTGAAAAGGCAATCTCCCTGTTTGTGGATAAGACAG
CTCCATAGTCCAGCCTAACTATGGGACACCATTATGAGCAAGAAAAAGATGAAGATGGATTCTTGTATGGGGCCTACCGT
GGAGAGAACACT

Alignment

ORF - retro_eeur_337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 71.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIVEKVSGSQIVDITKRKYIVPSDITVAQFMWIIRNRIHFPSERIFFLFVDXXXXXXXL-MGQYYEKKKD
          VIVEKVSGSQIVDI.KRKY.VPSDITVAQFMWIIR..I..PSE....LFVD.......L.MG..YE..KD
Retrocopy VIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIR*KIQLPSEKAISLFVDKTAP*SSLTMGHHYEQEKD

Parental  EDGFLYGAY-SENT
          EDGFLYGAY..ENT
Retrocopy EDGFLYGAYRGENT

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	9.51 RPM	17.73 RPM
SRP017611_kidney	11.06 RPM	21.75 RPM
SRP017611_liver	4.34 RPM	7.23 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_337 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Erinaceus europaeus	ENSEEUG00000011134	1 retrocopy	retro_eeur_337 ,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,