RetrogeneDB ID: retro_eeur_139

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_8598:341399..341718(+)
• Located in intron of: ENSEEUG00000008313

Retrocopy information

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

Parental gene information

• Parental gene symbol: LEPROTL1
• Ensembl ID: ENSEEUG00000001360
• Aliases: None
• Description: leptin receptor overlapping transcript-like 1 [Source:HGNC Symbol;Acc:6555]

Sequence

>retro_eeur_139
AGTTTGTTCTTTGGAGAAGCAATTGGGCTGATGTTTTTGATGCTTGGGCGTGCCCTTCCAAAATGCAACCAATACTGGCC
CCTCTTCGTCTTATTTTTCTATATCCTTTCACCTATTCCATAATGCATAGCCAAGAAGATTAGTGGATGATACAGATGCT
ATGAGTAATGCTTGTGAGAAGCTCGCCATATTTCTTACAACAGGCATTGTTGCCTCGGCTTTTGGACTCCCAATTGTATT
TGCCAGGGCACATCTGATTGAGTGGGGAGCCTATGCACTTGTTCCCACAGGAAATACAGTCATCTTTGCAACAATACTA

Alignment

ORF - retro_eeur_139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.72 %
• Parental protein coverage: 80.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLSFGGAIGLMFLMLGCALPKYNQYWPLFVLFFYILSPIPYCIA-RRLVDDTDAMSNACKELAIFLTTGI
          SL.FG.AIGLMFLMLG.ALPK.NQYWPLFVLFFYILSPIP.CIA.RRLVDDTDAMSNAC..LAIFLTTGI
Retrocopy SLFFGEAIGLMFLMLGRALPKCNQYWPLFVLFFYILSPIP*CIA>RRLVDDTDAMSNACEKLAIFLTTGI

Parental  VVSAFGLPIVFARAHLIEWGACALVLTGNTVIFATIL
          V.SAFGLPIVFARAHLIEWGA.ALV.TGNTVIFATIL
Retrocopy VASAFGLPIVFARAHLIEWGAYALVPTGNTVIFATIL

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	23.37 RPM
SRP017611_kidney	0.19 RPM	12.94 RPM
SRP017611_liver	0.00 RPM	27.65 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_139 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
Canis familiaris	ENSCAFG00000006530	1 retrocopy	retro_cfam_2171,
Choloepus hoffmanni	ENSCHOG00000012299	1 retrocopy	retro_chof_1305,
Dasypus novemcinctus	ENSDNOG00000014538	3 retrocopies	retro_dnov_1528, retro_dnov_2606, retro_dnov_876,
Erinaceus europaeus	ENSEEUG00000001360	1 retrocopy	retro_eeur_139 ,
Oryctolagus cuniculus	ENSOCUG00000013931	1 retrocopy	retro_ocun_832,