RetrogeneDB ID: retro_eeur_537

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_340907:69911..70155(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN1
• Ensembl ID: ENSEEUG00000005357
• Aliases: None
• Description: prefoldin subunit 1 [Source:HGNC Symbol;Acc:8866]

Sequence

>retro_eeur_537
CTTGCAGACATATAGACTGAACAACTAAACAGAACGAAAAAGCATGCACATCTCACAGACACAGAGATTATGACTTTGGT
ACATGAGATTAACATGTATGAAGGTGTAGGAAGAATGTTTATTCTTCAATCCAAGGAGGAAATTCACAGTCAGATGCTGG
AGAAACAGAAAATATCAGAAGAAAATATTAAGGAATTGGAACAGAAAAAAATCCTACCTGGAAAGGAGTGTGAAGGAAGC
TCAG

Alignment

ORF - retro_eeur_537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 85.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LADIQIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQSKEVIHSQLLEKQKIAEEKIKELEQ-K
          LADI..EQLNRTKKHAHLTDTEIMTLV.E.NMYEGVGRMFILQSKE.IHSQ.LEKQKI.EE.IKELEQ.K
Retrocopy LADI*TEQLNRTKKHAHLTDTEIMTLVHEINMYEGVGRMFILQSKEEIHSQMLEKQKISEENIKELEQ>K

Parental  KSYLERSVKEAE
          KSYLERSVKEA.
Retrocopy KSYLERSVKEAQ

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	1.61 RPM	11.28 RPM
SRP017611_kidney	3.00 RPM	21.00 RPM
SRP017611_liver	1.45 RPM	9.00 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_537 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 6 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893, retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53,
Erinaceus europaeus	ENSEEUG00000005357	1 retrocopy	retro_eeur_537 ,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,