RetrogeneDB ID: retro_eeur_158

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_108706:263..668(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000000499
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IAH1
• Ensembl ID: ENSEEUG00000003840
• Aliases: None
• Description: isoamyl acetate-hydrolyzing esterase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:27696]

Sequence

>retro_eeur_158
ATGGTGCAGTACCTGAAGTCTGTGGATATCCCCAAGAGCAGGGTTATTCTCATCACCCCACCCCCTCTGTGGGAGACAGC
GTGGGAAAAGGAATGCCACATGCAAGGCTGCAAATTAAACATCTTGAATGTTGTAGTTGGTGAATATGCCAGTGCTTGTT
TACAAGTAGCCCAAGACTGTGGGACTAACGCACTTGACCTGTGGACCATGATGCAGAAAGATGGTCAGGACTTCTCATCC
TATTTGTCAGATGGACTACACTTATCACCAAAGGGAAATGAGTTTTTGTTCTCATATCTTTGGCCTTTGATAGAGAAAAA
TGATTCTTCTCTGCCTTTGCTGCTCTCTTACTGGCGTGACTTAGCAGAAACAAAACCAGAACTCAGTCTTCTGGGAGATA
GAGAC

Alignment

ORF - retro_eeur_158 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVQYLKSVDIPKSRVILITPPPLWETAWEKECHMQGCKLNRLNAVVGEYASACLQVAQDCGTDALDLWTL
          MVQYLKSVDIPKSRVILITPPPLWETAWEKECHMQGCKLN.LN.VVGEYASACLQVAQDCGT.ALDLWT.
Retrocopy MVQYLKSVDIPKSRVILITPPPLWETAWEKECHMQGCKLNILNVVVGEYASACLQVAQDCGTNALDLWTM

Parental  MQKDSQDFSSYLSDGLHLSPKGNEFLFSHLWPLIEKKVSSLPLLLPYWRDVAEAKPELSLLGDGD
          MQKD.QDFSSYLSDGLHLSPKGNEFLFS.LWPLIEK..SSLPLLL.YWRD.AE.KPELSLLGD.D
Retrocopy MQKDGQDFSSYLSDGLHLSPKGNEFLFSYLWPLIEKNDSSLPLLLSYWRDLAETKPELSLLGDRD

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	2.74 RPM
SRP017611_kidney	0.75 RPM	42.20 RPM
SRP017611_liver	0.00 RPM	18.17 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_158 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000003840	1 retrocopy	retro_eeur_158 ,
Echinops telfairi	ENSETEG00000003899	2 retrocopies	retro_etel_629, retro_etel_63,
Ictidomys tridecemlineatus	ENSSTOG00000004500	1 retrocopy	retro_itri_219,