RetrogeneDB ID: retro_eeur_206

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_207677:505..1051(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000007648
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000007111
• Aliases: None
• Description: None

Sequence

>retro_eeur_206
GCTGACTGTGCAGGGAGGCTTATTAATGTCACCCTGGGAGTCCACAACATAGAGGAGCGTGAAGACACTTGGCAGACGCT
GATGGTCCAAAAACAATTCTGTCATCCAAAATACGGTGAGATGACTCTTCTCCATAACATCATGTTACTAAAGCTGGAGG
AGAAAGCCAACCTGACCCTGGCCGTGGGCACAGTCCCCCTGGCAGCTGAATTTGACTTCATTCCCCCTGGGAGAATGTGC
CGGGTGGCCGGCTCGGGGAGAACGGATGTGAAGGGGAAAGGGTCTGACACTCTGCAGGAGGTGAAGCAGAGACTTATGGA
CCCCCAAGACTGCAAGCACCACTCAGATTTTGACCACAATCTCCAGCTGTGTCTGGGAAACTCCAAGAAGAGAAACTCTG
CATTTAAGGGAGACTCCGGGGGCCCTCTCCTGTGTGCTGGGGTGGCCCATGGCATTGTGTCCTATGGAAGGATGGATGCC
AAACCCCTTGCTGTCTTCACCTGCATCTCCTATTACCGGCCCTGGATCAATATGATCCTGAAAGAG

Alignment

ORF - retro_eeur_206 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.76 %
• Parental protein coverage: 73.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHCAGRLINVALGVHNIDEREDTWQMLMVQKQFRHPKYDEMTLLHDIMLLKLEEKANLTLAVGTVPLAAE
          A.CAGRLINV.LGVHNI.EREDTWQ.LMVQKQF.HPKY.EMTLLH.IMLLKLEEKANLTLAVGTVPLAAE
Retrocopy ADCAGRLINVTLGVHNIEEREDTWQTLMVQKQFCHPKYGEMTLLHNIMLLKLEEKANLTLAVGTVPLAAE

Parental  FDFIPPGRMCRVAGWGRTDVKGKGSDTLQEVKQKLMDPQDCKHHSDFDHNLQLCVGNSKKRNSAFKGDSG
          FDFIPPGRMCRVAG.GRTDVKGKGSDTLQEVKQ.LMDPQDCKHHSDFDHNLQLC.GNSKKRNSAFKGDSG
Retrocopy FDFIPPGRMCRVAGSGRTDVKGKGSDTLQEVKQRLMDPQDCKHHSDFDHNLQLCLGNSKKRNSAFKGDSG

Parental  GPLLCAGVAHGIVSYGRMDAKPPAVFTRISHTWPWINMILKE
          GPLLCAGVAHGIVSYGRMDAKP.AVFT.IS...PWINMILKE
Retrocopy GPLLCAGVAHGIVSYGRMDAKPLAVFTCISYYRPWINMILKE

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	0.00 RPM
SRP017611_kidney	0.19 RPM	0.38 RPM
SRP017611_liver	0.00 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_206 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007111	1 retrocopy	retro_eeur_206 ,