RetrogeneDB ID: retro_eeur_3

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_128901:144..549(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003544
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000009817
• Aliases: None
• Description: None

Sequence

>retro_eeur_3
ATGTCGGTGGCCTTGCTGCGGCGCGGCCTGGAGCTGCTAGGGGCTCTGGCGCCCCAGGTCGCCTGCGGCCTGGCCAAAGC
CAGCGGGACTCCGGAGCAGCGGCCCAGGAAGGCGAAAGCGACCCAGGCACAAAAGCTGCGGAACTCTGCCAAGAGGAAAG
TGCCCAAGTCGGCGCTGGCTGGATTCCAGAAGCGAGAGAAGCAGAACTACCTTGGAGCAAACCTGAAGTTTATGACTGCT
TCCAGGAACACCATGGCTGAGAACGTCATCCGGAAGATTCTTTATCAGAACCGGGGCCGCAAGGCCTGTGACCCGCCTGT
AACCAAGACTAAAAAGAAGACTGAGGGCACTGTGTTCACTGAGGAAGACTTCCAGAAGTTCCAACAGGAATACTTCGGCA
GCTAG

Alignment

ORF - retro_eeur_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSAALLRRGLELLGAPEAPQVARGPAKASGTRGQRARKAKATQAQKLRNSAKGKVPKSALAEFQKREKQN
          MS.ALLRRGLELLGA..APQVA.G.AKASGT..QR.RKAKATQAQKLRNSAK.KVPKSALA.FQKREKQN
Retrocopy MSVALLRRGLELLGAL-APQVACGLAKASGTPEQRPRKAKATQAQKLRNSAKRKVPKSALAGFQKREKQN

Parental  YLGANLKFMTASRNTMAENVIRKILHQNRGRKACDRPVTKTKKKKTEGTVFTEEDFQKFQQEYFGS
          YLGANLKFMTASRNTMAENVIRKIL.QNRGRKACD.PVTKT.KKKTEGTVFTEEDFQKFQQEYFGS
Retrocopy YLGANLKFMTASRNTMAENVIRKILYQNRGRKACDPPVTKT-KKKTEGTVFTEEDFQKFQQEYFGS

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	13.86 RPM
SRP017611_kidney	0.00 RPM	26.63 RPM
SRP017611_liver	0.16 RPM	14.95 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_3 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010936	1 retrocopy	retro_amel_1552,
Erinaceus europaeus	ENSEEUG00000009817	1 retrocopy	retro_eeur_3 ,
Felis catus	ENSFCAG00000029275	1 retrocopy	retro_fcat_1374,