RetrogeneDB ID: retro_eeur_14

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_321283:16918..17722(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000001580
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000009723
• Aliases: None
• Description: None

Sequence

>retro_eeur_14
TGCTTCGAGTGCTGCATCAAGTGTCTGGGCGGAGTCCCCTATGCCTCGCTGGTGGCCACCATCCTCTGCTTTTCCGGGGT
CGCCCTGTTCTGCGGCTGTGGCCACGTGGCCCTGGCCGGCACCGTGGCACTTCTGGAGCAGCACTTCTCCACCAACGCCA
ACGACCACGCCCTGCTGAGCCAAGTGATTCAGCTGATGCAGTACGTCATCTACGGGATCGCGTCCTTCTTCTTCCTGTAC
GGGATCATTCTGCTGGCAGAAGGCTTCTACACCACCAGTGCTGTGAAGGAACTGCACGGGGAGTTCAAGACCACCGCCTG
TGGCCGATGCATCAGCGGAATGTTTGTTTGCCTCACCTACGTGCTGGGAGTGGCCTGGCTGGGTGTGTTTGGATTCTCTG
CCGTTCCTGTGTTTATGTTCTACAACATCTGGTCAACCTGTGAAGTCATCAAGTCACCCCAGACCAATGGGACGGCTGGT
GTGGAGCAGATCTGTGTGGATGTCCGGCAATATGGCATCGTCCCTTGGAATGCTTTCCCAGGAAGGATATGCGGCTCTGC
TCTTGAGAACATCTGCAACACCAGTGAGTTCTACATGTCTTACCACCTGTTCATTGTGGCTTGTGCCGGAGCTGGTGCCA
CTGTCATTGCCCTGATCCACTTCCTCATGATACTGTCTTCTAACTGGGCTTACTTAAAGGATGCAAGCAAAATGCAGGCT
TACCAGGATATCAAAGCAAAGGAGGAACAGGAGCTGCAAGATATCCAGTCTCGGTCAAAAGAGCAACTCAATTCTTACAC
TTAA

Alignment

ORF - retro_eeur_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 81.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CFECCIKCLGGVPYASLVATILCFSGVALFCGCGHVALAGTVALLEQHFSTNANDHALLSQVIQLMQYVI
          CFECCIKCLGGVPYASLVATILCFSGVALFCGCGHVALAGTVALLEQHFSTNANDHALLSQVIQLMQYVI
Retrocopy CFECCIKCLGGVPYASLVATILCFSGVALFCGCGHVALAGTVALLEQHFSTNANDHALLSQVIQLMQYVI

Parental  YGIASFFFLYGIILLAEGFYTTSAVKELHGEFKTTACGRCISGMFVCLTYVLGVAWLGVFGFSAVPVFMF
          YGIASFFFLYGIILLAEGFYTTSAVKELHGEFKTTACGRCISGMFVCLTYVLGVAWLGVFGFSAVPVFMF
Retrocopy YGIASFFFLYGIILLAEGFYTTSAVKELHGEFKTTACGRCISGMFVCLTYVLGVAWLGVFGFSAVPVFMF

Parental  YNIWSTCEVIKSPQTNGTAGVEQICVDVRQYGIVPWNAFPGRICGSALENICNTSEFYMSYHLFIVACAG
          YNIWSTCEVIKSPQTNGTAGVEQICVDVRQYGIVPWNAFPGRICGSALENICNTSEFYMSYHLFIVACAG
Retrocopy YNIWSTCEVIKSPQTNGTAGVEQICVDVRQYGIVPWNAFPGRICGSALENICNTSEFYMSYHLFIVACAG

Parental  AGATVIALIHFLMILSSNWAYLKDASKMQAYQDIKAKEEQELQDIQSRSKEQLNSYT
          AGATVIALIHFLMILSSNWAYLKDASKMQAYQDIKAKEEQELQDIQSRSKEQLNSYT
Retrocopy AGATVIALIHFLMILSSNWAYLKDASKMQAYQDIKAKEEQELQDIQSRSKEQLNSYT

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	31.58 RPM	344.85 RPM
SRP017611_kidney	0.00 RPM	2.25 RPM
SRP017611_liver	0.16 RPM	0.64 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_14 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	ENSEEUG00000009723	1 retrocopy	retro_eeur_14 ,