RetrogeneDB ID: retro_eeur_172

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_140388:831..1230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THAP1
• Ensembl ID: ENSEEUG00000003332
• Aliases: None
• Description: THAP domain containing, apoptosis associated protein 1 [Source:HGNC Symbol;Acc:20856]

Sequence

>retro_eeur_172
ATGGTGCAGTCCTGTACCGCCTACGGCTGCAAGAACCCATACAATAAGGATAAGCCCATTTCTTTTCACAAGTTTCGTCT
TACACGACCTAATCTTTGTAAAGAATGTGAAGCAGCTGATAGAAGAAAAAACTTTAAGTCAACAAAGTACACCCGTATTT
GTTCAGAACACTTTACTCCAGACTGCTTTAAGAGGGAATGCAACAACAAGTTATTGAAGGAGAATGCTGTGCCCATCATA
TTTCACTGTACTGAACCGGACGACAGAAAGGAAGAGCTACTTGGAACCACGGCGACAGCTTTCACCAGCCTTCCTTATAG
CACCTCTCATTTTCCAAGTTGATCCTGCTAATTGGGATTACTCAAGCTCTCCCTCTTTCGAACCCAGGATAATCTCTCA

Alignment

ORF - retro_eeur_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.56 %
• Parental protein coverage: 61.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVQSCSAYGCKNRYDKDKPVSFHKFPLTRPNLCKEWEAAVRRKNFKPTKYSSICSEHFTPDCFKRECNNK
          MVQSC.AYGCKN.Y.KDKP.SFHKF.LTRPNLCKE.EAA.RRKNFK.TKY..ICSEHFTPDCFKRECNNK
Retrocopy MVQSCTAYGCKNPYNKDKPISFHKFRLTRPNLCKECEAADRRKNFKSTKYTRICSEHFTPDCFKRECNNK

Parental  LLKENAVPTIFLCTEPHDKKEEL-LEPQGQLHPPPL-APPISQVDAA-IGLLMP-PLQTP-DNLS
          LLKENAVP.IF.CTEP.D.KEEL.LEP..QL.P..L.AP.I.QVD.A.IG.....PL..P.DNLS
Retrocopy LLKENAVPIIFHCTEPDDRKEEL>LEPRRQLSPAFLIAPLIFQVDPA>IGITQALPLSNP>DNLS

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	2.58 RPM
SRP017611_kidney	0.00 RPM	4.88 RPM
SRP017611_liver	0.00 RPM	2.25 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_172 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	ENSEEUG00000003332	2 retrocopies	retro_eeur_131, retro_eeur_172 ,
Myotis lucifugus	ENSMLUG00000003837	1 retrocopy	retro_mluc_1607,
Oryctolagus cuniculus	ENSOCUG00000001391	1 retrocopy	retro_ocun_1582,