RetrogeneDB ID: retro_eeur_70

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_4164:19006..19518(+)
• Located in intron of: ENSEEUG00000003713

Retrocopy information

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

Parental gene information

• Parental gene symbol: MS4A4A
• Ensembl ID: ENSEEUG00000003258
• Aliases: None
• Description: membrane-spanning 4-domains, subfamily A, member 4A [Source:HGNC Symbol;Acc:13371]

Sequence

>retro_eeur_70
GTTGTACAAATCATGATTGCCCTGATGAATTTCAGTTTTGGAGTCATAATTATGAGTGTCACAGTAACATATCATGGACA
GTATCCCTTCTCAGTATACACATGCTACACAATCTGGGGGTCAGTGATGTTTATTGTTTCAGGGTCATTATCAGTAGGAG
CAGGGAAAAGAACTACAAAGGGTATGGTCTGAGGTAGCCTAGAGTAAACACTACAAGCTCCATCTTTGCTGCAATAGGGA
TCATATTCATGGCAATCAGCTTGCACATTTATTCATTCCATCCTTACATCTGTTATGGCACTAAGATGCAAGAGGATTGT
GCCATGGTCATATCTATTATAACGGGTCTAGAATTCCTAGTGTTAATTTTAAGCATGCTGGAGTTCTGCATTGCTGTGTC
CCTATCTGCTTTTGGATGCAGAGTCACCTGTTGTAATCCTAGTGGGGTTGTACTCATTATGCCATCCAATTCTCACATGG
CAGAATCATCACCATCTGCACCATTTATGGAC

Alignment

ORF - retro_eeur_70 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.95 %
• Parental protein coverage: 84.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVQIVIALMNFSFGVITMSVTITYHGSIP-SVYTCYTIWGSVMFIVSGSLSIGAGKRTTKGMVRGSLG-V
          VVQI.IALMNFSFGVI.MSVT.TYHG..P.SVYTCYTIWGSVMFIVSGSLS.GAGKRTTKGMV.GSL..V
Retrocopy VVQIMIALMNFSFGVIIMSVTVTYHGQYPFSVYTCYTIWGSVMFIVSGSLSVGAGKRTTKGMV*GSLE<V

Parental  NITSSIFAAIGIIFMAISLHIYSFHPYICYG----DDCAMVVSIITGLEFLVLILSILEFCIAVSLSAFG
          N.TSSIFAAIGIIFMAISLHIYSFHPYICYG.....DCAMV.SIITGLEFLVLILS.LEFCIAVSLSAFG
Retrocopy NTTSSIFAAIGIIFMAISLHIYSFHPYICYGTKMQEDCAMVISIITGLEFLVLILSMLEFCIAVSLSAFG

Parental  CRVTCCNPGGVVLIMPSNSHMAESSPSAPFMD
          CRVTCCNP.GVVLIMPSNSHMAESSPSAPFMD
Retrocopy CRVTCCNPSGVVLIMPSNSHMAESSPSAPFMD

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	0.48 RPM	1.61 RPM
SRP017611_kidney	0.56 RPM	1.50 RPM
SRP017611_liver	1.77 RPM	5.95 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_70 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000003258	1 retrocopy	retro_eeur_70 ,