RetrogeneDB ID: retro_eeur_634

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_371511:43738..43963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SS18L2
• Ensembl ID: ENSEEUG00000014065
• Aliases: None
• Description: synovial sarcoma translocation gene on chromosome 18-like 2 [Source:HGNC Symbol;Acc:15593]

Sequence

>retro_eeur_634
ATGTCAGTGGCCTTCGTGCTGGACTGGATGCGAGGCAAGGCGGAAGTAAATCAGGAGACCATCCAGCGGCTCCTGGAGGA
GAATGACCAGTTGATCTGCTGCATCGTGAAATATCAGAATAAGGGTCGAGCACATGAGTGTGTCCAGTACCAGCAGGTGT
TACCCAGAAAGCTCATTTTTCTGGCTACCACTGCAGATGCCAGCCCAACCAACACTGCGAAGAAA

Alignment

ORF - retro_eeur_634 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVAFVPDWMRGKAEVNQETIQRLLEENDQLIRCIVEYQNKGRAHECVQ-RQVLHRNLIYLASIADASPT
          MSVAFV.DWMRGKAEVNQETIQRLLEENDQLI.CIV.YQNKGRAHECVQ..QVL.R.LI.LA..ADASPT
Retrocopy MSVAFVLDWMRGKAEVNQETIQRLLEENDQLICCIVKYQNKGRAHECVQYQQVLPRKLIFLATTADASPT

Parental  NTAKE
          NTAK.
Retrocopy NTAKK

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	6.28 RPM
SRP017611_kidney	0.00 RPM	4.88 RPM
SRP017611_liver	0.00 RPM	3.54 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_634 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000989	1 retrocopy	retro_acar_189,
Dipodomys ordii	ENSDORG00000015005	4 retrocopies	retro_dord_286, retro_dord_39, retro_dord_643, retro_dord_658,
Erinaceus europaeus	ENSEEUG00000014065	1 retrocopy	retro_eeur_634 ,
Echinops telfairi	ENSETEG00000007192	2 retrocopies	retro_etel_1749, retro_etel_2074,
Loxodonta africana	ENSLAFG00000021542	2 retrocopies	retro_lafr_754, retro_lafr_92,
Myotis lucifugus	ENSMLUG00000013024	1 retrocopy	retro_mluc_21,
Mus musculus	ENSMUSG00000032526	3 retrocopies	retro_mmus_1247, retro_mmus_1827, retro_mmus_3284,
Ochotona princeps	ENSOPRG00000015198	4 retrocopies	retro_opri_401, retro_opri_516, retro_opri_542, retro_opri_593,
Sorex araneus	ENSSARG00000014056	1 retrocopy	retro_sara_465,
Tarsius syrichta	ENSTSYG00000007658	1 retrocopy	retro_tsyr_1687,