RetrogeneDB ID: retro_eeur_41

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2436:15805..16142(+)
• Located in intron of: ENSEEUG00000001984

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2W
• Ensembl ID: ENSEEUG00000011886
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2W (putative) [Source:HGNC Symbol;Acc:25616]

Sequence

>retro_eeur_41
ATTGTAGTCCTAGAAGGTGCACCAGGTACCTTATATGATGGGGAAAAGTTTCAACTTCTATTTAAATTTAGTAGTAGATA
CCCTTTTGACTCTCCTCAGGTCATGTTTACTGGTGAAAATATTCCTGTTCATCCTCATGTTTATAGCAATGGGCATGTCT
GTTTATCCATTCTAATGGAAGACTGGTCTCCAGCGCTCTCAGTCCAGTCAGTGTGTCTTAGCATTATTAGCATGCTTTCC
AGCTGCAAAGAAAAGAGACAACCACCAGATAATGCATTTTCTGTTCGACATGTAACAGAACCCAAAGAAAAACAAAATGG
TGTATCATGAGTCCAGT

Alignment

ORF - retro_eeur_41 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.35 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IVDMEGAPGTLYEGEKFQLLFKFSSRYPFDSPQVMFTGENIPVHPHVYSNGHICLSILTEDWSPALSVQS
          IV..EGAPGTLY.GEKFQLLFKFSSRYPFDSPQVMFTGENIPVHPHVYSNGH.CLSIL.EDWSPALSVQS
Retrocopy IVVLEGAPGTLYDGEKFQLLFKFSSRYPFDSPQVMFTGENIPVHPHVYSNGHVCLSILMEDWSPALSVQS

Parental  VCLSIISMLSSCKEKRRPPDNSFYVR-TCNKNPKKTKWW-YHDDT
          VCLSIISMLSSCKEKR.PPDN.F.VR.TCN....KTKW..YH...
Retrocopy VCLSIISMLSSCKEKRQPPDNAFSVR<TCNRTQRKTKWC<YHESS

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	0.32 RPM	25.78 RPM
SRP017611_kidney	0.19 RPM	13.13 RPM
SRP017611_liver	0.00 RPM	6.27 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_41 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 8 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005910	4 retrocopies	retro_chof_1114, retro_chof_1974, retro_chof_889, retro_chof_957,
Dasypus novemcinctus	ENSDNOG00000012909	2 retrocopies	retro_dnov_1378, retro_dnov_962,
Erinaceus europaeus	ENSEEUG00000010643	14 retrocopies	retro_eeur_113, retro_eeur_177, retro_eeur_249, retro_eeur_253, retro_eeur_266, retro_eeur_272, retro_eeur_294, retro_eeur_346, retro_eeur_375, retro_eeur_518, retro_eeur_592, retro_eeur_604, retro_eeur_641, retro_eeur_80,
Erinaceus europaeus	ENSEEUG00000011886	1 retrocopy	retro_eeur_41 ,
Myotis lucifugus	ENSMLUG00000027009	3 retrocopies	retro_mluc_1510, retro_mluc_1900, retro_mluc_619,
Sorex araneus	ENSSARG00000007886	2 retrocopies	retro_sara_306, retro_sara_464,
Tupaia belangeri	ENSTBEG00000011410	3 retrocopies	retro_tbel_1929, retro_tbel_4440, retro_tbel_682,
Vicugna pacos	ENSVPAG00000001527	2 retrocopies	retro_vpac_115, retro_vpac_227,