RetrogeneDB ID: retro_eeur_84

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_510:1790..2112(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003438
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2D3
• Ensembl ID: ENSEEUG00000010820
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476]

Sequence

>retro_eeur_84
GAACTTAGTGATTTGACCCATGACCCTCCATCACAATGTTCTGTAGACCCAGTTAGAGATATGTTTCATTAGCAAGTCAC
AATTACGGGAACTAATTACAGCCCCTACCAAGACTATGTACTCTTTCTGACAATTCATTTGACTACAGACTACCCCTCAA
ACCACCTAAGGCTGAATTAACAACAAGAATCTATCATCCAAATATTAACAGTAAGGCAGCATTTGGCTTGATATTCTAAG
ATCACAGCAGTCTCCTGCTGCAACTCTTCCCAAAGTTCTTTTATCCATTTATTCACTGCTATGTGATTCAAACCTAGAAG
AG

Alignment

ORF - retro_eeur_84 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.64 %
• Parental protein coverage: 78.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP-FKPPKAVAFTTRIYHP
          ELSDL..DPP.QCS..PV.D.MFH.Q.TI.G.N.SPYQ..V.FLTIH..TDYP..KPPKA...TTRIYHP
Retrocopy ELSDLTHDPPSQCSVDPVRD-MFH*QVTITGTNYSPYQDYVLFLTIHLTTDYP<LKPPKA-ELTTRIYHP

Parental  NINSN-GSICLDILRSQWSPALTISKVLLSICSLLCDPNPDD
          NINS..GSI.LDILRSQ.SPA.T..KVLLSI.SLLCD.N...
Retrocopy NINSK<GSIWLDILRSQQSPAATLPKVLLSIYSLLCDSNLEE

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	42.54 RPM
SRP017611_kidney	0.00 RPM	60.39 RPM
SRP017611_liver	0.00 RPM	40.68 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_84 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Erinaceus europaeus	ENSEEUG00000010820	1 retrocopy	retro_eeur_84 ,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Otolemur garnettii	ENSOGAG00000012860	6 retrocopies	retro_ogar_1124, retro_ogar_3047, retro_ogar_3048, retro_ogar_3110, retro_ogar_544, retro_ogar_599,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,