RetrogeneDB ID: retro_eeur_573

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_346849:12251..12611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSEEUG00000002185
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]

Sequence

>retro_eeur_573
GTGGAGGACAGGGCTCTGGGCTCCCTGCTGGCCCCCACCTGCATGTTCTGCTTCTGCTTCCCCTCACCGTCCAGCGGGAG
AAATTCAGGAAAAAAAGAAAAAACAGATTGAGAACTGAAGGGACAAGAAGTCAGTTCTAAAGTCTACTTCATTAAGCAGA
CAGCTGGCAACTCCTGTAGGGCCATCAGGCAGATACATTGATTATTGGCCAATAATCAAGACAAGCTGGAGTTTGAGGAT
GAGAAAGCCTTGAAGAAGTTTCTTTCTGAAACAGAGACGTTGTCCCCTGAACACAGGGCAAAATGCTTTGAAAAGAATGA
GGCTATTTAAGCCGTCCATGACGCTGTGGCACAGGAAGGC

Alignment

ORF - retro_eeur_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 52.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEDESLGSVPAPACALLLLF--PLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIH-AVA
          .ED..LGS..AP.C.....F..P..............ELKGQEVS.KVYF.KQT.GNSC..I..IH...A
Retrocopy VEDRALGSLLAPTCMFCFCFPSPSSGRNSXXXXXXD*ELKGQEVSSKVYFIKQTAGNSCRAIRQIH*LLA

Parental  NNQDKLEFEDGSVLKQFLSETEKLSPEDRAKCFEKNEAIQAAHDAVAQEG
          NNQDKLEFED...LK.FLSETE.LSPE.RAKCFEKNEAI.A.HDAVAQEG
Retrocopy NNQDKLEFEDEKALKKFLSETETLSPEHRAKCFEKNEAI*AVHDAVAQEG

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	197.40 RPM
SRP017611_kidney	0.00 RPM	3.38 RPM
SRP017611_liver	0.00 RPM	0.48 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_573 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Erinaceus europaeus	ENSEEUG00000002185	3 retrocopies	retro_eeur_150, retro_eeur_573 , retro_eeur_598,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Homo sapiens	ENSG00000154277	2 retrocopies	retro_hsap_781, retro_hsap_782,
Gorilla gorilla	ENSGGOG00000008809	1 retrocopy	retro_ggor_648,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Myotis lucifugus	ENSMLUG00000010138	2 retrocopies	retro_mluc_1216, retro_mluc_2113,
Nomascus leucogenys	ENSNLEG00000017176	2 retrocopies	retro_nleu_2582, retro_nleu_2583,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Pan troglodytes	ENSPTRG00000016009	2 retrocopies	retro_ptro_3028, retro_ptro_3029,
Tarsius syrichta	ENSTSYG00000008305	1 retrocopy	retro_tsyr_1191,