RetrogeneDB ID: retro_eeur_199

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_207085:3833..4172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCK2
• Ensembl ID: ENSEEUG00000013484
• Aliases: None
• Description: uridine-cytidine kinase 2 [Source:HGNC Symbol;Acc:12562]

Sequence

>retro_eeur_199
TACCGTGTCCTCACCTCTGAGCAGAAGGCCAAAGCCCTCAAGGGCCAGTTCAACTTTGATCACCCAGATGCCTTTGACAA
TGAACTCATCTTCAAGATGCTCAAAGAAATTATGGACGGGAAGACAGTGCAGATCCCAGTGTATGACTCTGTCTCTAATT
GCGGAAGGAGGAGACTTTCACCGTGTTATCCTGCCGACGTGGTGCCCTTTGAGAGGATCCTGGCCTTCTACTCCCAGGAA
GTGCAAAACCTGATCCAGATGAAGCTTTTTGTGGACAGAGATGCTGATACCCTGCTGTCCCGCAGAGTATTGGCGGACAT
CAGTGAACCAGGGAGGGAC

Alignment

ORF - retro_eeur_199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.87 %
• Parental protein coverage: 73.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YRVLTSEQK-KALKGQFNFDHPDAFDNELIFMTLKEIMEGKTVQIPVYDFVSHS-RKEETVTV-YPADVV
          YRVLTSEQK.KALKGQFNFDHPDAFDNELIF..LKEIM.GKTVQIPVYD.VS...RKEET.TV.YPADVV
Retrocopy YRVLTSEQKAKALKGQFNFDHPDAFDNELIFKMLKEIMDGKTVQIPVYDSVSNC<RKEETFTV>YPADVV

Parental  LFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRELRDISCKGPD
          .FE.ILAFYSQEV..L.QMKLFVD.DADT.LSRR.L.DIS..G.D
Retrocopy PFERILAFYSQEVQNLIQMKLFVDRDADTLLSRRVLADISEPGRD

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	4.67 RPM
SRP017611_kidney	0.00 RPM	0.94 RPM
SRP017611_liver	0.00 RPM	0.96 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_199 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013484	1 retrocopy	retro_eeur_199 ,
Myotis lucifugus	ENSMLUG00000016012	1 retrocopy	retro_mluc_589,
Oryctolagus cuniculus	ENSOCUG00000008446	1 retrocopy	retro_ocun_1924,
Pteropus vampyrus	ENSPVAG00000007694	1 retrocopy	retro_pvam_793,