RetrogeneDB ID: retro_eeur_690

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_75386:2..821(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDK3
• Ensembl ID: ENSEEUG00000014090
• Aliases: None
• Description: pyruvate dehydrogenase kinase, isozyme 3 [Source:HGNC Symbol;Acc:8811]

Sequence

>retro_eeur_690
GATGCTTGTGAGAAAACATCATTCGTGTTTCTACGGAAAGAACTTCCCGTGCGCCTCGCCAGTACAGCGAGGGAAGTTGG
TCTTCTGCCAGATAAATTGCTACACCACCCTTCGGTAAACCTGGTGCGAAATGGGTACTTGCAGAGTTTCCTTGAGCTCT
TAGAATATGAGAACAAAAGCCCTGAGGATCCACAGGTCTTGGTCAACTTTCTTCAAGTTCTGATTAATATCAGAAATAGA
CACAATGATGTGGCACCTATGATAGCACAAGGAGTGATCGAATACAAAGAAAAGTTTGGCTTTGACCCGTTCACTAGTAG
TAACATCCAATATTTTCTGGATCGGTTTTATATCAACCGCATCTCTTTCCGCATGCTCATTAACCAACACACACTCCTGT
TTGGCGGTGACATCAATCCTGCTCATCCTAAACACATCGGAAGTATTGACCCCACCTGCAATGTGGCTGATGTTGTGAGA
GATGCTTATGAGAAGGCCAAGATGCTGTGTGAACAGTATTACCTCGTAGCTCCAGAACTGAAAATCGAAGAATTCAATGC
CCAAGCTCTAGACAAACCTATACAGGTAGTTTATGTGCCTTCACATCTGTTTCACATGTTATTTGAGTTGTTCAAGAACT
CAATGAGAGCAACAGTTGAACTGTATGAAGGTAGAAAGGAGGGTTGCCCAGCTATTAAGACCCTCGTTACTCTAGGTCAG
GAAGACTTGTCCATTAAGATAAGCGACCAAGGTGGTGGGGTCCCACTTCGAAAAATAGACCGTCTTTTTAACTACATGTA
TTCAACTGCTCCAGACCCA

Alignment

ORF - retro_eeur_690 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.91 %
• Parental protein coverage: 73.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NACEKTSYMFLRKELPVRLANTMREVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNF
          .ACEKTS..FLRKELPVRLA.T.REV.LLPD.LL..PSV.LV...Y.QSFLELLEYENKSPEDPQVL.NF
Retrocopy DACEKTSFVFLRKELPVRLASTAREVGLLPDKLLHHPSVNLVRNGYLQSFLELLEYENKSPEDPQVLVNF

Parental  LQVLINVRNRHNDVVPTMAQGVIEYKEKFGFDPFISSNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNP
          LQVLIN.RNRHNDV.P..AQGVIEYKEKFGFDPF.SSNIQYFLDRFY.NRISFRMLINQHTLLFGGD.NP
Retrocopy LQVLINIRNRHNDVAPMIAQGVIEYKEKFGFDPFTSSNIQYFLDRFYINRISFRMLINQHTLLFGGDINP

Parental  AHPKHIGSIDPTCNVADVVKDAYETAKMLCEQYYLVAPELEIEEFNAKAPDKPIQVVYVPSHLFHMLFEL
          AHPKHIGSIDPTCNVADVV.DAYE.AKMLCEQYYLVAPEL.IEEFNA.A.DKPIQVVYVPSHLFHMLFEL
Retrocopy AHPKHIGSIDPTCNVADVVRDAYEKAKMLCEQYYLVAPELKIEEFNAQALDKPIQVVYVPSHLFHMLFEL

Parental  FKNSMRATVELYEDRKEAYPAVKTLVTLGKEDLSIKISDQGGGVPLRKIDRLFNYMYSTAPRP
          FKNSMRATVELYE.RKE..PA.KTLVTLG.EDLSIKISDQGGGVPLRKIDRLFNYMYSTAP.P
Retrocopy FKNSMRATVELYEGRKEGCPAIKTLVTLGQEDLSIKISDQGGGVPLRKIDRLFNYMYSTAPDP

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	20.95 RPM
SRP017611_kidney	0.19 RPM	96.02 RPM
SRP017611_liver	0.00 RPM	1.45 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_690 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017832	1 retrocopy	retro_btau_911,
Erinaceus europaeus	ENSEEUG00000014090	2 retrocopies	retro_eeur_100, retro_eeur_690 ,
Otolemur garnettii	ENSOGAG00000005598	2 retrocopies	retro_ogar_1213, retro_ogar_1980,