RetrogeneDB ID: retro_eeur_664

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_378031:56192..56457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA6
• Ensembl ID: ENSEEUG00000004117
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa [Source:HGNC Symbol;Acc:7690]

Sequence

>retro_eeur_664
ATTTTCACCCAGGACATGAAGGCCAAGCAGATGGTGTACGCCAAGCTCTGCTGTGCCTGGTATTAAGAGGTGCTAACAAC
TGTGCACTTATACCTAGCTAGATATCTCTGCTAAATGGGGATGGGATAAAGTTTGAGAAATGTTAATGCTGAGTGCCTTT
TCCACAGATCCCAGAATGGTCAATCTTCCAGTCATTAAAGGATAGATAGAACTGGAAGAAACGATTCAAGTATGGAAGCA
GCAGACACATACTATGTGGTTCTTC

Alignment

ORF - retro_eeur_664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.3 %
• Parental protein coverage: 68.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFSRDLKEAKRRVRELYRAWYREVPNTVHLFQ-LDISVKQGRDKVREMFMKNAHVTDPRVLDLLVIKGKM
          IF..D.K........L..AWY.EV..TVHL...LDIS.K.G.DKV.EM.M..A..TDPR...L.VIKG..
Retrocopy IFTQDMKAKQMVYAKLCCAWY*EVLTTVHLYL>LDISAKWGWDKV*EMLMLSAFSTDPRMVNLPVIKG*I

Parental  ELEETIKVWKQRTHIMRFF
          ELEETI.VWKQ.TH.M.FF
Retrocopy ELEETIQVWKQQTHTMWFF

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	29.01 RPM
SRP017611_kidney	0.00 RPM	81.77 RPM
SRP017611_liver	0.00 RPM	40.52 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_664 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000001466	1 retrocopy	retro_csav_29,
Erinaceus europaeus	ENSEEUG00000004117	1 retrocopy	retro_eeur_664 ,
Monodelphis domestica	ENSMODG00000007030	1 retrocopy	retro_mdom_397,
Mus musculus	ENSMUSG00000022450	1 retrocopy	retro_mmus_2693,
Oryctolagus cuniculus	ENSOCUG00000015446	1 retrocopy	retro_ocun_1128,
Otolemur garnettii	ENSOGAG00000014762	2 retrocopies	retro_ogar_1656, retro_ogar_312,
Procavia capensis	ENSPCAG00000004570	1 retrocopy	retro_pcap_18,
Rattus norvegicus	ENSRNOG00000008569	1 retrocopy	retro_rnor_604,
Sorex araneus	ENSSARG00000003814	1 retrocopy	retro_sara_75,