RetrogeneDB ID: retro_eeur_52

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2825:42186..42840(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS3
• Ensembl ID: ENSEEUG00000007356
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7710]

Sequence

>retro_eeur_52
ACTGTCAGACCACGGGTTGATGTAACCCACAAGCAACTCTCAGCTTTTGGAGAGTATGTGGCTGAAATCCTGCCCAAATA
TGTCCAACAAGTTCAGGTGACATGCTTCAATGAGTTGGAGATCTGTATCCATCTAGATGGAGTCATTCCAGTGTTGACTT
TTCTCCGAGATTACACGAATGCACAGTTTAAATCCTTGGTTGACTTGACAGCAGTTGACATCCCCACCTGGCAGAATCAT
TTTGAGACTGTTTACAACCTGCTCTCTCTGCGCTACAACTCTTGCATCCATGTGAAGACCTATACAGACGAGCTGACACC
CACTGACTCCACAGTCCCTGTGAACAAGGCAGCCAACTGGTATGAGAGGGAGATCTGGGACATGTTTGGAGTCTTCTTTG
CTAACCATCCTGATCTGAGGAGGATCCTGACAGACTATGGCTTTGAGGGGCATCCTTTCAGAAAAGATTTCCCCTTGTCT
GACTATGTTGAGTTACACTATGATGATAAGGTGAAGCGGGTGGTGGCTGAGCCAGTGGAGTTGGCCCAAGAGTTCCACAG
GTTTGACCTGAACAGCCCATGGGAGGCTTTTCCTGCCTACTGGCAGCCCCCTGAAAACCTCAAGCTTGAAGCTGGAGAAA
AAACAGAAACCAAG

Alignment

ORF - retro_eeur_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVRLRDDVTHKQLSAFGEYVAEILPKYVQQVQVTCFSELEICIHPDGVIPVLTFLRDHTNAQFKSLADLT
          TVR.R.DVTHKQLSAFGEYVAEILPKYVQQVQVTCF.ELEICIH.DGVIPVLTFLRD.TNAQFKSL.DLT
Retrocopy TVRPRVDVTHKQLSAFGEYVAEILPKYVQQVQVTCFNELEICIHLDGVIPVLTFLRDYTNAQFKSLVDLT

Parental  AVDIPTRQNRFEIVYNLLSLRYNSRIRVKTYTDELTPIDSTVPVYKAANWYEREIWDMFGVFFANHPDLR
          AVDIPT.QN.FE.VYNLLSLRYNS.I.VKTYTDELTP.DSTVPV.KAANWYEREIWDMFGVFFANHPDLR
Retrocopy AVDIPTWQNHFETVYNLLSLRYNSCIHVKTYTDELTPTDSTVPVNKAANWYEREIWDMFGVFFANHPDLR

Parental  RILTDYGFEGHPFRKDFPLSGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEAFPAYRQPPENLKLE
          RILTDYGFEGHPFRKDFPLS.YVEL.YDD.VKRVVAEPVELAQEF..FDLNSPWEAFPAY.QPPENLKLE
Retrocopy RILTDYGFEGHPFRKDFPLSDYVELHYDDKVKRVVAEPVELAQEFHRFDLNSPWEAFPAYWQPPENLKLE

Parental  AGEKTETK
          AGEKTETK
Retrocopy AGEKTETK

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	5.48 RPM	86.37 RPM
SRP017611_kidney	10.50 RPM	222.80 RPM
SRP017611_liver	4.02 RPM	83.44 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_52 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008411	1 retrocopy	retro_cfam_1052,
Callithrix jacchus	ENSCJAG00000020194	1 retrocopy	retro_cjac_4059,
Equus caballus	ENSECAG00000013454	1 retrocopy	retro_ecab_431,
Erinaceus europaeus	ENSEEUG00000007356	1 retrocopy	retro_eeur_52 ,
Mus musculus	ENSMUSG00000005510	2 retrocopies	retro_mmus_2338, retro_mmus_792,