RetrogeneDB ID: retro_eeur_133

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_8372:65301..65780(+)
• Located in intron of: ENSEEUG00000010089

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS4
• Ensembl ID: ENSEEUG00000015851
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7711]

Sequence

>retro_eeur_133
GGGTGAAGGGCAATGGCTGCCATGGCCTTTTCCACGTCCAGGCTTCCGATCAGGTTGTTGAGCACATCCTCATGGTGACT
GGCACAGGACCAGACTCGAGACAGGCAGCTCATAACAGTTGATGAAAAATTGGGTATCACTACTTTAACTGGGGTTCCAG
AAGAACATATCAAAACTAGAAAAGTCAGGGTCTTTGTTCCTGCTCTCAATAATATGCATTCTGGAGTAAACAATACAAAG
AAATGGAAGATGGAGTTTGATACAAGGGAACACTGGGAAAATTCTTTGATGGGCTGGGCATGAACGGCTGATCCCTTATC
CAACATGGTTTTGACTTTCTGTACTAAGAAGATGCAATTGTCTTTGCAGAGAAAAATGGATGGAGCTATGGCATTGAAGA
AAGGAAGGTTCCGAAACCCAAGTCCAAGTCTTATGGCACAAACTTTTCTTGGAACAAAGGAACAAGAGTATTCACAAAA

Alignment

ORF - retro_eeur_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRRAMAAAAFSVSRLPIRLLSTSAWRPAQDQTRDRQLITVDEKLDITTLTGVPEEHIKTRKVRIFVPARN
          G.RAMAA.AFS.SRLPIRLLSTS.W..AQDQTRDRQLITVDEKL.ITTLTGVPEEHIKTRKVR.FVPA.N
Retrocopy G*RAMAAMAFSTSRLPIRLLSTSSW*LAQDQTRDRQLITVDEKLGITTLTGVPEEHIKTRKVRVFVPALN

Parental  NMQSGVHNTKKWKMEFDTRERWENPLMGWASTADPLSNMVLTFSTK-EDAIVFAEKNGWSYDVEERKVPK
          NM.SGV.NTKKWKMEFDTRE.WEN.LMGWA.TADPLSNMVLTF.TK.EDAIVFAEKNGWSY..EERKVPK
Retrocopy NMHSGVNNTKKWKMEFDTREHWENSLMGWA*TADPLSNMVLTFCTK<EDAIVFAEKNGWSYGIEERKVPK

Parental  PKSNFYGANFSWNKRTRVSTK
          PKS..YG.NFSWNK.TRV.TK
Retrocopy PKSKSYGTNFSWNKGTRVFTK

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	29.17 RPM
SRP017611_kidney	0.00 RPM	67.33 RPM
SRP017611_liver	0.00 RPM	35.21 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_133 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005452	1 retrocopy	retro_cpor_1111,
Erinaceus europaeus	ENSEEUG00000015851	3 retrocopies	retro_eeur_133 , retro_eeur_30, retro_eeur_347,
Macropus eugenii	ENSMEUG00000001362	1 retrocopy	retro_meug_651,
Microcebus murinus	ENSMICG00000015138	1 retrocopy	retro_mmur_355,
Monodelphis domestica	ENSMODG00000019465	1 retrocopy	retro_mdom_1227,
Mus musculus	ENSMUSG00000021764	1 retrocopy	retro_mmus_3372,
Ochotona princeps	ENSOPRG00000013784	1 retrocopy	retro_opri_508,
Procavia capensis	ENSPCAG00000013496	1 retrocopy	retro_pcap_268,
Pongo abelii	ENSPPYG00000015455	1 retrocopy	retro_pabe_193,
Sus scrofa	ENSSSCG00000016893	1 retrocopy	retro_sscr_999,
Tupaia belangeri	ENSTBEG00000004605	1 retrocopy	retro_tbel_2068,