RetrogeneDB ID: retro_eeur_43

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2543:38759..38974(-)
• Located in intron of: ENSEEUG00000014042

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSEEUG00000011640
• Aliases: None
• Description: neural precursor cell expressed, developmentally down-regulated 8 [Source:HGNC Symbol;Acc:7732]

Sequence

>retro_eeur_43
ATGAAGACCCTGATTGGTAAGACCATCACCCTCGAGGTGGAGCCCAGTGACACCATCGAGAATGTCAAGGCAAAGATCCA
GGACAGGAGGGCATAACCCCAGACCAGCAGAGGCTGATCTTTGCTGGCAAGCAGCTGGAAGATGGATGCACTGTGTCTGA
CTACAAAATCCAGAAGGAGTCCACCCTGTACCTGGTCCTGTGCCTGAGGGGTGGT

Alignment

ORF - retro_eeur_43 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.05 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKTLTGKEIEIDIEPTDKVERIKERVEEK-EGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL
          .KTL.GK.I....EP.D..E..K.......EGI.P.QQRLI..GKQ..D..T..DYKI...S.L.LVL.L
Retrocopy MKTLIGKTITLEVEPSDTIENVKAKIQDR<EGITPDQQRLIFAGKQLEDGCTVSDYKIQKESTLYLVLCL

Parental  RGG
          RGG
Retrocopy RGG

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	39.80 RPM
SRP017611_kidney	0.00 RPM	60.39 RPM
SRP017611_liver	0.00 RPM	27.49 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_43 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Erinaceus europaeus	ENSEEUG00000011640	2 retrocopies	retro_eeur_165, retro_eeur_43 ,
Echinops telfairi	ENSETEG00000018391	2 retrocopies	retro_etel_1118, retro_etel_1677,
Homo sapiens	ENSG00000129559	1 retrocopy	retro_hsap_180,
Macaca mulatta	ENSMMUG00000029409	1 retrocopy	retro_mmul_2236,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,
Vicugna pacos	ENSVPAG00000009104	4 retrocopies	retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,