RetrogeneDB ID: retro_eeur_42

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2520:9069..9452(-)
• Located in intron of: ENSEEUG00000003530

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBP1
• Ensembl ID: ENSEEUG00000005367
• Aliases: None
• Description: retinol binding protein 1, cellular [Source:HGNC Symbol;Acc:9919]

Sequence

>retro_eeur_42
ATGCCAGTGGACTTCAGCGGGTACTGGAATTGCAGAGCAACGACAACTTTGAGTAATACCTGCAAGCTCTGGATGTGAAT
GTGGGCCTGCGCAAGATCGCCAGCCTGCTGAAGCAGGACAAAGAGATCATGCAGGAGGGCGAGCACATAATTATCCACAG
GCTGAGCACCTTCAGGAACTACATCATGGACTTCCAGCTTGGCCAGCAGTTTGAGGAGGATCTGACAGGCATAGATGACT
GAAAGTGCATGACCATAGTGAGCTGGGATGGGAACAAGCTGGAGTGTGTGCAGAAGGGTGAGAAGGAGGGGCGCGGCTGG
ACACAGTGGAACGCAGGGGATGAGATGCACTTGGAGATGCAAGCGCAGGGTGTGGCCTGCAAG

Alignment

ORF - retro_eeur_42 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.72 %
• Parental protein coverage: 94.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVDFSGYW-KMQSNDNFEEYLRALDVNVALRKIASLLKPDKEIVQEGEHMIIRTLSTFRNYIMDFQVGQ
          MPVDFSGYW...QSNDNFE.YL.ALDVNV.LRKIASLLK.DKEI.QEGEH.II..LSTFRNYIMDFQ.GQ
Retrocopy MPVDFSGYW<ELQSNDNFE*YLQALDVNVGLRKIASLLKQDKEIMQEGEHIIIHRLSTFRNYIMDFQLGQ

Parental  EFEEDLTGIDDRKCMTTVSWDGDKLECVQKGEKEGRGWTQWIEGDELHLEMRAQGVICK
          .FEEDLTGIDD.KCMT.VSWDG.KLECVQKGEKEGRGWTQW..GDE.HLEM.AQGV.CK
Retrocopy QFEEDLTGIDD*KCMTIVSWDGNKLECVQKGEKEGRGWTQWNAGDEMHLEMQAQGVACK

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	0.16 RPM	11.12 RPM
SRP017611_kidney	0.00 RPM	24.94 RPM
SRP017611_liver	0.00 RPM	8.84 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_42 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020028	1 retrocopy	retro_btau_1290,
Erinaceus europaeus	ENSEEUG00000005367	1 retrocopy	retro_eeur_42 ,
Erinaceus europaeus	ENSEEUG00000014023	2 retrocopies	retro_eeur_405, retro_eeur_627,
Macropus eugenii	ENSMEUG00000003195	2 retrocopies	retro_meug_1379, retro_meug_511,
Ictidomys tridecemlineatus	ENSSTOG00000005673	1 retrocopy	retro_itri_749,