RetrogeneDB ID: retro_eeur_7

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_263976:3..306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000000886
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000002930
• Aliases: None
• Description: None

Sequence

>retro_eeur_7
AGCCTGGAGCGGGTGTCCAACGAGGAGATACTGAACCTGTGTCGGAAGTACTATCTGGGTGGGTTCGCTTTTCTCCCATT
TCTCTGGTTGGTCAACATCTTCTGGTTCTTCCGAGAAGCCTTCCTTGTCCCAGCTTACACTGAGCAGAGCCAAATCAAAG
GCTATGTCTGGCGCTCAGCTGTGGGCTTCCTCTTCTGGGTGATTGTACTTGCCACCTGGATCACCATCTTCCAGATCTAC
CGGCCCCGGTGGGGCGCCCTTGGAGACTACCTCTCTTTCACTATACCACTGGGTAGCCCCTGA

Alignment

ORF - retro_eeur_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.0 %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRSAVGFLFWVIVL
          .LERVSNEE.LNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRSAVGFLFWVIVL
Retrocopy SLERVSNEEILNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRSAVGFLFWVIVL

Parental  ATWITIFQIYRPRWGALGDYLSFTIPLGSP
          ATWITIFQIYRPRWGALGDYLSFTIPLGSP
Retrocopy ATWITIFQIYRPRWGALGDYLSFTIPLGSP

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	6.77 RPM
SRP017611_kidney	0.38 RPM	17.25 RPM
SRP017611_liver	0.16 RPM	11.58 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_7 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002930	1 retrocopy	retro_eeur_7 ,
Macropus eugenii	ENSMEUG00000012358	1 retrocopy	retro_meug_524,
Myotis lucifugus	ENSMLUG00000011528	2 retrocopies	retro_mluc_1385, retro_mluc_1860,
Mus musculus	ENSMUSG00000036835	2 retrocopies	retro_mmus_1415, retro_mmus_2454,
Sorex araneus	ENSSARG00000002056	1 retrocopy	retro_sara_708,
Sus scrofa	ENSSSCG00000024330	1 retrocopy	retro_sscr_664,
Tupaia belangeri	ENSTBEG00000001589	1 retrocopy	retro_tbel_447,