RetrogeneDB ID: retro_eeur_525

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_338447:4693..5017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX3
• Ensembl ID: ENSEEUG00000015256
• Aliases: None
• Description: sorting nexin 3 [Source:HGNC Symbol;Acc:11174]

Sequence

>retro_eeur_525
ACAAATCTACCTATTTTCAAGCTGAAGGAATCCACTGTTAGAAGAAGATACAGTGACTTTGAATGGCTGAGAAGTGAATT
AGAAAGAGAGAGCAAGGTCGTGGTTCCCCCGCTCCCTGGGAAAGCATTTTTGCGTCAGCTTCCCTTTAGTGGAGACGATG
GAATATTTGATGACAGTTTTATTGAAGAAAGAAAGCAAGGGCTGGAGCAGTTTATAAACAAGGTCGCTGGTCATCCCCTG
GCACAGAACGAACGTTGTCTCCACATGTTTTTACAGGACGAAATTATAGATAAAAGCTATACTCTGTCTAAGATAAGACA
TGCT

Alignment

ORF - retro_eeur_525 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDSFIEERKQGLEQ
          TNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPF.GDDGIFDDSFIEERKQGLEQ
Retrocopy TNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFSGDDGIFDDSFIEERKQGLEQ

Parental  FINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA
          FINKVAGHPLAQNERCLHMFLQDEIIDKSYT.SKIRHA
Retrocopy FINKVAGHPLAQNERCLHMFLQDEIIDKSYTLSKIRHA

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	3.22 RPM	14.18 RPM
SRP017611_kidney	2.44 RPM	13.50 RPM
SRP017611_liver	0.64 RPM	7.88 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_525 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015256	1 retrocopy	retro_eeur_525 ,
Echinops telfairi	ENSETEG00000003537	3 retrocopies	retro_etel_1331, retro_etel_645, retro_etel_924,
Felis catus	ENSFCAG00000024997	1 retrocopy	retro_fcat_1705,
Loxodonta africana	ENSLAFG00000018131	1 retrocopy	retro_lafr_579,
Oryctolagus cuniculus	ENSOCUG00000005858	2 retrocopies	retro_ocun_1022, retro_ocun_750,
Tupaia belangeri	ENSTBEG00000011755	3 retrocopies	retro_tbel_2964, retro_tbel_3503, retro_tbel_3929,
Tursiops truncatus	ENSTTRG00000008868	2 retrocopies	retro_ttru_1028, retro_ttru_1103,