RetrogeneDB ID: retro_eeur_382

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_278185:998..1261(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000005674
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000011989
• Aliases: None
• Description: None

Sequence

>retro_eeur_382
TTTCTGTGCAGCCTGCTGGCTCCCATGGTCATGGTCAGTGCTGAGCAACAGAAAGAACAGAATCTCTTTCATTATGACTA
CCAGACCCTGAGGATCAGGGGATTAGTGTCTGCTGTGGTCCTTTTCTTGGTGGTGATCCTCCTACTCCTGAGTCTCAGAT
GCAAGTGCAATTTCAATTCGAAATCCCAGGTGCCAGGGGACCAGGAGACCCAGGTGGAGATGCTCATCACTGCAAAGCAA
CAGAGGCCCAGAAGGCAGAGAAC

Alignment

ORF - retro_eeur_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 93.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLCSLLAPMVLVHAAEQEKEQDPFHYDYQTLRIGGLVFAVVLFLVGILLILSRRCKCNFNQKPRAPGDEE
          FLCSLLAPMV.V..AEQ.KEQ..FHYDYQTLRI.GLV.AVVLFLV.ILL.LS.RCKCNFN.K...PGD.E
Retrocopy FLCSLLAPMVMV-SAEQQKEQNLFHYDYQTLRIRGLVSAVVLFLVVILLLLSLRCKCNFNSKSQVPGDQE

Parental  AQVETLITA-NATEPQKAEN
          .QVE.LITA..ATE.QKAEN
Retrocopy TQVEMLITA<KATEAQKAEN

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	39.48 RPM
SRP017611_kidney	0.00 RPM	0.75 RPM
SRP017611_liver	0.00 RPM	0.48 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_382 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
Callithrix jacchus	ENSCJAG00000013044	1 retrocopy	retro_cjac_2098,
Erinaceus europaeus	ENSEEUG00000011989	1 retrocopy	retro_eeur_382 ,
Homo sapiens	ENSG00000137726	2 retrocopies	retro_hsap_562, retro_hsap_662,
Gorilla gorilla	ENSGGOG00000006473	2 retrocopies	retro_ggor_507, retro_ggor_574,
Macaca mulatta	ENSMMUG00000007617	2 retrocopies	retro_mmul_2439, retro_mmul_2440,
Nomascus leucogenys	ENSNLEG00000007348	2 retrocopies	retro_nleu_1982, retro_nleu_2890,
Otolemur garnettii	ENSOGAG00000015394	2 retrocopies	retro_ogar_2451, retro_ogar_3061,
Pongo abelii	ENSPPYG00000003918	3 retrocopies	retro_pabe_583, retro_pabe_644, retro_pabe_648,
Pan troglodytes	ENSPTRG00000004329	3 retrocopies	retro_ptro_3127, retro_ptro_421, retro_ptro_481,