RetrogeneDB ID: retro_eeur_9

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_176806:858..1176(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000010178
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000010549
• Aliases: None
• Description: None

Sequence

>retro_eeur_9
CTGCTGAATCCCCCTCAGGCTGCTGCTCTTGCTGTTAGATATGCATCCAAGAAGACAGATGGCAGCTCCGAAAACCATGG
TGGAAGGTCACCAGGCAAACACTTTGGCATAAAGGAATTAGAGAGTAACTACATTCACGCTGGCAATATCCTTGCTACTC
AGCGTCACTTTCGCTGGCACCCAGGTGCCCATGTGGGATTGGGGAAGAACAAGTGCCTGTATGCCCTGGAGGAGGGCATA
GTTCGCTACACCAAGGACGTTTATGTGCCCAACCCTAGCAATTCGGGGGCTGTAGATCTGATTGCCAAGCTACCCAGG

Alignment

ORF - retro_eeur_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 71.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLNPPQAAALAVRYASKKTGGSSKNHGGKSPGKHFGIKKLEGHYVHAGNILATQRHFRWHPGAHVGLGKN
          LLNPPQAAALAVRYASKKT.GSS.NHGG.SPGKHFGIK.LE..Y.HAGNILATQRHFRWHPGAHVGLGKN
Retrocopy LLNPPQAAALAVRYASKKTDGSSENHGGRSPGKHFGIKELESNYIHAGNILATQRHFRWHPGAHVGLGKN

Parental  KCLYALEEGIVRYTKEVYVPNPSNSEAVDLVTKLPR
          KCLYALEEGIVRYTK.VYVPNPSNS.AVDL..KLPR
Retrocopy KCLYALEEGIVRYTKDVYVPNPSNSGAVDLIAKLPR

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	0.48 RPM	22.88 RPM
SRP017611_kidney	1.13 RPM	55.32 RPM
SRP017611_liver	0.32 RPM	25.56 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_9 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017031	1 retrocopy	retro_cfam_1454,
Choloepus hoffmanni	ENSCHOG00000005103	1 retrocopy	retro_chof_943,
Callithrix jacchus	ENSCJAG00000018851	2 retrocopies	retro_cjac_28, retro_cjac_378,
Dasypus novemcinctus	ENSDNOG00000023845	2 retrocopies	retro_dnov_1233, retro_dnov_1731,
Erinaceus europaeus	ENSEEUG00000010549	3 retrocopies	retro_eeur_126, retro_eeur_22, retro_eeur_9 ,
Echinops telfairi	ENSETEG00000014252	2 retrocopies	retro_etel_13, retro_etel_893,
Microcebus murinus	ENSMICG00000009698	1 retrocopy	retro_mmur_624,
Macaca mulatta	ENSMMUG00000017231	1 retrocopy	retro_mmul_64,
Mus musculus	ENSMUSG00000024414	2 retrocopies	retro_mmus_1696, retro_mmus_2918,
Oryctolagus cuniculus	ENSOCUG00000004601	2 retrocopies	retro_ocun_1026, retro_ocun_1936,
Otolemur garnettii	ENSOGAG00000005385	1 retrocopy	retro_ogar_53,