RetrogeneDB ID: retro_eeur_563

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_344818:45238..45727(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000004274
• Aliases: None
• Description: None

Sequence

>retro_eeur_563
AAGGATATTTTATTTCCTTACATCAAGGAAAATGTTGAAGAGTATCTGCAGACACATTGGGAGGAAGAGGAGTGCCAGCA
GGATGTCAATCTTCTGAGGAAACAGGCTGAAGAAGACTCTCACCTGGACGGCACTTTCCCCGTCCCAGTGGCTCGTGGGA
ATAGTGCTGAAGACCTGCAGCAGACCATCCAGGCTGTGGTGGATAATGTCCACTGGCATATGTCCCTGGACCAGAAGACC
ACAGCTCTGAAACAGCTGCAGGGCCACATGTGGAGGGCAGCCTTCACAGCTGGGTGCATAAAAACAGAGTTCTTTGAAGA
TGTAGTTCCAGCAGTCAGGAAATGGAGAGAGGCTGGAATAAAGGTATATATCTATTCTTCAGGGTGTGTGGAGGCCCAGA
AGTTATTATTTGGGCATTCTACAGAAGGAGATATTCTTGAGCTTGTTGATGGTCACTTTGACACCAAGATTGGACACAAA
GTGGAGAGT

Alignment

ORF - retro_eeur_563 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.18 %
• Parental protein coverage: 62.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDILFPYIKENVEEYLQTHWEEEECQXXXXXXXXXAEEDSHLDGAVPIPVARGNSAEDLQQTIQAVVDNV
          KDILFPYIKENVEEYLQTHWEEEECQ.........AEEDSHLDG..P.PVARGNSAEDLQQTIQAVVDNV
Retrocopy KDILFPYIKENVEEYLQTHWEEEECQQDVNLLRKQAEEDSHLDGTFPVPVARGNSAEDLQQTIQAVVDNV

Parental  HWQMSLDRKTTALKQLQGHMWRAAFTAGCIKAEFFEDVVPAVRKWREAGIKVYIYSSGSVEAQKLLFGHS
          HW.MSLD.KTTALKQLQGHMWRAAFTAGCIK.EFFEDVVPAVRKWREAGIKVYIYSSG.VEAQKLLFGHS
Retrocopy HWHMSLDQKTTALKQLQGHMWRAAFTAGCIKTEFFEDVVPAVRKWREAGIKVYIYSSGCVEAQKLLFGHS

Parental  TEGDILELVDGHFDTKIGHKVES
          TEGDILELVDGHFDTKIGHKVES
Retrocopy TEGDILELVDGHFDTKIGHKVES

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	2.42 RPM	29.49 RPM
SRP017611_kidney	0.75 RPM	9.75 RPM
SRP017611_liver	0.48 RPM	3.54 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_563 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005140	2 retrocopies	retro_amel_1186, retro_amel_930,
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus	ENSCJAG00000015251	2 retrocopies	retro_cjac_1376, retro_cjac_2375,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563 ,
Homo sapiens	ENSG00000145293	1 retrocopy	retro_hsap_2900,
Gorilla gorilla	ENSGGOG00000003719	1 retrocopy	retro_ggor_2010,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Myotis lucifugus	ENSMLUG00000014460	1 retrocopy	retro_mluc_2504,
Otolemur garnettii	ENSOGAG00000002502	1 retrocopy	retro_ogar_1549,
Pongo abelii	ENSPPYG00000014887	1 retrocopy	retro_pabe_2399,
Pan troglodytes	ENSPTRG00000016218	1 retrocopy	retro_ptro_1960,
Ictidomys tridecemlineatus	ENSSTOG00000013987	2 retrocopies	retro_itri_1067, retro_itri_1587,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,