RetrogeneDB ID: retro_eeur_357

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_26920:1020..1347(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSEEUG00000012759
• Aliases: None
• Description: signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]

Sequence

>retro_eeur_357
ATGGTGCTGCTGGAGAGCGAGCAGTTCCTGACGGAGCTGACCAGGCTCTTCCAGAAGTGCCGGCTGTCGGACAGCGTGTT
CATCACCCTGAAGATGTATGACGGTCGCACCAAGCCCATCCCCAGGAAGGGCTCCGTGGAGGGCTTCGAGCCCGCGGACA
AGTGCCTGCTGCGAGCCACTGACGGCAAGAAGAAGATCAGCACGGTGGTGAGCTCCAAAGAAGTGAATAAGTTTCAGATG
GCTGATTCAAACTTGCTGAGAGCCAACATGGATGGCCTGAAGAAGAGGGACAAAAAGAGCAAGAGTAAGAAGAGCAAAGC
AGCACAG

Alignment

ORF - retro_eeur_357 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.25 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRLSGSVFITLKKYDGRTKPIPRKGSVEGFEPADKCLLRATDGKKKISTVV
          MVLLESEQFLTELTRLFQKCRLS.SVFITLK.YDGRTKPIPRKGSVEGFEPADKCLLRATDGKKKISTVV
Retrocopy MVLLESEQFLTELTRLFQKCRLSDSVFITLKMYDGRTKPIPRKGSVEGFEPADKCLLRATDGKKKISTVV

Parental  SSKEVNKFQMAYSNLLRANMDGLKKRDKKSKSKKSKAAQ
          SSKEVNKFQMA.SNLLRANMDGLKKRDKKSKSKKSKAAQ
Retrocopy SSKEVNKFQMADSNLLRANMDGLKKRDKKSKSKKSKAAQ

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	11.12 RPM	22.56 RPM
SRP017611_kidney	6.38 RPM	17.82 RPM
SRP017611_liver	4.18 RPM	10.45 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_357 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017231	1 retrocopy	retro_amel_1566,
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Erinaceus europaeus	ENSEEUG00000012759	1 retrocopy	retro_eeur_357 ,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Myotis lucifugus	ENSMLUG00000010531	5 retrocopies	retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Ochotona princeps	ENSOPRG00000008599	1 retrocopy	retro_opri_619,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Rattus norvegicus	ENSRNOG00000007512	1 retrocopy	retro_rnor_2702,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,