RetrogeneDB ID: retro_eeur_25

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_1142:85293..85593(+)
• Located in intron of: ENSEEUG00000001695

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSEEUG00000007914
• Aliases: None
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:23401]

Sequence

>retro_eeur_25
CTGGAGCGCCTGAGCTCGCTGCCCACGCAGATGGATTACAAAGGCCAGAGCTAGCTGAGCAGATGTTTCAGGCAATCATA
CTCTTCTGCGGTCGCTGGGTTCATCTACAGATACGTAGCCCAACAGTTCGGGTGGACTGTCTACATAGTTATGGCGAGAT
TTGCTTTTTCATGTTTGCTAACACTTCCTCCATGGCCCTTTTATCGCCGGCACCCTCTCAAGTGGTTACCTGTTCAAGAC
TCAGGCACAGAAGACAAGAAACCAGGGGAAAGAAAAGCGAAGCGGCAGGCTAAAAATAAC

Alignment

ORF - retro_eeur_25 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEHLNSLPTQMDYKGQKLAEQMFQGIILVSAVVGFAYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIYR
          LE.L.SLPTQMDYKGQ......F......SAV.GF.Y.YVA.QFGWTVYIVMA.FAFSCLLTLPPWP.YR
Retrocopy LERLSSLPTQMDYKGQS*LSRCFRQSYS-SAVAGFIYRYVAQQFGWTVYIVMARFAFSCLLTLPPWPFYR

Parental  RHPLKWLPVQDSATEDKKPGERKAKRHAKNN
          RHPLKWLPVQDS.TEDKKPGERKAKR.AKNN
Retrocopy RHPLKWLPVQDSGTEDKKPGERKAKRQAKNN

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	1.13 RPM	12.73 RPM
SRP017611_kidney	2.44 RPM	31.32 RPM
SRP017611_liver	0.64 RPM	14.95 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_25 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 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008426	1 retrocopy	retro_amel_1899,
Canis familiaris	ENSCAFG00000008927	1 retrocopy	retro_cfam_2079,
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245, retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686, retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25 ,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056,
Homo sapiens	ENSG00000114902	1 retrocopy	retro_hsap_294,
Gorilla gorilla	ENSGGOG00000028027	1 retrocopy	retro_ggor_332,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575, retro_lafr_625,
Microcebus murinus	ENSMICG00000014061	1 retrocopy	retro_mmur_292,
Myotis lucifugus	ENSMLUG00000000744	1 retrocopy	retro_mluc_2104,
Macaca mulatta	ENSMMUG00000017370	1 retrocopy	retro_mmul_549,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928,
Otolemur garnettii	ENSOGAG00000004106	3 retrocopies	retro_ogar_2119, retro_ogar_2315, retro_ogar_2788,
Pongo abelii	ENSPPYG00000013798	1 retrocopy	retro_pabe_380,
Pan troglodytes	ENSPTRG00000015011	1 retrocopy	retro_ptro_241,
Tarsius syrichta	ENSTSYG00000006854	2 retrocopies	retro_tsyr_1359, retro_tsyr_599,
Tursiops truncatus	ENSTTRG00000008576	1 retrocopy	retro_ttru_806,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,