RetrogeneDB ID: retro_eeur_617

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_366845:27448..27802(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSEEUG00000010462
• Aliases: None
• Description: ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]

Sequence

>retro_eeur_617
TTTGGTGTCTGCCACATCTTTGCATCCTTCAATGGCACTTTTGACCATGTCACTGATCTTTCTGGCAAGGAAACCATCTG
CCCTGTAACTGGTGGGATGAAGGTGAAAGCTGACAGAGATGAATCATCTCCATATGCTGCCATGTTGGCTGCCCAGGACG
TCACCCAAAGGTGCAAGGAGTTGGGCATCACTGCCCTCCACATCAAACTCCATGCCACAGGAGGAAATTGGACCAAGACA
CCTGGACCTGGGGCCCAGTCAGCCCTCAGAGTCCTGGCCCATTCAGGGATGAAAATTGGGAGGATTGAAGCTATCACTCC
CATCCCCTCCAATAGCACTCACAGGAAGGGGGGG

Alignment

ORF - retro_eeur_617 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 77.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGVCHIFASFNDTFVHVTDLSGKETI-RVTGGMKVK-DRDESSPYAAMLAAQDVAQRCKELGITALHIKL
          FGVCHIFASFN.TF.HVTDLSGKETI..VTGGMKVK.DRDESSPYAAMLAAQDV.QRCKELGITALHIKL
Retrocopy FGVCHIFASFNGTFDHVTDLSGKETICPVTGGMKVKADRDESSPYAAMLAAQDVTQRCKELGITALHIKL

Parental  RATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPSDSTRRKGG
          .ATGGN.TKTPGPGAQSALR.LA.SGMKIGRIE..TPIPS.ST.RKGG
Retrocopy HATGGNWTKTPGPGAQSALRVLAHSGMKIGRIEAITPIPSNSTHRKGG

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	1.77 RPM	165.33 RPM
SRP017611_kidney	2.63 RPM	368.33 RPM
SRP017611_liver	3.70 RPM	228.46 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_617 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 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Erinaceus europaeus	ENSEEUG00000010462	3 retrocopies	retro_eeur_330, retro_eeur_423, retro_eeur_617 ,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Mus musculus	ENSMUSG00000024608	5 retrocopies	retro_mmus_1362, retro_mmus_1924, retro_mmus_2178, retro_mmus_2252, retro_mmus_2380,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Tursiops truncatus	ENSTTRG00000013035	1 retrocopy	retro_ttru_566,