RetrogeneDB ID: retro_eeur_566

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_345904:84664..84930(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000014658
• Aliases: None
• Description: None

Sequence

>retro_eeur_566
TTTAATTGGCACGTCACAATTACAGCACCTGATAGACGTAGCATATTCTTTCAACAATTCACTTTCCTACATATTACCCA
CACAAACTGCCTGAGGTTAAATTCACAACAAAAATCTATCACCCAAATGGTAACAGTAGTGGTGATATTTGATTTGGTAT
TTTAAGATCACAGTGGATTCCTGTTTCAACTATTTCTAAAGTCATTTTATCAGCTTGTGCATAGCTATATTATCTAAACC
CAGATGACTTCTCTCCCCTGCCTCCA

Alignment

ORF - retro_eeur_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.38 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FHWQATIMGPNDSPYQGGVFFL-TIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTI
          F.W..TI......P.....FF..TIHFPT.YP.K.P.V.FTT.IYHPN.NS.G.I...ILRSQW.P..TI
Retrocopy FNWHVTIT----APDRRSIFFQ<TIHFPTYYPHKLPEVKFTTKIYHPNGNSSGDI*FGILRSQWIPVSTI

Parental  SKVLLSICSLLCDPNPDD--PLVP
          SKV.LS.C..L...NPDD..PL.P
Retrocopy SKVILSACA*LYYLNPDDFSPLPP

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	0.00 RPM	42.86 RPM
SRP017611_kidney	0.00 RPM	37.51 RPM
SRP017611_liver	0.00 RPM	21.54 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_566 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 37 parental genes, and 161 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002183	1 retrocopy	retro_acar_182,
Ailuropoda melanoleuca	ENSAMEG00000011216	6 retrocopies	retro_amel_1295, retro_amel_1427, retro_amel_1648, retro_amel_1750, retro_amel_620, retro_amel_995,
Bos taurus	ENSBTAG00000004161	6 retrocopies	retro_btau_1421, retro_btau_1602, retro_btau_1739, retro_btau_1775, retro_btau_1851, retro_btau_1852,
Canis familiaris	ENSCAFG00000031041	5 retrocopies	retro_cfam_1191, retro_cfam_1439, retro_cfam_1602, retro_cfam_2034, retro_cfam_785,
Choloepus hoffmanni	ENSCHOG00000004649	2 retrocopies	retro_chof_2549, retro_chof_439,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Callithrix jacchus	ENSCJAG00000015492	3 retrocopies	retro_cjac_512, retro_cjac_657, retro_cjac_791,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Dasypus novemcinctus	ENSDNOG00000009320	30 retrocopies	retro_dnov_1061, retro_dnov_1125, retro_dnov_113, retro_dnov_114, retro_dnov_1167, retro_dnov_1193, retro_dnov_1198, retro_dnov_1257, retro_dnov_141, retro_dnov_1544, retro_dnov_1752, retro_dnov_1761, retro_dnov_1831, retro_dnov_1862, retro_dnov_1912, retro_dnov_1934, retro_dnov_1995, retro_dnov_2084, retro_dnov_2135, retro_dnov_2289, retro_dnov_2362, retro_dnov_2457, retro_dnov_2622, retro_dnov_436, retro_dnov_574, retro_dnov_750, retro_dnov_795, retro_dnov_83, retro_dnov_889, retro_dnov_917,
Dipodomys ordii	ENSDORG00000006762	2 retrocopies	retro_dord_172, retro_dord_323,
Equus caballus	ENSECAG00000020678	1 retrocopy	retro_ecab_859,
Erinaceus europaeus	ENSEEUG00000010820	1 retrocopy	retro_eeur_84,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566 , retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Felis catus	ENSFCAG00000024918	2 retrocopies	retro_fcat_1106, retro_fcat_785,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
Loxodonta africana	ENSLAFG00000006878	2 retrocopies	retro_lafr_288, retro_lafr_290,
Macropus eugenii	ENSMEUG00000004256	6 retrocopies	retro_meug_1034, retro_meug_1503, retro_meug_2138, retro_meug_564, retro_meug_787, retro_meug_89,
Macaca mulatta	ENSMMUG00000020666	3 retrocopies	retro_mmul_1298, retro_mmul_2143, retro_mmul_2246,
Monodelphis domestica	ENSMODG00000011783	2 retrocopies	retro_mdom_17, retro_mdom_884,
Mustela putorius furo	ENSMPUG00000009110	5 retrocopies	retro_mputfur_1263, retro_mputfur_1637, retro_mputfur_263, retro_mputfur_682, retro_mputfur_703,
Mus musculus	ENSMUSG00000078578	11 retrocopies	retro_mmus_1818, retro_mmus_1895, retro_mmus_1913, retro_mmus_2293, retro_mmus_2635, retro_mmus_2643, retro_mmus_3119, retro_mmus_3636, retro_mmus_850, retro_mmus_875, retro_mmus_923,
Mus musculus	ENSMUSG00000091896	3 retrocopies	retro_mmus_2267, retro_mmus_27, retro_mmus_629,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Oryctolagus cuniculus	ENSOCUG00000029448	10 retrocopies	retro_ocun_1220, retro_ocun_1426, retro_ocun_1536, retro_ocun_1660, retro_ocun_1856, retro_ocun_1941, retro_ocun_261, retro_ocun_467, retro_ocun_887, retro_ocun_988,
Otolemur garnettii	ENSOGAG00000012860	6 retrocopies	retro_ogar_1124, retro_ogar_3047, retro_ogar_3048, retro_ogar_3110, retro_ogar_544, retro_ogar_599,
Ochotona princeps	ENSOPRG00000011695	9 retrocopies	retro_opri_1042, retro_opri_1189, retro_opri_206, retro_opri_310, retro_opri_447, retro_opri_457, retro_opri_627, retro_opri_77, retro_opri_838,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pongo abelii	ENSPPYG00000015844	6 retrocopies	retro_pabe_1016, retro_pabe_1164, retro_pabe_1257, retro_pabe_2330, retro_pabe_30, retro_pabe_3670,
Pan troglodytes	ENSPTRG00000017303	3 retrocopies	retro_ptro_26, retro_ptro_3141, retro_ptro_341,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Rattus norvegicus	ENSRNOG00000013741	9 retrocopies	retro_rnor_2777, retro_rnor_342, retro_rnor_345, retro_rnor_539, retro_rnor_650, retro_rnor_724, retro_rnor_725, retro_rnor_772, retro_rnor_784,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tarsius syrichta	ENSTSYG00000005459	1 retrocopy	retro_tsyr_1421,