RetrogeneDB ID: retro_eeur_278

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_236602:3563..3849(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPE1
• Ensembl ID: ENSEEUG00000005040
• Aliases: None
• Description: heat shock 10kDa protein 1 (chaperonin 10) [Source:HGNC Symbol;Acc:5269]

Sequence

>retro_eeur_278
TTAGGAATTTTCTTCCCCTTTGACTGAGTAATAGTTGAATGGAGCATAGCTAAAACGGTAACTAAAGGAGGCATTATGCT
TCCAGAAAACTCTCAAGATAAAGTATTGTAAGCAACAGTAGTAGTTGTTGGACCCAGCTCTAAAGAGAAGGGTGGAGAGA
TTAAACAAGTTAGTGTGAATGTTGGGAGATAAAGTTCTTCTACCAGAATATAGAGGCATCAAACTGATTCTAGATGACAA
AGTTTATTTCTTATTTAGAGATGATATTCTTGGAAAGCATGTAGAC

Alignment

ORF - retro_eeur_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.2 %
• Parental protein coverage: 96. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGKFFPLFDQVLAEWSAGETVTEEGIMLPEKCQ-RVLLTAVAAXXXXXXXXTGEIQPVSVKV-GDKVLLP
          LG.FFP.FD.V..EWS...TVT..GIMLPE..Q..VL...V...........GEI..VSV.V.GDKVLLP
Retrocopy LGIFFP-FD*VIVEWSIAKTVTKGGIMLPENSQDKVL*ATVVVVGPSSKEKGGEIKQVSVNV>GDKVLLP

Parental  EYGGTKVVLDDKDYFLFRDGDILGKYVD
          EY.G.K..LDDK.YFLFRD.DILGK.VD
Retrocopy EYRGIKLILDDKVYFLFRD-DILGKHVD

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	5.48 RPM	13.21 RPM
SRP017611_kidney	0.94 RPM	58.32 RPM
SRP017611_liver	0.48 RPM	43.09 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_278 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 13 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013769	18 retrocopies	retro_amel_1027, retro_amel_1083, retro_amel_1084, retro_amel_1100, retro_amel_133, retro_amel_1504, retro_amel_1513, retro_amel_1623, retro_amel_1699, retro_amel_1819, retro_amel_199, retro_amel_23, retro_amel_269, retro_amel_310, retro_amel_329, retro_amel_491, retro_amel_506, retro_amel_922,
Canis familiaris	ENSCAFG00000010890	4 retrocopies	retro_cfam_1768, retro_cfam_1883, retro_cfam_208, retro_cfam_556,
Callithrix jacchus	ENSCJAG00000004008	1 retrocopy	retro_cjac_254,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Erinaceus europaeus	ENSEEUG00000005040	6 retrocopies	retro_eeur_132, retro_eeur_278 , retro_eeur_474, retro_eeur_611, retro_eeur_657, retro_eeur_698,
Felis catus	ENSFCAG00000014455	9 retrocopies	retro_fcat_114, retro_fcat_1174, retro_fcat_1406, retro_fcat_1686, retro_fcat_1723, retro_fcat_457, retro_fcat_681, retro_fcat_794, retro_fcat_97,
Gorilla gorilla	ENSGGOG00000027944	17 retrocopies	retro_ggor_1051, retro_ggor_117, retro_ggor_1243, retro_ggor_1545, retro_ggor_157, retro_ggor_1676, retro_ggor_1821, retro_ggor_1956, retro_ggor_1957, retro_ggor_1958, retro_ggor_2331, retro_ggor_2391, retro_ggor_2476, retro_ggor_2492, retro_ggor_775, retro_ggor_841, retro_ggor_897,
Loxodonta africana	ENSLAFG00000000057	1 retrocopy	retro_lafr_69,
Macaca mulatta	ENSMMUG00000010491	1 retrocopy	retro_mmul_344,
Oryctolagus cuniculus	ENSOCUG00000010360	1 retrocopy	retro_ocun_127,
Otolemur garnettii	ENSOGAG00000034434	24 retrocopies	retro_ogar_1018, retro_ogar_1441, retro_ogar_1512, retro_ogar_1690, retro_ogar_1744, retro_ogar_1899, retro_ogar_191, retro_ogar_1921, retro_ogar_200, retro_ogar_2030, retro_ogar_2129, retro_ogar_2310, retro_ogar_235, retro_ogar_2439, retro_ogar_2636, retro_ogar_2928, retro_ogar_3088, retro_ogar_3350, retro_ogar_3419, retro_ogar_389, retro_ogar_777, retro_ogar_824, retro_ogar_829, retro_ogar_834,
Pongo abelii	ENSPPYG00000025876	1 retrocopy	retro_pabe_179,
Rattus norvegicus	ENSRNOG00000014868	6 retrocopies	retro_rnor_1094, retro_rnor_1320, retro_rnor_1334, retro_rnor_2245, retro_rnor_2296, retro_rnor_984,