RetrogeneDB ID: retro_eeur_334

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_259312:3632..4148(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NACA
• Ensembl ID: ENSEEUG00000010458
• Aliases: None
• Description: nascent polypeptide-associated complex alpha subunit [Source:HGNC Symbol;Acc:7629]

Sequence

>retro_eeur_334
AGCATTCCTGCTACAGAGCAGGAGCTGCCACAGCCGCAGGCTCAGACAGCATCTGGGTCAGAATCTGACAGCGATGAGTG
AGGACCAGAGCTTGAGGGACAGGATTCCACACAAGCAACCACACCACAGGCTCAGCTGAAATCCATGAAGAACCAGTGAG
CAAAGCAAAACAGAGCTGGAGTGAAAAGAAGACTCAAAAGGTTTTGTCCAAACTGGGTCTTCAGCAGGTAATGGGTTACT
AGAGTTACTATCCGGAAATCAAAGAATACCCTCTTTGTCATCACAAAGCCAGATGTCTACAAAAGCCCAGCATCAGATTC
CTACACAGTTTTTGGAGAAGCAAAGAGGGAGGATTTGTCTCAGCAAGCACAGCTGTCAGCTGCTGAGAAATTCCAAGTTC
CAGGTGAGGCTGTCGCAAACATTCAAGAAAGCATGCAAAGTTCAACTGTGCAAGGAAAGAGTGAAGAGGAGGAGGCTGAC
GAAACTGGTATAGAAGTTAAGGACAGAGAACTTTTG

Alignment

ORF - retro_eeur_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 82.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TVPATEQELPQPQAETGSGTESDSDESVPELEEQDSTQATTQQAQLAA-AAEIDEEPVSKAKQSRSE-KK
          ..PATEQELPQPQA.....T.S.S.....E.......Q..TQ.....A..AEI.EEPVSKAKQS.SE.K.
Retrocopy SIPATEQELPQPQAQ----TASGSESDSDE*GPELEGQDSTQATTPQA<SAEIHEEPVSKAKQSWSE<KE

Parental  ARKAMSKLGLRQVTG-VTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQLAAAEKFK
          ..K.....G.....G.VTRVTIRKSKN.LFVITKPDVYKSPASD.Y.VFGEAK.EDLSQQAQL.AAEKF.
Retrocopy DSKGFVQTGSSAGNG<VTRVTIRKSKNTLFVITKPDVYKSPASDSYTVFGEAKREDLSQQAQLSAAEKFQ

Parental  VQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVKDIELV
          V.GEAV.NIQE..Q..TVQ..SEEEE.DETG.EVKD.EL.
Retrocopy VPGEAVANIQESMQSSTVQGKSEEEEADETGIEVKDRELL

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	136.49 RPM
SRP017611_kidney	0.00 RPM	303.06 RPM
SRP017611_liver	0.00 RPM	208.04 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_334 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 12 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004175	3 retrocopies	retro_amel_1725, retro_amel_1821, retro_amel_643,
Bos taurus	ENSBTAG00000010701	2 retrocopies	retro_btau_1237, retro_btau_1620,
Canis familiaris	ENSCAFG00000000141	8 retrocopies	retro_cfam_1502, retro_cfam_1561, retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus	ENSCJAG00000010701	8 retrocopies	retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Erinaceus europaeus	ENSEEUG00000010458	5 retrocopies	retro_eeur_170, retro_eeur_207, retro_eeur_242, retro_eeur_334 , retro_eeur_520,
Loxodonta africana	ENSLAFG00000004598	6 retrocopies	retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491, retro_lafr_958,
Myotis lucifugus	ENSMLUG00000001169	16 retrocopies	retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Nomascus leucogenys	ENSNLEG00000017449	7 retrocopies	retro_nleu_1358, retro_nleu_20, retro_nleu_2522, retro_nleu_478, retro_nleu_754, retro_nleu_839, retro_nleu_941,
Pongo abelii	ENSPPYG00000004670	6 retrocopies	retro_pabe_2507, retro_pabe_26, retro_pabe_3279, retro_pabe_633, retro_pabe_656, retro_pabe_764,
Sarcophilus harrisii	ENSSHAG00000002175	1 retrocopy	retro_shar_213,
Ictidomys tridecemlineatus	ENSSTOG00000009028	1 retrocopy	retro_itri_367,
Vicugna pacos	ENSVPAG00000004028	2 retrocopies	retro_vpac_485, retro_vpac_611,