RetrogeneDB ID: retro_eeur_542

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_341584:50495..51025(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000012698
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAF10
• Ensembl ID: ENSEEUG00000008412
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa [Source:HGNC Symbol;Acc:11543]

Sequence

>retro_eeur_542
ACTCCTACCACACTGCCTGCCAGCCCCACTGCAGGAAACAAGGCCAGCCCTGTGGGGACAGCGGGGTGGCCCAGGACTGG
AGCCGCGGAGGGGGGCTTGAGACCTGTGGAGGTGCAGGCAAGGGAGCCTGCAGAGCAGCATGAGGGGGGCTTGTCTAAGG
GTGACTACGACCTGCTGAACATGGCCGAAGGTGGCATGAGGCCTTTGGTGTCCAGCACTCCGCTGGTGGACTTCTTGATA
CAGCTGGAGGACTACACGCCTACACTCCCAGATGCAGTGACCGGCTACTACTTGAACCGCGCAGGCTTTGAGGCTACAGA
CCTACGCATAGTACGGCTCATCTCCCTAGCTGACCAGAAATTCATCTCAGATATTGCCAGAGATGCCCTTCAGCACTGCA
AAATGAAGGGCGCAGCCTCTGGCAGCTCCAGAAACAAAAGCAAGGACCGCAAGTACACTCTAACCATGGAGGACCTGACC
TCTGCCCTCAGCGAGTATGGGATAATGTGAAGAAGCCACACTACTTCACC

Alignment

ORF - retro_eeur_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.04 %
• Parental protein coverage: 81.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPAGTPGGPGTGAAAGGAGPVAARAGEPAERRGAAPVSAGGAAPP---EGALSNGVYVLPSAANGDVKPV
          .P...P..P..G..A...G..A......A...G..PV......P....EG.LS.G.Y.L...A.G...P.
Retrocopy TPTTLPASPTAGNKASPVG-TAGWPRTGAAEGGLRPVEVQAREPAEQHEGGLSKGDYDLLNMAEGGMRPL

Parental  VSSTPLVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQHCKMKGTA
          VSSTPLVDFL.QLEDYTPT.PDAVTGYYLNRAGFEA.D.RI.RLISLA.QKFISDIA.DALQHCKMKG.A
Retrocopy VSSTPLVDFLIQLEDYTPTLPDAVTGYYLNRAGFEATDLRIVRLISLADQKFISDIARDALQHCKMKGAA

Parental  SGSSRSKSKDRKYTLTMEDLTPALSEYGI-NVKKPHYFT
          SGSSR.KSKDRKYTLTMEDLT.ALSEYGI.NVKKPHYFT
Retrocopy SGSSRNKSKDRKYTLTMEDLTSALSEYGI<NVKKPHYFT

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	9.83 RPM
SRP017611_kidney	0.00 RPM	31.13 RPM
SRP017611_liver	0.00 RPM	22.03 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_542 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006498	2 retrocopies	retro_cfam_1041, retro_cfam_992,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525,
Erinaceus europaeus	ENSEEUG00000008412	3 retrocopies	retro_eeur_542 , retro_eeur_692, retro_eeur_709,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090,
Felis catus	ENSFCAG00000015390	1 retrocopy	retro_fcat_1458,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645, retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35,
Tursiops truncatus	ENSTTRG00000004894	1 retrocopy	retro_ttru_1113,