RetrogeneDB ID: retro_eeur_706

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_95229:444..1068(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP6C
• Ensembl ID: ENSEEUG00000010197
• Aliases: None
• Description: protein phosphatase 6, catalytic subunit [Source:HGNC Symbol;Acc:9323]

Sequence

>retro_eeur_706
ATGGAAGAATCCAATGTGCAAGAAGTTCGATGTCCAATCACCATCTATGGAGATGTACATGGGCAATTTAATGATCTCAT
GGAACTATTTAGAATTGGAGGCAAATCACCAGATACAAATTGCTTGTTTATGGGAGATTATGTTGACAGAGGATATTATT
CAGTTGAAACAGTTACTTTACTTGTAGCTCTTAAGGTTCATTATTAGGAATGTATCACTATTCTTTGAGGAAATGATGAG
AGCAGACAGATCACACAAGTATATGGTTTCTATGATGAGGGTTTAAGGAAATATGGAAATAGAAATGTTTGGAAATATTT
TACAGATCTGTTTGACTATCTTCCTCTTACTGCCTTGGTGGATGGGCAGATCTTTTGTCTACATGGTGGCCTCTCACCAT
CCACAGATACAATGGATCACATTAGAGCACTTGATCGCCTACAAGAATTTCCTCATGAGGGTCCAATGTGTGGCTTGCTG
TGCTCAGATCCAGACGACCATGGTGGTTGGGGTCTATCTCCTCAAAGAGGAGCTGGTTATCCTTTTGAGCAAGATATTTC
TGAGACATTTAACCATGCCAATGTCCTCATGTTGATGTCTAGAGATCACCAGCATGATGGAGGG

Alignment

ORF - retro_eeur_706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 74.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEESNVQPVSTPVTVCGDIHGQFYDLCELFRTGGQVPDTNYIFMGDFVDRGYYSLETFTYLLALKAKWPD
          .EESNVQ.V..P.T..GD.HGQF.DL.ELFR.GG..PDTN..FMGD.VDRGYYS.ET.T.L.ALK.....
Retrocopy MEESNVQEVRCPITIYGDVHGQFNDLMELFRIGGKSPDTNCLFMGDYVDRGYYSVETVTLLVALKVHY*E

Parental  RITLLRGNHESRQITQVYGFYDECQTKYGNANAWRYCTKVFDMLTVAALIDEQILCVHGGLSPDIKTLDQ
          .IT.L.GN.ESRQITQVYGFYDE...KYGN.N.W.Y.T..FD.L...AL.D.QI.C.HGGLSP...T.D.
Retrocopy CITIL*GNDESRQITQVYGFYDEGLRKYGNRNVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSTDTMDH

Parental  IRTIERNQEIPHKGAFCDLVWSDPEDVDTWAISP-RGAGWLFGAKVTNEFVHISSLKLNCRAHRLMHDCG
          IR...R.QE.PH.G..C.L..SDP.D...W..SP.RGAG..F.......F.H...L.L..R.H...HD.G
Retrocopy IRALDRLQEFPHEGPMCGLLCSDPDDHGGWGLSPQRGAGYPFEQDISETFNHANVLMLMSRDHQ--HDGG

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	2.74 RPM	19.50 RPM
SRP017611_kidney	6.56 RPM	35.26 RPM
SRP017611_liver	2.41 RPM	19.13 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_706 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012357	3 retrocopies	retro_chof_1759, retro_chof_183, retro_chof_608,
Dasypus novemcinctus	ENSDNOG00000015319	1 retrocopy	retro_dnov_1700,
Erinaceus europaeus	ENSEEUG00000010197	1 retrocopy	retro_eeur_706 ,
Macaca mulatta	ENSMMUG00000020549	1 retrocopy	retro_mmul_698,
Rattus norvegicus	ENSRNOG00000015145	1 retrocopy	retro_rnor_2074,
Sarcophilus harrisii	ENSSHAG00000008282	1 retrocopy	retro_shar_146,
Sus scrofa	ENSSSCG00000005600	1 retrocopy	retro_sscr_243,