RetrogeneDB ID: retro_eeur_112

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7127:60280..60763(-)
• Located in intron of: ENSEEUG00000003035

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM3
• Ensembl ID: ENSEEUG00000014211
• Aliases: None
• Description: glutathione S-transferase mu 3 (brain) [Source:HGNC Symbol;Acc:4635]

Sequence

>retro_eeur_112
CCCTGTCTCATGGATGGTAAGAACAAGATCACCCAGAGTAAAGCTATCATGCGCTATATTGCTTGCAAGCACAATCTCTG
TGGCGAGACTGAAGAAGAAAAGATTCAAGTGGACATCATGGAAAACCAAATAATGGATTTCTGCATGCAGCTAGTCAGGC
TCTGCTATAACCCTGACCATGAAAAACTGAAGCCTCAGTACCTGGAACAGCTCCTGGGACAACTGAAACTATTCTCCTTG
TTCTTAGGGAAATTCTCCTGGTTTGCAGGGGAAAAGATCACCTTTGTGGATTTCCTTATCTATGATGTCTTGGATCAGAA
CCATATGTTTGAGCCCAAATGTCTGGATGAATCTCCAAATTGGAAAGATTTCATGTGCCATTTTGAGACTTTGGAGAAAA
TAGCCTCCTACACGCAATCTGATCGCTTATTCAAATTGCCCATCAACAACAAGATGTCCCAGTGGGGCAACAAGAGATTA
TGC

Alignment

ORF - retro_eeur_112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.06 %
• Parental protein coverage: 71.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PYLMDGKNKITQSNAIMRYIARKHNLCGETEEEKIRVDIMENQIMDFRMQLVKLCYNPDHEKLKPQYLEQ
          P.LMDGKNKITQS.AIMRYIA.KHNLCGETEEEKI.VDIMENQIMDF.MQLV.LCYNPDHEKLKPQYLEQ
Retrocopy PCLMDGKNKITQSKAIMRYIACKHNLCGETEEEKIQVDIMENQIMDFCMQLVRLCYNPDHEKLKPQYLEQ

Parental  LPGQLKLFSLFLGKFSWFAGEKITFVDFLTYDVLDQNRMFEPKCLDEFPNLKDFMCRFEALEKIASYMQS
          L.GQLKLFSLFLGKFSWFAGEKITFVDFL.YDVLDQN.MFEPKCLDE.PN.KDFMC.FE.LEKIASY.QS
Retrocopy LLGQLKLFSLFLGKFSWFAGEKITFVDFLIYDVLDQNHMFEPKCLDESPNWKDFMCHFETLEKIASYTQS

Parental  DRFFKLPINNKMAQWGNKRLC
          DR.FKLPINNKM.QWGNKRLC
Retrocopy DRLFKLPINNKMSQWGNKRLC

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	3.22 RPM	42.38 RPM
SRP017611_kidney	15.00 RPM	221.48 RPM
SRP017611_liver	7.40 RPM	95.50 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_112 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112 ,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,