RetrogeneDB ID: retro_eeur_508

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_331247:18758..19361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INSIG2
• Ensembl ID: ENSEEUG00000008765
• Aliases: None
• Description: insulin induced gene 2 [Source:HGNC Symbol;Acc:20452]

Sequence

>retro_eeur_508
GGACCCCTCTCAGCCGGCCCCCACACGTCCCCCATCTGGCACCACCGCCTGGCGGCCTGCGGCCTGGTGCTGTTCTCGGT
GGGCGTGGGGCTGGCCCTCGTGCTCAACCTGCCGCAGGTGCAGCGCCACATCACCCTGTTCCCAGACGAGGTGGCCGCCA
CCAGCTTCTCCTCCACCTGGTGGGTGGCCCTCTGCTGCGGCACGGCGGCCGCTGTGGTGAGCCTGCTGTACCCCTGCATC
AACAGGCACCTAGGGGAGCCCCACGAGTTCAAGCGCGAGTGGACCAGCATCATGCGCTGCGTGGCAGTCTTTGTGGGCAT
CAACCACGCCAGTGCTAAGTTGGACTTCGCCAACTACGTGCAGCTGTCGCTGACGCTGGCCTCGCTGTCCCTGGGGCTGT
GGTGGGCATTCGACCATTCCCGTAGTGGCCTGGGACTCGGCATCACCATCGCCTTCCTGGCCACGCTCATCACACAGCTG
CTGGTGCACAACGCGGTCTACCAGAACACCTCCCCTGACTTCCTCTACATTCTCTTCTGGCTGCCCTGCATCTTCTTCTC
TGGAGGCGTGCCCATGGGCAACATCGGGCGGCAGCTGGCCATG

Alignment

ORF - retro_eeur_508 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.01 %
• Parental protein coverage: 95.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPKKRGPYISSITSRSVNLVIRGVVLFFIGVFLALVLNLLQIQRNVTLFPPDVIASIFSSAWWVPPCCGT
          GP...GP..S.I......L...G.VLF..GV.LALVLNL.Q.QR..TLFP..V.A..FSS.WWV..CCGT
Retrocopy GPLSAGPHTSPIWHH--RLAACGLVLFSVGVGLALVLNLPQVQRHITLFPDEVAATSFSSTWWVALCCGT

Parental  ASAVIGLLYPCIDRHLGEPHKFKREWSSVMRCVAVFVGINHASAXXXXXXXXXXXLTLAALSIGL-WTFD
          A.AV..LLYPCI.RHLGEPH.FKREW.S.MRCVAVFVGINHASA...........LTLA.LS.GL.W.FD
Retrocopy AAAVVSLLYPCINRHLGEPHEFKREWTSIMRCVAVFVGINHASAKLDFANYVQLSLTLASLSLGLWWAFD

Parental  KPAS-FGLGVGIAFLATLITQLLVYNGVYQYTSPDFLYVRSWLPCIFFAGGITMGNIGRQLAM
          ...S..GLG..IAFLATLITQLLV.N.VYQ.TSPDFLY...WLPCIFF.GG..MGNIGRQLAM
Retrocopy HSRSGLGLGITIAFLATLITQLLVHNAVYQNTSPDFLYILFWLPCIFFSGGVPMGNIGRQLAM

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	0.32 RPM	17.08 RPM
SRP017611_kidney	0.56 RPM	14.44 RPM
SRP017611_liver	2.73 RPM	16.40 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_508 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008765	1 retrocopy	retro_eeur_508 ,
Myotis lucifugus	ENSMLUG00000028113	1 retrocopy	retro_mluc_2270,
Macaca mulatta	ENSMMUG00000006354	1 retrocopy	retro_mmul_703,
Monodelphis domestica	ENSMODG00000000458	2 retrocopies	retro_mdom_1872, retro_mdom_542,
Otolemur garnettii	ENSOGAG00000007739	1 retrocopy	retro_ogar_940,