RetrogeneDB ID: retro_eeur_665

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_378237:46007..46313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC1
• Ensembl ID: ENSEEUG00000004320
• Aliases: None
• Description: trafficking protein particle complex 1 [Source:HGNC Symbol;Acc:19894]

Sequence

>retro_eeur_665
ATGACTGTCCACAATTTGTATCTGTTCGACCGAAATGGAATGTGTCTGCATTACGAGTGGCATCACAAGAAGCAAGCAGG
GATCCCTAAGGTGGAGGAGCAGAAGCTGAGGAATGGGATGCTCTTCTCTATCTGTTCATTTGTCAGCAAGATGTCCCCAC
TAGACATGAACGATGGCTTCCTGTCATTCCAAACTAGCCGTTACAAACTCCATTACTATGAAATGCCCACGGGGATCAAG
GTTGTCATGAATATTGACTTGGGCGTGGGACCTATCTGAGATGTTCTACACCACATCTACAGTGCA

Alignment

ORF - retro_eeur_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTVHNLYLFDRNGVCLHYSEWHRKKQAGIPKEEEYKLMYGMLFSIRSFVSKMSPLDMKDGFLSFQTSRYK
          MTVHNLYLFDRNG.CLHY.EWH.KKQAGIPK.EE.KL..GMLFSI.SFVSKMSPLDM.DGFLSFQTSRYK
Retrocopy MTVHNLYLFDRNGMCLHY-EWHHKKQAGIPKVEEQKLRNGMLFSICSFVSKMSPLDMNDGFLSFQTSRYK

Parental  LHYYETPTGIKVVMNTDLGVGPIRDVLHHIYSA
          LHYYE.PTGIKVVMN.DLGVGPI.DVLHHIYSA
Retrocopy LHYYEMPTGIKVVMNIDLGVGPI*DVLHHIYSA

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	0.81 RPM	3.55 RPM
SRP017611_kidney	0.94 RPM	8.06 RPM
SRP017611_liver	0.32 RPM	6.27 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_665 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047214	1 retrocopy	retro_btau_280,
Callithrix jacchus	ENSCJAG00000014756	1 retrocopy	retro_cjac_1057,
Erinaceus europaeus	ENSEEUG00000004320	1 retrocopy	retro_eeur_665 ,
Sorex araneus	ENSSARG00000010582	1 retrocopy	retro_sara_590,
Tursiops truncatus	ENSTTRG00000010306	1 retrocopy	retro_ttru_403,