RetrogeneDB ID: retro_eeur_203

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_207212:1582..1867(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSEEUG00000002083
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_eeur_203
ACCACTATTATGGCTGTGCAGTTTGACAGGGATGTGGTTTCTGGAGCTGACTCCAGAACTACCACTGGGTCCTACATTGC
CAGCTGAGTGACTGACAAGCTGACCCCCATTCATGAGTGAATCTTCTGCTGTCACTTGGGCTCAGCAACTGATACCCAGA
CAGTAGCTGATGCAGTCACATATCAGCTTGGTTTCCACAGCATTGAACTGAATGAGCCTCCACTGGTACACACAGCTGCC
AGCCTCTTTAAGGAGAGATGTTACCGATACTGAGAAGAGCTAGTC

Alignment

ORF - retro_eeur_203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.26 %
• Parental protein coverage: 53.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIEL
          TTIMAVQFD..VV.GADSRTTTGSYIA..VTDKLTPIH..IFCC..GSA.DTQ.VADAVTYQLGFHSIEL
Retrocopy TTIMAVQFDRDVVSGADSRTTTGSYIAS*VTDKLTPIHE*IFCCHLGSATDTQTVADAVTYQLGFHSIEL

Parental  NEPPLVHTAASLFKEMCYRYREELM
          NEPPLVHTAASLFKE.CYRY.EEL.
Retrocopy NEPPLVHTAASLFKERCYRY*EELV

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	35.94 RPM
SRP017611_kidney	0.00 RPM	77.83 RPM
SRP017611_liver	0.00 RPM	42.93 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_203 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000005851	1 retrocopy	retro_dord_613,
Erinaceus europaeus	ENSEEUG00000002083	3 retrocopies	retro_eeur_203 , retro_eeur_607, retro_eeur_71,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Vicugna pacos	ENSVPAG00000000595	1 retrocopy	retro_vpac_400,