RetrogeneDB ID: retro_eeur_71

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_4175:37453..37912(-)
• Located in intron of: ENSEEUG00000014603

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_71
TCTGACTCCAGAGCTACCACTGGGTCCTACATTGCCAACCGACTGACTGACAAGCTGCCCCCATTCATGACGGAATCTTC
TGCAGTGGCTCAGACTCAGCAGCTAATACCCAGGCAGTCACTGATGCAGTCACTTATCAGCTTGGCTTCCACAGCACTGG
ACTGAATGAGCCTCCACTGGTACACACAGCTGCCAGACTCTTTAAGGAGATGTGTTACTGATACCGAGAAGAGCTAATGG
CAGGAATCATCACTGCAGGCTTGGTCCCAAGAAAGAGGACAGGTGTACTCAGTGCTCGTGGGAGGTATGATGGCTAGGCA
GTCCTTCGCCACTGGGGGTTCTGGGAGCTCCTACATCTATGGCTATATTGATGCTACCTACTGGGAAGGCATGGGCAAGG
AAGAATGTCTTCAGTTCACTGCTAATGCTCTTGCTTTGGCCATGGAGCGGGATGGCTCA

Alignment

ORF - retro_eeur_71 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.41 %
• Parental protein coverage: 86.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADSRTTTGSYIANRVTDKL-TPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK
          .DSR.TTGSYIANR.TDKL..PIHD.IFC..S.SAA.TQAV.DAVTYQLGFHS..LNEPPLVHTAA.LFK
Retrocopy SDSRATTGSYIANRLTDKL<APIHDGIFCSGSDSAANTQAVTDAVTYQLGFHSTGLNEPPLVHTAARLFK

Parental  EMCYRYREELMAGIIIAG-WDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECL
          EMCY.YREELMAGII.AG.W..QE.GQVYSV..GGMM.RQSFA.GGSGSSYIYGY.DATY.EGM.KEECL
Retrocopy EMCY*YREELMAGIITAG>WS-QERGQVYSVLVGGMMARQSFATGGSGSSYIYGYIDATYWEGMGKEECL

Parental  QFTANAPALAMERDSS
          QFTANA.ALAMERD.S
Retrocopy QFTANALALAMERDGS

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	2.90 RPM	35.94 RPM
SRP017611_kidney	4.31 RPM	77.83 RPM
SRP017611_liver	3.54 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_71 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,