RetrogeneDB ID: retro_eeur_444

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_305990:18769..19252(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL43
• Ensembl ID: ENSEEUG00000004807
• Aliases: None
• Description: mitochondrial ribosomal protein L43 [Source:HGNC Symbol;Acc:14517]

Sequence

>retro_eeur_444
ACGGCGCGCGGGACCCCGAGCTGCTTCCTGGCTAGTGTCCTCCACAACAGGGTGGGCCGCTAGCAGCTGCAGTGCCTCAG
CTTCAGCCTCAGCCGCGACAAGCCGTCGTCCCTGGGCACCAGGGAGTTCCTGGAACGGGAGGTGACAGACTTTGCCCGGC
GGAACCCAGGGGTCGTCATCTACGTGAACGCCCAGCAGTGCTCTGCGCCCACGGTAGTGGCCGAATACCTGAACGGGGCT
GTGCGCGAGGAGAGCATCCAGTCCAAGTCGGCAGACGCAGAAGCTGGCGAGCCAGTCGGGTTTGGACGTGATCGGCATCC
GCAAGCCCTACCACACCGACACCCCGAACATCCAGGGCCAGTGGCACCCCTTCACCAACAAGCCCACGAAGCCGGGCGGC
CTGTGTCGCCGAGAGCTCCAGGGCCCCGGCCCGGCCCACGTGCAGGCAGTGAAGCGACCGCACCCACCTGGCTCTCACGG
CGG

Alignment

ORF - retro_eeur_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.9 %
• Parental protein coverage: 63.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TARGTPSRFLASVLHNGVGRYVQQLQRLSFSLSRDKPSSLGAREFVEREVTDFARRNPGVVIYVNVQRCS
          TARGTPS.FLASVLHN.VGR...QLQ.LSFSLSRDKPSSLG.REF.EREVTDFARRNPGVVIYVN.Q.CS
Retrocopy TARGTPSCFLASVLHNRVGR*--QLQCLSFSLSRDKPSSLGTREFLEREVTDFARRNPGVVIYVNAQQCS

Parental  APTVVAEYLNGAVREESVQSKSADEIAALVQKLASQSGLDVIRIRKPYHTDTPSIQGQWHPFTNKPTKPG
          APTVVAEYLNGAVREES.QSKSAD..A.................R.P.H........Q.......P..P.
Retrocopy APTVVAEYLNGAVREESIQSKSADAEAGEPVGFGRDRHPQALPHRHPEHPGPVAPLHQQAHEAGRPVSPR

Parental  SLRPRELQGPGPAHDSAELLSKR
          ...PR.....G........LS.R
Retrocopy APGPRPGPRAGSEATAPTWLSRR

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	1.29 RPM	5.32 RPM
SRP017611_kidney	5.63 RPM	23.07 RPM
SRP017611_liver	3.54 RPM	14.15 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_444 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009742	1 retrocopy	retro_cfam_1720,
Erinaceus europaeus	ENSEEUG00000004807	1 retrocopy	retro_eeur_444 ,
Echinops telfairi	ENSETEG00000012498	1 retrocopy	retro_etel_2213,
Microcebus murinus	ENSMICG00000000014	1 retrocopy	retro_mmur_370,
Macaca mulatta	ENSMMUG00000010679	1 retrocopy	retro_mmul_1882,
Nomascus leucogenys	ENSNLEG00000014812	1 retrocopy	retro_nleu_17,