RetrogeneDB ID: retro_eeur_485

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_323397:23936..24424(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL19
• Ensembl ID: ENSEEUG00000002266
• Aliases: None
• Description: mitochondrial ribosomal protein L19 [Source:HGNC Symbol;Acc:14052]

Sequence

>retro_eeur_485
ATGGCCCTGGTCGGGCGCTTTCGAGCCAACAGGGAGCTGATTCCTGTGCCGGCCTCCTTTGCCTGCGGTGTGTGGCCGGC
CCTGGCCGTTGGCAGAGCACAGGACCCTCGGAGTCAGGCGCCTTCCGGCCGCCCTCGAAACCCGTGATCGTGGACAAACG
CAGCCCGCCGCTCCCGGAAACCGGGTTCCTGAGTCCTGAATTCATTCCTCCACGGGGAAGAACAAATCCTCTGAAATTTC
AACTAGAAAGAAAAGATATGCCAGAAAGGAGAAAAATACTCCACATTCCAGAGTTCTATGTTGGAAGCATTTGAGTTACT
ACAGCTGACCCTTATGCCAGTGGAAAAACTAGCCAGTTTCTGGGGATTTGCATTCAGAGATCAGGATCAGGATTTGGAGC
CACTTTTATCCTTCGAAACATTATAGATGGACAAGGTATTGAGATTTGCTTTGAACTTTATAATCCTCGAATCCAGGAGA
TCCAGGTG

Alignment

ORF - retro_eeur_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.52 %
• Parental protein coverage: 58.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALVGRFRANRALIPVPASFACGAR-AGPSRPQSTGPAESGAFRPPSKPVIVDKRSPPLRETRFLSPEFI
          MALVGRFRANR.LIPVPASFACG...AGP.R.QSTGP.ESGAFRPPSKPVIVDKRSPPL.ET.FLSPEFI
Retrocopy MALVGRFRANRELIPVPASFACGVW<AGPGRWQSTGPSESGAFRPPSKPVIVDKRSPPLPETGFLSPEFI

Parental  PPRGRTNPLKFQLERKDMLERRKILHIPEFYVGYILRVTTADPYASGKTSHFLGICIQRSGSGFGATFIL
          PPRGRTNPLKFQLERKDM.ERRKILHIPEFYVG.I..VTTADPYASGKTS.FLGICIQRSGSGFGATFIL
Retrocopy PPRGRTNPLKFQLERKDMPERRKILHIPEFYVGSI-*VTTADPYASGKTSQFLGICIQRSGSGFGATFIL

Parental  RNIIDGQGIEICFELYNPRIQEIQV
          RNIIDGQGIEICFELYNPRIQEIQV
Retrocopy RNIIDGQGIEICFELYNPRIQEIQV

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	6.12 RPM	5.16 RPM
SRP017611_kidney	17.07 RPM	14.63 RPM
SRP017611_liver	6.75 RPM	6.91 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_485 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002266	1 retrocopy	retro_eeur_485 ,
Homo sapiens	ENSG00000115364	1 retrocopy	retro_hsap_2957,
Gorilla gorilla	ENSGGOG00000027896	1 retrocopy	retro_ggor_2048,
Loxodonta africana	ENSLAFG00000000146	1 retrocopy	retro_lafr_472,
Myotis lucifugus	ENSMLUG00000012774	1 retrocopy	retro_mluc_1308,
Pongo abelii	ENSPPYG00000012255	1 retrocopy	retro_pabe_2453,
Pan troglodytes	ENSPTRG00000012108	1 retrocopy	retro_ptro_2002,
Ictidomys tridecemlineatus	ENSSTOG00000002873	1 retrocopy	retro_itri_549,
Tupaia belangeri	ENSTBEG00000016470	1 retrocopy	retro_tbel_326,