RetrogeneDB ID: retro_eeur_128

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7864:10708..11551(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL15
• Ensembl ID: ENSEEUG00000001454
• Aliases: None
• Description: mitochondrial ribosomal protein L15 [Source:HGNC Symbol;Acc:14054]

Sequence

>retro_eeur_128
ATGGTGGCTCCTGTGGGCGGTGGCAGGTCCTGGGCCCTGGACCTGCTCAGAGCTCTGCCTCATATGAGTCTGGCCAATTT
AAAGCCAAATCCAGGGTTCAGAAAACAGGAAAGACAACCAAGAGGTCGAAGGAGAGGTAGGAAATGTGGCAGAGGCCATA
AAGGAGAGCAACAGAGAGGAACCTGTCCCCGACTGGGCTTTGAGGGAGGCCAGACTCCATTTTACATCCAAATTCCAAAA
TATGGGTTTAATGAGGGACATAGCTTCCAACGCCAGTATCAGCCTTTGAGTCTCCATAGACTGCAGTATCTTATTGATTT
GGGCCGAGATGATCCTACTCAGCCTATTGACTTAACCCAGCTAGTCAATGGGCGAGGTGTGACCATCCAGCCTCTTAAAA
GGGACTGTAGTGTCTAGCTGGTAGAGGAGGGTGCTGATACATTTAAGGCAAAAGTTAATATCGAAGTACAGTTGGCTTCA
GAGGTAGCCATTGCTGCAATTGAGAAAAATAGTGGTGTTGTCACTACAGCCTTCTATGATCCAAGAAGTCTGGACATTTT
ATGCAAACCTATTCCATTCTTTCTGTGTGGACAACCCATTCCCAAACGAATGCTTCCTCTGGAAGAACTGGTCCTGTATT
ACACTGATGCAAAGAATCATGGCTACCTGGCTGATCCTGGCAAATATCCTGAAGGAAGACTTGAACTTGCCAAGAAATAT
GGTTATATTTTACCTGATATCACAAAAGATGAACTCTTCAAAATGCTTGGTACTCAGAAGGACCCAAGGCAGAGTTTCTT
TGGTCTCGCTCCTGGATGGGCGGTGAACATGGCAGATAGGAAA

Alignment

ORF - retro_eeur_128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.54 %
• Parental protein coverage: 94.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPVRGGGSRALDLLRGLPRVSLANLKPNPGSRKQERRPRGKRRGRKCGRGHKGNRQKGTRPRLGFEGS
          M.APV.GG.S.ALDLLR.LP..SLANLKPNPG.RKQER.PRG.RRGRKCGRGHKG..Q.GT.PRLGFEG.
Retrocopy MVAPVGGGRSWALDLLRALPHMSLANLKPNPGFRKQERQPRGRRRGRKCGRGHKGEQQRGTCPRLGFEGG

Parental  QTP-YLLFPKYGFNEGHSFRRQYHPLSLHRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDYGVHL
          QTP.Y...PKYGFNEGHSF.RQY.PLSLHRLQYLIDLGR.DPTQPIDLTQLVNGRGVTIQPLKRD..V.L
Retrocopy QTPFYIQIPKYGFNEGHSFQRQYQPLSLHRLQYLIDLGRDDPTQPIDLTQLVNGRGVTIQPLKRDCSV*L

Parental  VEEGADTFKAKVNIEVQLASEVAIAAIEKNGGVVTTAFYDPRSLDILCKPIPFFLRGQPIPKRMLPPEEL
          VEEGADTFKAKVNIEVQLASEVAIAAIEKN.GVVTTAFYDPRSLDILCKPIPFFL.GQPIPKRMLP.EEL
Retrocopy VEEGADTFKAKVNIEVQLASEVAIAAIEKNSGVVTTAFYDPRSLDILCKPIPFFLCGQPIPKRMLPLEEL

Parental  VPYYTDAKNRGYLADPGKYPEARLELAKKYGYILPDITKDELFKMLSTRKDPRQIFFGLAPGWVVNMADR
          V.YYTDAKN.GYLADPGKYPE.RLELAKKYGYILPDITKDELFKML.T.KDPRQ.FFGLAPGW.VNMADR
Retrocopy VLYYTDAKNHGYLADPGKYPEGRLELAKKYGYILPDITKDELFKMLGTQKDPRQSFFGLAPGWAVNMADR

Parental  K
          K
Retrocopy K

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	3.71 RPM	26.43 RPM
SRP017611_kidney	7.13 RPM	54.20 RPM
SRP017611_liver	6.11 RPM	36.17 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_128 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128 , retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709, retro_mmus_3534,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241, retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,