RetrogeneDB ID: retro_sscr_617

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:53809269..53809791(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL15
• Ensembl ID: ENSSSCG00000030578
• Aliases: None
• Description: mitochondrial ribosomal protein L15 [Source:HGNC Symbol;Acc:14054]

Sequence

>retro_sscr_617
ACCCAGCTTGCCAATGGGAGAGGTGTGACCATTCAGCCATTTAAAAGCAATTATGGAATCCAGCTGGTAGAGGAGGGTAC
TGGCACCTTTGAGGCTAAAGATAATATTGAAGTACAGCTGGCTTCAGAGCTGGCCATTGCTGCGATCAGGAAGAATGGGG
GTATTGTCACAATGGTCTTCTATGATCCGAGAAGCCTGGAAATTCTGTGCAAACCTATTCCATTCTTTCTCCGTGGACAA
CCCATCCCAAAGTGAATGTTTTCCCCCAAGGCAATGGAACCATATTACACTGATGCAAAGAATCACGGGTATTTGTCAGA
TCCTGCCAAATTTCCTGAGCTCACCAAGAACCATGGTTCTATTTTACCTGATATCACTAAAGATGAACTCTTCGAAATGC
TCAGTACTTAAAAGGACCCAAGGCAGATTTTCTTTGATCTTGCACCTGGATGGGAGGTGAAGATAGCAGATAAGAAATTC
CTAAAACATGCAGATGAGAATCTCCTCAAGTACTACAGCTCA

Alignment

ORF - retro_sscr_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.84 %
• Parental protein coverage: 60.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQLVNGRGVTIQPSKRDYGVQLVEEGADTFKAKVNIEVQMASELAIAAIEKNGGVVTTAFYDPRSLEILC
          TQL.NGRGVTIQP.K..YG.QLVEEG..TF.AK.NIEVQ.ASELAIAAI.KNGG.VT..FYDPRSLEILC
Retrocopy TQLANGRGVTIQPFKSNYGIQLVEEGTGTFEAKDNIEVQLASELAIAAIRKNGGIVTMVFYDPRSLEILC

Parental  KPVPFFLRGQPIPKRMLPPEALVPYYTDAKNRGYLADPARFPEARLELARKYGYVLPDITKDELFKMLST
          KP.PFFLRGQPIPK.M..P.A..PYYTDAKN.GYL.DPA.FPE....L....G..LPDITKDELF.MLST
Retrocopy KPIPFFLRGQPIPK*MFSPKAMEPYYTDAKNHGYLSDPAKFPE----LTKNHGSILPDITKDELFEMLST

Parental  RKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYSS
          .KDPRQIFF.LAPGW.V..ADKK.LK..DENLLKYYSS
Retrocopy *KDPRQIFFDLAPGWEVKIADKKFLKHADENLLKYYSS

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
SRP014902_placenta	0.00 RPM	14.20 RPM
SRP014902_testis	0.28 RPM	40.74 RPM
SRP018288_heart	0.05 RPM	33.61 RPM
SRP018288_kidney	0.20 RPM	45.81 RPM
SRP018288_liver	0.00 RPM	29.10 RPM
SRP018288_lung	0.10 RPM	31.46 RPM
SRP018856_adipose	0.11 RPM	35.18 RPM
SRP035408_brain	0.00 RPM	51.61 RPM
SRP035408_liver	0.00 RPM	23.69 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_617 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_617 has 0 orthologous retrocopies within eutheria group .

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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,