RetrogeneDB ID: retro_sscr_217

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:13430650..13431043(+)
• Located in intron of: ENSSSCG00000010832

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL17
• Ensembl ID: ENSSSCG00000024693
• Aliases: None
• Description: mitochondrial ribosomal protein L17 [Source:HGNC Symbol;Acc:14053]

Sequence

>retro_sscr_217
TATGAACGCATCGAGGTGTCATGGGCATGCGTGGACGAGCTGAGGGGCTACACAGAGAAGCTCATCGACTCTGGGAAGCT
GGAAGACACCAACAAATGAGCCATGCGCACAGCTGACTTGTGGCCCACGGAGAGAGACTCAATCCCAAAGCTGTTTCAAG
TACTGGCCCCTGGGTTCCACGTCCAGACTGGGGACTACAGGAGAATGCTGCAGATCCCAAATCGGAATGAGCAGGATCGG
GCCAGGATGGCAGTGATTGCATATAAAGGGAACTGCCTGCCACCTTTGCCCCTGCCTCGCAGGGACAGCAATCCTACACT
CCTAAACCAGCTACTTCAGGGGCTGCAGCAGAACCAGGAAGCAAACAGCCACACAGCTCAAACACCAGCAATT

Alignment

ORF - retro_sscr_217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.15 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HERIEASWARVDELRGYAEKLIDYGKLGDTNERAMRMADFWLTEKDLIPKLFQVLAPRFQGQNGGYTRML
          .ERIE.SWA.VDELRGY.EKLID.GKL.DTN..AMR.AD.W.TE.D.IPKLFQVLAP.F..Q.G.Y.RML
Retrocopy YERIEVSWACVDELRGYTEKLIDSGKLEDTNK*AMRTADLWPTERDSIPKLFQVLAPGFHVQTGDYRRML

Parental  QIPNRNEQDRAKMAVIEYKGNCLPPLPLPRRDSNLTLLNQLLQGLRQDQEASSHTAQTPAV
          QIPNRNEQDRA.MAVI.YKGNCLPPLPLPRRDSN.TLLNQLLQGL.Q.QEA.SHTAQTPA.
Retrocopy QIPNRNEQDRARMAVIAYKGNCLPPLPLPRRDSNPTLLNQLLQGLQQNQEANSHTAQTPAI

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	65.44 RPM
SRP014902_testis	0.14 RPM	50.92 RPM
SRP018288_heart	0.00 RPM	41.31 RPM
SRP018288_kidney	0.20 RPM	49.35 RPM
SRP018288_liver	0.48 RPM	23.51 RPM
SRP018288_lung	0.00 RPM	28.31 RPM
SRP018856_adipose	0.38 RPM	72.12 RPM
SRP035408_brain	0.00 RPM	56.76 RPM
SRP035408_liver	0.06 RPM	33.03 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_217 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027536	1 retrocopy	retro_cpor_1430,
Macropus eugenii	ENSMEUG00000013588	1 retrocopy	retro_meug_1822,
Myotis lucifugus	ENSMLUG00000001144	2 retrocopies	retro_mluc_2368, retro_mluc_679,
Mustela putorius furo	ENSMPUG00000005449	1 retrocopy	retro_mputfur_125,
Rattus norvegicus	ENSRNOG00000019497	1 retrocopy	retro_rnor_1979,
Sus scrofa	ENSSSCG00000024693	1 retrocopy	retro_sscr_217 ,
Ictidomys tridecemlineatus	ENSSTOG00000003313	3 retrocopies	retro_itri_1019, retro_itri_1156, retro_itri_240,