RetrogeneDB ID: retro_sscr_284

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:47385614..47385952(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSSSCG00000015040
• Aliases: None
• Description: 6-pyruvoyltetrahydropterin synthase [Source:HGNC Symbol;Acc:9689]

Sequence

>retro_sscr_284
AGCACTTCCCATCACCTCACAGCAAGTTTCTGAATAATGAAGAAAACTTGAAACTCTTTGGGAAATGCAACAACCCAAAT
GGCCATGGGCACAATTATAAAGTTGTGGTGATAGCACATGGAGAGATTGATTCTGTTATAGGAATGATTTTGAATTCGAC
TGACCTCAAGCAGTATATTGGGAAGGCAATCATGAAGCCACTTGATCATAAGAATCTGGACATGGATGTGCTATACTTTG
CAGATGTTGTAAGCATGACAGAAAATGTAGCTGTATATATCTGGGAAAACCTCCAGAAATTTCTTCTTGTGGGAGTTCTT
TATAAAGTACAAGTATAT

Alignment

ORF - retro_sscr_284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.82 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SASHRL-HSKSLSNEENLKLFGKCNNPNGHGHNYKVVVTVHGEIDPVTGMVMNLTDLKKYMEEAIMKPLD
          S.SH.L.HSK.L.NEENLKLFGKCNNPNGHGHNYKVVV..HGEID.V.GM..N.TDLK.Y...AIMKPLD
Retrocopy STSHHL<HSKFLNNEENLKLFGKCNNPNGHGHNYKVVVIAHGEIDSVIGMILNSTDLKQYIGKAIMKPLD

Parental  HKNLDLDVPYFADVVSTTENVAVYIWENLQKYLPAGVLYKVKVY
          HKNLD.DV.YFADVVS.TENVAVYIWENLQK.L..GVLYKV.VY
Retrocopy HKNLDMDVLYFADVVSMTENVAVYIWENLQKFLLVGVLYKVQVY

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	8.23 RPM
SRP014902_testis	0.00 RPM	26.31 RPM
SRP018288_heart	0.00 RPM	42.59 RPM
SRP018288_kidney	0.00 RPM	60.58 RPM
SRP018288_liver	0.00 RPM	23.51 RPM
SRP018288_lung	0.00 RPM	14.05 RPM
SRP018856_adipose	0.00 RPM	9.33 RPM
SRP035408_brain	0.00 RPM	29.79 RPM
SRP035408_liver	0.00 RPM	19.46 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_284 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_284 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003968	3 retrocopies	retro_amel_1001, retro_amel_1480, retro_amel_691,
Bos taurus	ENSBTAG00000003770	3 retrocopies	retro_btau_1182, retro_btau_1762, retro_btau_682,
Canis familiaris	ENSCAFG00000013915	2 retrocopies	retro_cfam_1386, retro_cfam_1859,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Felis catus	ENSFCAG00000024702	3 retrocopies	retro_fcat_1546, retro_fcat_212, retro_fcat_564,
Myotis lucifugus	ENSMLUG00000023388	1 retrocopy	retro_mluc_946,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Sorex araneus	ENSSARG00000001975	2 retrocopies	retro_sara_163, retro_sara_72,
Sus scrofa	ENSSSCG00000015040	1 retrocopy	retro_sscr_284 ,
Tursiops truncatus	ENSTTRG00000010526	1 retrocopy	retro_ttru_1710,
Vicugna pacos	ENSVPAG00000000061	1 retrocopy	retro_vpac_363,