RetrogeneDB ID: retro_sscr_325

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:102050346..102050637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APH1B
• Ensembl ID: ENSSSCG00000004567
• Aliases: None
• Description: APH1B gamma secretase subunit [Source:HGNC Symbol;Acc:24080]

Sequence

>retro_sscr_325
TTTCTCCTGCTTTTTGCAGTGTTAGCCTCAGTCTGTATCCAAGAAATGTTCTGGCTTGCATATTTTAAACTTTTTAAGAA
AGCCAGTGAGCGTTTGAAGAGTTTAAACCCAGGTGAGACAGCACTCTCTATGCAACTGCTGGCCTGTGTTTCTGGCTTAG
ACTTTGGAATCATGAGTGGAATATTTTCCTTTATAAATACCCAGTCTGACTCCTTGGGGCTGAGCACAGTGGGAACTCAT
GGAGACCCTCCCCAGGGATTCCCAATTTCAGCTTTCGCGTTGATGGTGATC

Alignment

ORF - retro_sscr_325 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.07 %
• Parental protein coverage: 55.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLLIFGVLVSVLIQETFRFAYYKLLKKASEGLKSLNPDETAPSMRLLAYVSGLGFGIMSGVFSFVNTLSD
          .LL.F.VL.SV.IQE.F..AY.KL.KKASE.LKSLNP.ETA.SM.LLA.VSGL.FGIMSG.FSF.NT.SD
Retrocopy FLLLFAVLASVCIQEMFWLAYFKLFKKASERLKSLNPGETALSMQLLACVSGLDFGIMSGIFSFINTQSD

Parental  SLGPGTVGIHGDPPQFFLNSGMCLVVV
          SLG..TVG.HGDPPQ.F..S...L.V.
Retrocopy SLGLSTVGTHGDPPQGFPISAFALMVI

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	0.27 RPM
SRP014902_testis	0.00 RPM	1.98 RPM
SRP018288_heart	0.00 RPM	0.42 RPM
SRP018288_kidney	0.00 RPM	0.69 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	1.53 RPM
SRP018856_adipose	0.00 RPM	4.34 RPM
SRP035408_brain	0.00 RPM	0.32 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_325 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010641	1 retrocopy	retro_btau_1423,
Sus scrofa	ENSSSCG00000004567	1 retrocopy	retro_sscr_325 ,
Tursiops truncatus	ENSTTRG00000006865	2 retrocopies	retro_ttru_1673, retro_ttru_983,