RetrogeneDB ID: retro_sscr_446

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:101179128..101179297(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SVIP
• Ensembl ID: ENSSSCG00000022838
• Aliases: None
• Description: small VCP/p97-interacting protein [Source:HGNC Symbol;Acc:25238]

Sequence

>retro_sscr_446
GGATTGTATTTTTCCTGTCCCATGGAAGTGGCATCTCCATCACTGGACCTGGAATAAAAAAGAGCAAAGCTTGCAGAGGC
TGCAGAGAGAAGACAAAACAATGCTACATCTCAGGGCATTTTGGATGTTCCGTCTGTGGAAGGGAGAGAGAAAGAAAAAG
GAAAAAATG

Alignment

ORF - retro_sscr_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.18 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLCFPCPTEEAPPSPDPEEKRAKLAEAAERRQKEAASRGILDVRSVEEK-RKKKEKI
          GL.F.CP.E.A.PS.D.E.KRAKLAEAAERRQ..A.S.GILDV.SVE...RKKKEK.
Retrocopy GLYFSCPMEVASPSLDLE*KRAKLAEAAERRQNNATSQGILDVPSVEGR>RKKKEKM

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	0.71 RPM
SRP018288_heart	0.00 RPM	2.54 RPM
SRP018288_kidney	0.00 RPM	5.32 RPM
SRP018288_liver	0.00 RPM	1.76 RPM
SRP018288_lung	0.00 RPM	2.44 RPM
SRP018856_adipose	0.00 RPM	0.80 RPM
SRP035408_brain	0.00 RPM	13.69 RPM
SRP035408_liver	0.00 RPM	2.67 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_446 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_446 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_446 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013152	4 retrocopies	retro_chof_1571, retro_chof_2005, retro_chof_2442, retro_chof_668,
Dasypus novemcinctus	ENSDNOG00000016735	4 retrocopies	retro_dnov_2035, retro_dnov_2072, retro_dnov_928, retro_dnov_945,
Sus scrofa	ENSSSCG00000022838	1 retrocopy	retro_sscr_446 ,