RetrogeneDB ID: retro_sscr_1119

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL895852.1:1175..1361(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000023484
• Aliases: None
• Description: None

Sequence

>retro_sscr_1119
TCAACCAGCTGTCCCGGGTGACTCGGGCCCGTGCCTGATGTCCCACGGTGTCAACCAGCCGTCCTGGGTGACTCAGGCCC
GTGCCCAAGGGCCCGCGGGGTCCTCCAGTTGTCCCGGGCAACTCGGGACCATGCCGCAGGGCCCAGATGTTGAACAGCTG
TCCCGGGCGACTCACGCTTGGGTCCG

Alignment

ORF - retro_sscr_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 82.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STSCPRRLGPVSE-DHGVDQISQATRLRIRVPAGLTSCPGQLVPWTVPKVP-RCRPAVPGD--LGP
          STSCP..LGPV....HGV.Q.S..T..R...PAG..SCPGQL...T.P..P.RC..AVPGD..LGP
Retrocopy STSCPG*LGPVPD>SHGVNQPSWVTQARAQGPAGSSSCPGQL--GTMPQGP<RC*TAVPGDSRLGP

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	0.00 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_1119 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1119 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000023015	6 retrocopies	retro_sscr_1120, retro_sscr_265, retro_sscr_632, retro_sscr_777, retro_sscr_797, retro_sscr_815,
Sus scrofa	ENSSSCG00000023484	7 retrocopies	retro_sscr_1057, retro_sscr_1078, retro_sscr_1119 , retro_sscr_630, retro_sscr_631, retro_sscr_633, retro_sscr_816,
Sus scrofa	ENSSSCG00000024741	1 retrocopy	retro_sscr_266,