RetrogeneDB ID: retro_sscr_1032

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:80022997..80023267(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000022982
• Aliases: None
• Description: None

Sequence

>retro_sscr_1032
TTTAACCATAGCATTTGTTTGTGTTTTTCTCTTATTGTACACGTTAGATATGCCAACGTCAAGAAGTGCAGTAATGAGGG
TCGTGCCTTGATGCAATTGGATTTTCAACAGTTTTTAATGAAACTTGAAAAACTCACAGATATCCGGCCCATTCCTGATA
AAGAATTTGTGGAAACCTATATTAAAGCCTACTACCTAACTGAGAATGACATGGAACGCTGGATCAAAGAGCATAGGGTG
AGAGCTGAGAAGCAGTTAATTAAGTTTGTT

Alignment

ORF - retro_sscr_1032 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.11 %
• Parental protein coverage: 64.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WEHCIRLANRTIVE-GYANVKKCSNEGRALMQLDFQQFLMKLEKLTDIRPIPDKEFVETYIKAYYLTEND
          ..H.I.L....IV...YANVKKCSNEGRALMQLDFQQFLMKLEKLTDIRPIPDKEFVETYIKAYYLTEND
Retrocopy FNHSICLCFSLIVHVRYANVKKCSNEGRALMQLDFQQFLMKLEKLTDIRPIPDKEFVETYIKAYYLTEND

Parental  MERWIKEHREYSTKQLINLV
          MERWIKEHR....KQLI..V
Retrocopy MERWIKEHRVRAEKQLIKFV

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	1.06 RPM
SRP014902_testis	0.28 RPM	1.13 RPM
SRP018288_heart	0.03 RPM	6.00 RPM
SRP018288_kidney	0.00 RPM	2.86 RPM
SRP018288_liver	0.16 RPM	2.24 RPM
SRP018288_lung	0.00 RPM	3.87 RPM
SRP018856_adipose	0.00 RPM	1.87 RPM
SRP035408_brain	0.00 RPM	10.35 RPM
SRP035408_liver	0.00 RPM	3.43 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1032 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1032 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000022982	1 retrocopy	retro_sscr_1032 ,