RetrogeneDB ID: retro_sscr_704

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:68363863..68364204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000017579
• Aliases: None
• Description: None

Sequence

>retro_sscr_704
GGAAAGCTTAGTGGCCCTGGTGAAATTGGAAAATCTGGTCAGATGGGCCCCCATGGTCTGCCTGGTGAGAGAGGTCATCC
TGAACGCCCTGGCCTTGATAGTGCTCATGGAAATGATGGTGCTACTGGTGCTGCTGGATCCCCTGGTCCCACTGACCCTG
CTGGTCCACCTGGCTTCCCTGGTGCTGTTGGTGCTAAGGGTGAAGTTTGTCCCTGAGGAGCCCGAGGCTAAAGGTGCCAA
CAAATGCTCCTAGTATTGCTGGTTCTCCTGGCTTCCCTGGTGCCCAAGGCCCCTGTAGACCCCAGGGCTCCAGTGGCCCC
CCTGGTCCAAAGAGTAACAAC

Alignment

ORF - retro_sscr_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.87 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GEPGSPGENGAPGQMGPRGLPGERGRPGPPGPAGARGNDGATGAAGPPGPTGPAGPPGFPGAVGAKGEAG
          G....PGE.G..GQMGP.GLPGERG.P..PG...A.GNDGATGAAG.PGPT.PAGPPGFPGAVGAKGE..
Retrocopy GKLSGPGEIGKSGQMGPHGLPGERGHPERPGLDSAHGNDGATGAAGSPGPTDPAGPPGFPGAVGAKGEVC

Parental  PQGARG-SEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGGKGAN
          P.GARG....P.......G.PG..GA.GP....G..G.PG.K..N
Retrocopy P*GARG<LKVPTNAPSIAGSPGFPGAQGPCRPQGSSGPPGPKSNN

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	137.51 RPM
SRP014902_testis	0.00 RPM	156.44 RPM
SRP018288_heart	0.00 RPM	20.88 RPM
SRP018288_kidney	0.00 RPM	10.84 RPM
SRP018288_liver	0.00 RPM	6.88 RPM
SRP018288_lung	0.00 RPM	61.60 RPM
SRP018856_adipose	0.00 RPM	166.70 RPM
SRP035408_brain	0.00 RPM	0.83 RPM
SRP035408_liver	0.00 RPM	0.88 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_704 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_704 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000017579	2 retrocopies	retro_sscr_704 , retro_sscr_727,