RetrogeneDB ID: retro_sscr_816

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:43520424..43520642(-)
• 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_816
TCGACCAGCTGTCCCCGCCGACTCGGACCCAGGTCCGAGGAGCTGTGGGGTCGAGCAGCTCTCCTGGCCTGCTCGTCCCG
GGTTCGAGGGGACGCTGGCTCGACCAGTTTCCCCGGCCAACTCGGTCCCGGATCCAAGGTGCCGCACGTCGACGAGCTCT
CCCGGCCGACTCGGTCCCTGTACCTTTCTGACACGTGATAGACCAGCTATCCCGGCCC

Alignment

ORF - retro_sscr_816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  STSCPRRLGPVSED-HGVDQISQATR-LRIRVPAGLTSCPGQLVPWTVPKVPRC-RPAVPGD-LGPCLRV
          STSCPRRLGP.SE...GV.Q.S...R..R.R..AG.TS.PGQL.P....KVP...R.A.P.D.LGPC...
Retrocopy STSCPRRLGPRSEE>CGVEQLSWPAR<SRVRGDAGSTSFPGQLGPGS--KVPHV<RRALPAD<LGPCTFL

Parental  CR-LDQLSRP
          .R..DQLSRP
Retrocopy TR>IDQLSRP

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_816 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_816 has 0 orthologous retrocopies within eutheria group .

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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,