RetrogeneDB ID: retro_sscr_273

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:76673390..76673803(+)
• Located in intron of: ENSSSCG00000009524

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM208
• Ensembl ID: ENSSSCG00000002790
• Aliases: None
• Description: transmembrane protein 208 [Source:HGNC Symbol;Acc:25015]

Sequence

>retro_sscr_273
ATGGCACCCAAGGGCAAAGTGGGCACAAGAGGGAAGCAGCAGGTATTTGAGGAGAACAAAGAGTCCCTGGCATGTACCTG
CGGATCCCACCGGAAGCCAACACCATTTACTGTCATGGGACCTTGGTCGTCTTCTCATCTGCCTTGTTTGGGGCCCAGAT
GGCTCTGGGCTTCAGTCTGGCAGTTTATGGGGCTGGCTACCACTCTATGCGCTCGATGGCAAGAGCAGCCTGCTCTGAGC
AGGGGGCCCTGATGGATGGGGGAATGCACCTCAGCATGGAGCAGGGCATGGCCGAGCACCTTAAGGATCTGATCCTACTG
ACAGCCACTCTGCAGATGCTCAGCGGCTTCTCTCTCTGCATCTGGCCCTCCTGGCTTCTGGCACCAGGCAGAGCCCTTTA
CCTCCTGTGGATC

Alignment

ORF - retro_sscr_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 80.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPKGKVGTRGKKQIFEENKETLK-FYLRIILGANAIYCLVTLVIFYSSASFWAWMALGFSLAVYGASYH
          MAPKGKVGTRGK.Q.FEENKE.L...YLRI...AN.IYC..TLV.F.SSA.F.A.MALGFSLAVYGA.YH
Retrocopy MAPKGKVGTRGKQQVFEENKESLA<MYLRIPPEANTIYCHGTLVVF-SSALFGAQMALGFSLAVYGAGYH

Parental  SMSSMARAAFSEDGALMDGGMDLNMEQGMAEHLKDVILLTAIVQVLSCFSLYIWSFWLLAPGRALYLLWV
          SM.SMARAA.SE.GALMDGGM.L.MEQGMAEHLKD.ILLTA..Q.LS.FSL.IW..WLLAPGRALYLLW.
Retrocopy SMRSMARAACSEQGALMDGGMHLSMEQGMAEHLKDLILLTATLQMLSGFSLCIWPSWLLAPGRALYLLWI

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	17.52 RPM
SRP014902_testis	0.14 RPM	9.05 RPM
SRP018288_heart	0.00 RPM	10.16 RPM
SRP018288_kidney	0.00 RPM	33.89 RPM
SRP018288_liver	0.00 RPM	30.86 RPM
SRP018288_lung	0.10 RPM	23.01 RPM
SRP018856_adipose	0.00 RPM	41.17 RPM
SRP035408_brain	0.06 RPM	15.98 RPM
SRP035408_liver	0.00 RPM	24.28 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_273 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_273 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000026215	2 retrocopies	retro_ocun_1721, retro_ocun_1722,
Ochotona princeps	ENSOPRG00000002571	2 retrocopies	retro_opri_944, retro_opri_959,
Sus scrofa	ENSSSCG00000002790	1 retrocopy	retro_sscr_273 ,