RetrogeneDB ID: retro_sscr_285

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:59811932..59812358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRNP27
• Ensembl ID: ENSSSCG00000025674
• Aliases: None
• Description: small nuclear ribonucleoprotein 27kDa (U4/U6.U5) [Source:HGNC Symbol;Acc:30240]

Sequence

>retro_sscr_285
AGGCGGTCCCCGTCCACATCCTGGGAGAGAGAACTAAGGCGCCAAGAAAAGTCCCGGTCCCAAAAGCGAGATCTGAGAAG
GAGCCGCTCTCGTTGCCCCCACAGAAGACGTTCCAGGTCTCCAAGGCGACATAGATCCACATCTCCCTCCCCTTCTCGAC
TGAAAGAAAGAAGAGACGAAGAGAAGAAAGAAACAAAAGAAATAAAGAGCAAAGAACGTCAGATTACTGAGGAAGACTTA
GAGGGCAAAACAGAGGAAGAAATAGAAATGATGAAGTTAATGGGATTTGCCTCCTTTGACTCTACAAAAGGAAAAAATGT
GGATGGCTCTGTAAATGCCTATGCCATAAATGTGTCTCAGAAGAGGAAGTATAGGCACTACAGGAATCGAAAAGGTGGAT
TTAACAGACCTTTGGATTTCATTGCA

Alignment

ORF - retro_sscr_285 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRSRSTSRERERRRRERSRSRERDRRRSRSRSPHRRRSRSPRRHRSTSPSPSRLKERRDEEKKETKEIKS
          RRS.STS.ERE.RR.E.SRS..RD.RRSRSR.PHRRRSRSPRRHRSTSPSPSR.................
Retrocopy RRSPSTSWERELRRQEKSRSQKRDLRRSRSRCPHRRRSRSPRRHRSTSPSPSRXXXXXXXXXXXXXXXXX

Parental  KERQITVEEDLEGKTEEEIEMMKLMGFASFDSTKGKKVDGSVNAYAINVSQKRKYRQYMNRKGGFNRPLD
          ...QIT.EEDLEGKTEEEIEMMKLMGFASFDSTKGK.VDGSVNAYAINVSQKRKYR.Y.NRKGGFNRPLD
Retrocopy XXXQIT-EEDLEGKTEEEIEMMKLMGFASFDSTKGKNVDGSVNAYAINVSQKRKYRHYRNRKGGFNRPLD

Parental  FIA
          FIA
Retrocopy FIA

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	3.45 RPM
SRP014902_testis	0.28 RPM	9.76 RPM
SRP018288_heart	3.43 RPM	26.95 RPM
SRP018288_kidney	1.97 RPM	18.22 RPM
SRP018288_liver	0.64 RPM	11.35 RPM
SRP018288_lung	0.31 RPM	9.98 RPM
SRP018856_adipose	1.09 RPM	8.30 RPM
SRP035408_brain	10.80 RPM	62.41 RPM
SRP035408_liver	4.99 RPM	27.74 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_285 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_285 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037746	4 retrocopies	retro_btau_1352, retro_btau_375, retro_btau_514, retro_btau_515,
Choloepus hoffmanni	ENSCHOG00000003042	1 retrocopy	retro_chof_2589,
Echinops telfairi	ENSETEG00000017344	1 retrocopy	retro_etel_655,
Homo sapiens	ENSG00000124380	1 retrocopy	retro_hsap_3387,
Mus musculus	ENSMUSG00000001158	2 retrocopies	retro_mmus_1977, retro_mmus_2105,
Oryctolagus cuniculus	ENSOCUG00000022967	1 retrocopy	retro_ocun_1281,
Pongo abelii	ENSPPYG00000012332	2 retrocopies	retro_pabe_1990, retro_pabe_2782,
Pan troglodytes	ENSPTRG00000012022	1 retrocopy	retro_ptro_2300,
Sus scrofa	ENSSSCG00000025674	1 retrocopy	retro_sscr_285 ,