RetrogeneDB ID: retro_sscr_1037

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:118108931..118109204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000011459
• Aliases: None
• Description: Sus scrofa selenoprotein K (SELK), mRNA. [Source:RefSeq mRNA;Acc:NM_001044553]

Sequence

>retro_sscr_1037
ATGGTTCACACCTTGAGTGGACAAGTGTCGAACAGCAGGAGCCTGTCCTCATGGAGATGATCTTTTATAATGGATTTCTT
CTCGGGCATAGCTGTATTTGTGGCTTGTTTTTCAGAACTCTGCTTCAGCAAGATATGAAAAAGAGAACAGGCTATAGAAG
CTCATCTGATTCTAGACATGATGATGGAAGAGGGCCACCAGGAAACCCCCTCAGTAAAATGGGTCCGATTAATCATCTGT
GTGGCCTGAATCCTCCACCAGTGGGCTGGTGGA

Alignment

ORF - retro_sscr_1037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVYISNGQVLDSRSQSPWRLSFITDFFWGIAEFVV-LFFRTLLQQDVKKRRGYGGSSDSRYDDGRGPPGN
          MV....GQV..SRS.S.WR.SFI.DFF.GIA.FV..LFFRTLLQQD.KKR.GY..SSDSR.DDGRGPPGN
Retrocopy MVHTLSGQVSNSRSLSSWR*SFIMDFFSGIAVFVA<LFFRTLLQQDMKKRTGYRSSSDSRHDDGRGPPGN

Parental  PPRRMGRINHLRGPNPPPM-AGG
          P...MG.INHL.G.NPPP..AGG
Retrocopy PLSKMGPINHLCGLNPPPV>AGG

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	11.68 RPM
SRP014902_testis	0.00 RPM	16.83 RPM
SRP018288_heart	0.00 RPM	71.04 RPM
SRP018288_kidney	0.00 RPM	48.27 RPM
SRP018288_liver	0.00 RPM	54.37 RPM
SRP018288_lung	0.00 RPM	19.55 RPM
SRP018856_adipose	0.03 RPM	56.07 RPM
SRP035408_brain	0.00 RPM	43.70 RPM
SRP035408_liver	0.00 RPM	36.20 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1037 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1037 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007612	8 retrocopies	retro_cjac_1748, retro_cjac_2086, retro_cjac_2144, retro_cjac_2374, retro_cjac_2684, retro_cjac_2825, retro_cjac_3897, retro_cjac_726,
Cavia porcellus	ENSCPOG00000007172	4 retrocopies	retro_cpor_255, retro_cpor_320, retro_cpor_467, retro_cpor_562,
Homo sapiens	ENSG00000113811	3 retrocopies	retro_hsap_2027, retro_hsap_2055, retro_hsap_3513,
Gorilla gorilla	ENSGGOG00000000681	2 retrocopies	retro_ggor_1481, retro_ggor_2375,
Microcebus murinus	ENSMICG00000017513	2 retrocopies	retro_mmur_1054, retro_mmur_202,
Myotis lucifugus	ENSMLUG00000012622	3 retrocopies	retro_mluc_122, retro_mluc_1930, retro_mluc_2276,
Macaca mulatta	ENSMMUG00000019272	4 retrocopies	retro_mmul_1308, retro_mmul_1388, retro_mmul_1861, retro_mmul_625,
Mus musculus	ENSMUSG00000042682	9 retrocopies	retro_mmus_1015, retro_mmus_1017, retro_mmus_1019, retro_mmus_1106, retro_mmus_1855, retro_mmus_2704, retro_mmus_2705, retro_mmus_3495, retro_mmus_772,
Nomascus leucogenys	ENSNLEG00000026533	2 retrocopies	retro_nleu_2443, retro_nleu_483,
Ochotona princeps	ENSOPRG00000002266	6 retrocopies	retro_opri_167, retro_opri_389, retro_opri_571, retro_opri_679, retro_opri_745, retro_opri_975,
Pongo abelii	ENSPPYG00000025894	3 retrocopies	retro_pabe_107, retro_pabe_1658, retro_pabe_2904,
Pan troglodytes	ENSPTRG00000015030	3 retrocopies	retro_ptro_1348, retro_ptro_1370, retro_ptro_2386,
Pteropus vampyrus	ENSPVAG00000016291	1 retrocopy	retro_pvam_891,
Rattus norvegicus	ENSRNOG00000014624	4 retrocopies	retro_rnor_1064, retro_rnor_1065, retro_rnor_2580, retro_rnor_2947,
Sus scrofa	ENSSSCG00000011459	1 retrocopy	retro_sscr_1037 ,
Ictidomys tridecemlineatus	ENSSTOG00000000506	2 retrocopies	retro_itri_218, retro_itri_509,