RetrogeneDB ID: retro_sscr_648

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:142594765..142595113(+)
• Located in intron of: ENSSSCG00000026644

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS2
• Ensembl ID: ENSSSCG00000014850
• Aliases: None
• Description: signal peptidase complex subunit 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28962]

Sequence

>retro_sscr_648
AGAACCAGTGGTGGCGGAGGCAGTAGCAGGCTGGCGGTGGTCCCAGCTGCGGGACAGGCAGTAGCTGCGGCAGGTCTTTG
GACATGTGGAAGATTGATGATAAGCCTGTAAAAATGGACAGATGGGATGGATCACTTGTGAAAATCTTCAGGTGATTCTG
CCAAAAAGGTACTTCTGGAAAAGTACAAGTATGTGGAGAATTTTGCTTTAATTGACAGTCGCCTCACTGTCTGTACTGTC
TCTTGTTTCTTTGCCACAGTGGCTTCGATTGGGGATTATACACACCCCTTTCCAGAGTCGAAGCCTGTTTTGGCTTTGCA
CATCCTATCATATCCTTTAACCTCAGGC

Alignment

ORF - retro_sscr_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.11 %
• Parental protein coverage: 51.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSGGGGGSSG-AGGGPSCGTGSSRSGLLDKWKIDDKPVKIDKWDGSAV-KNSLDDSAKKVLLEKYKYVEN
          R..GGGGSS..AGGGPSCGTGSS....LD.WKIDDKPVK.D.WDGS.V.K.S..DSAKKVLLEKYKYVEN
Retrocopy RTSGGGGSSR<AGGGPSCGTGSSCGRSLDMWKIDDKPVKMDRWDGSLV>KSS-GDSAKKVLLEKYKYVEN

Parental  FGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLALCVITYFVMMG
          F.LID.RLT.CT.SCFFA.VA.I.DY.HPFPESKPVLAL....Y....G
Retrocopy FALIDSRLTVCTVSCFFATVASIGDYTHPFPESKPVLALHILSYPLTSG

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	33.98 RPM
SRP014902_testis	0.00 RPM	84.30 RPM
SRP018288_heart	0.03 RPM	70.17 RPM
SRP018288_kidney	0.00 RPM	112.39 RPM
SRP018288_liver	0.00 RPM	143.76 RPM
SRP018288_lung	0.00 RPM	114.76 RPM
SRP018856_adipose	0.05 RPM	53.64 RPM
SRP035408_brain	0.00 RPM	79.24 RPM
SRP035408_liver	0.00 RPM	124.94 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_648 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017127	1 retrocopy	retro_amel_1372,
Choloepus hoffmanni	ENSCHOG00000002974	3 retrocopies	retro_chof_1392, retro_chof_1588, retro_chof_2300,
Callithrix jacchus	ENSCJAG00000015576	2 retrocopies	retro_cjac_1500, retro_cjac_1929,
Cavia porcellus	ENSCPOG00000007273	2 retrocopies	retro_cpor_438, retro_cpor_578,
Dipodomys ordii	ENSDORG00000009679	1 retrocopy	retro_dord_423,
Homo sapiens	ENSG00000118363	4 retrocopies	retro_hsap_1488, retro_hsap_3137, retro_hsap_360, retro_hsap_723,
Gorilla gorilla	ENSGGOG00000014500	3 retrocopies	retro_ggor_1141, retro_ggor_372, retro_ggor_610,
Microcebus murinus	ENSMICG00000011153	2 retrocopies	retro_mmur_1566, retro_mmur_656,
Macaca mulatta	ENSMMUG00000010685	1 retrocopy	retro_mmul_26,
Monodelphis domestica	ENSMODG00000007130	2 retrocopies	retro_mdom_1127, retro_mdom_1454,
Mus musculus	ENSMUSG00000035227	1 retrocopy	retro_mmus_2088,
Nomascus leucogenys	ENSNLEG00000016949	2 retrocopies	retro_nleu_1710, retro_nleu_470,
Otolemur garnettii	ENSOGAG00000015621	1 retrocopy	retro_ogar_2649,
Ochotona princeps	ENSOPRG00000014459	2 retrocopies	retro_opri_266, retro_opri_948,
Pongo abelii	ENSPPYG00000003682	4 retrocopies	retro_pabe_1237, retro_pabe_2619, retro_pabe_2817, retro_pabe_625,
Pan troglodytes	ENSPTRG00000004073	1 retrocopy	retro_ptro_1007,
Rattus norvegicus	ENSRNOG00000018164	2 retrocopies	retro_rnor_2078, retro_rnor_2168,
Sarcophilus harrisii	ENSSHAG00000005389	1 retrocopy	retro_shar_787,
Sus scrofa	ENSSSCG00000014850	1 retrocopy	retro_sscr_648 ,
Ictidomys tridecemlineatus	ENSSTOG00000012647	2 retrocopies	retro_itri_1283, retro_itri_1584,
Tursiops truncatus	ENSTTRG00000005830	3 retrocopies	retro_ttru_1478, retro_ttru_1496, retro_ttru_1867,