Aliases for SPCS3 Gene

Aliases for SPCS3 Gene

  • Signal Peptidase Complex Subunit 3 2 3 4 5
  • SPC22/23 2 3 4
  • Microsomal Signal Peptidase 22/23 KDa Subunit 3 4
  • SPase 22/23 KDa Subunit 3 4
  • PRO3567 2 3
  • YLR066W 2 3
  • SPC22 3 4
  • SPC3 2 3
  • Signal Peptidase Complex Subunit 3 Homolog (S. Cerevisiae) 2
  • Microsomal Signal Peptidase 23 KDa Subunit 3
  • Signal Peptidase Complex Subunit 3 Homolog 3
  • SPase 22 KDa Subunit 3
  • EC 3.4.-.- 4
  • FLJ22649 2
  • SPC23 3
  • SPCS3 5

External Ids for SPCS3 Gene

Previous GeneCards Identifiers for SPCS3 Gene

  • GC04P177617
  • GC04P177478
  • GC04P177241
  • GC04P172992

Summaries for SPCS3 Gene

GeneCards Summary for SPCS3 Gene

SPCS3 (Signal Peptidase Complex Subunit 3) is a Protein Coding gene. Diseases associated with SPCS3 include Omsk Hemorrhagic Fever and Retinitis Pigmentosa 29. Among its related pathways are Incretin synthesis, secretion, and inactivation and Viral mRNA Translation. Gene Ontology (GO) annotations related to this gene include peptidase activity.

UniProtKB/Swiss-Prot Summary for SPCS3 Gene

  • Component of the microsomal signal peptidase complex which removes signal peptides and other N-terminal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum.
  • (Microbial infection) Plays an important role in virion production of flaviviruses such as West Nile virus, Japanese enchephalitis virus, Dengue virus type 2 and Yellow Fever virus.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPCS3 Gene

Genomics for SPCS3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPCS3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J176318 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +1.2 1235 5.6 BCLAF1 SP1 MYC ZNF600 ZNF592 POLR2A YY1 MXD4 SMAD5 BHLHE40 SPCS3-AS1 SPCS3 HSALNG0038702 VEGFC
GH04J176265 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.3 -49.9 -49932 10.5 ZNF600 JUND ATF2 CEBPB ZNF639 ZEB1 MAX EP300 PRDM1 RAD21 ASB5 lnc-SPATA4-1 SPCS3 HSALNG0038699 SPATA4
GH04J176295 Enhancer 0.3 Ensembl 12.1 -24.5 -24465 0.6 FOXA2 lnc-SPCS3-3 SPCS3 SPCS3-AS1 ASB5 HSALNG0038699
GH04J176357 Enhancer 0.7 Ensembl ENCODE 4.9 +38.7 38740 3 FOXA2 IRF4 BATF ATF2 JUNB ARID3A RUNX3 CEBPB WDR17 SPCS3 HSALNG0038703 lnc-SPCS3-1 VEGFC
GH04J176296 Enhancer 0.2 Ensembl 12.1 -23.6 -23565 0.8 lnc-SPCS3-3 SPCS3 SPCS3-AS1 piR-48950-156 ASB5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPCS3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPCS3

Top Transcription factor binding sites by QIAGEN in the SPCS3 gene promoter:
  • aMEF-2
  • Lhx3a
  • LHX3b
  • MEF-2
  • MEF-2A
  • Meis-1
  • Meis-1a
  • Meis-1b
  • Pbx1a
  • S8

Genomic Locations for SPCS3 Gene

Latest Assembly
chr4:176,319,966-176,332,245
(GRCh38/hg38)
Size:
12,280 bases
Orientation:
Plus strand

Previous Assembly
chr4:177,241,117-177,253,396
(GRCh37/hg19 by Entrez Gene)
Size:
12,280 bases
Orientation:
Plus strand

chr4:177,241,115-177,253,396
(GRCh37/hg19 by Ensembl)
Size:
12,282 bases
Orientation:
Plus strand

Genomic View for SPCS3 Gene

Genes around SPCS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPCS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPCS3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPCS3 Gene

Proteins for SPCS3 Gene

  • Protein details for SPCS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P61009-SPCS3_HUMAN
    Recommended name:
    Signal peptidase complex subunit 3
    Protein Accession:
    P61009
    Secondary Accessions:
    • P12280
    • Q9H0S7

    Protein attributes for SPCS3 Gene

    Size:
    180 amino acids
    Molecular mass:
    20313 Da
    Quaternary structure:
    • Component of the microsomal signal peptidase complex which consists of five members: SEC11A, SEC11C, SPCS1, SPCS2 and SPCS3.

neXtProt entry for SPCS3 Gene

Post-translational modifications for SPCS3 Gene

  • Glycosylation at Asn141
  • Ubiquitination at Lys49, Lys117, and Lys137
  • Modification sites at PhosphoSitePlus

Other Protein References for SPCS3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for SPCS3
  • Santa Cruz Biotechnology (SCBT) Antibodies for SPCS3

No data available for DME Specific Peptides for SPCS3 Gene

Domains & Families for SPCS3 Gene

Gene Families for SPCS3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SPCS3 Gene

InterPro:
Blocks:
  • Signal peptidase subunit

Suggested Antigen Peptide Sequences for SPCS3 Gene

GenScript: Design optimal peptide antigens:
  • Signal peptidase complex subunit 3 homolog (S. cerevisiae), isoform CRA_a (D3DP46_HUMAN)
  • Microsomal signal peptidase 22/23 kDa subunit (SPCS3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P61009

UniProtKB/Swiss-Prot:

SPCS3_HUMAN :
  • Belongs to the SPCS3 family.
Family:
  • Belongs to the SPCS3 family.
genes like me logo Genes that share domains with SPCS3: view

Function for SPCS3 Gene

Molecular function for SPCS3 Gene

UniProtKB/Swiss-Prot Function:
Component of the microsomal signal peptidase complex which removes signal peptides and other N-terminal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Plays an important role in virion production of flaviviruses such as West Nile virus, Japanese enchephalitis virus, Dengue virus type 2 and Yellow Fever virus.

Enzyme Numbers (IUBMB) for SPCS3 Gene

Phenotypes From GWAS Catalog for SPCS3 Gene

Gene Ontology (GO) - Molecular Function for SPCS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004252 serine-type endopeptidase activity IEA --
GO:0005515 protein binding IPI 25959826
GO:0008233 peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with SPCS3: view
genes like me logo Genes that share phenotypes with SPCS3: view

miRNA for SPCS3 Gene

miRTarBase miRNAs that target SPCS3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPCS3

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPCS3 Gene

Localization for SPCS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPCS3 Gene

Microsome membrane. Single-pass type II membrane protein. Endoplasmic reticulum membrane. Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPCS3 gene
Compartment Confidence
endoplasmic reticulum 4
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SPCS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA --
GO:0005787 signal peptidase complex IBA 21873635
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SPCS3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SPCS3 Gene

Pathways & Interactions for SPCS3 Gene

genes like me logo Genes that share pathways with SPCS3: view

Gene Ontology (GO) - Biological Process for SPCS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006465 signal peptide processing IBA 21873635
GO:0006508 proteolysis IEA,IDA 27499293
GO:0019082 viral protein processing IMP 27383988
GO:0045047 protein targeting to ER IBA 21873635
genes like me logo Genes that share ontologies with SPCS3: view

No data available for SIGNOR curated interactions for SPCS3 Gene

Drugs & Compounds for SPCS3 Gene

No Compound Related Data Available

Transcripts for SPCS3 Gene

mRNA/cDNA for SPCS3 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPCS3

Alternative Splicing Database (ASD) splice patterns (SP) for SPCS3 Gene

No ASD Table

Relevant External Links for SPCS3 Gene

GeneLoc Exon Structure for
SPCS3

Expression for SPCS3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPCS3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPCS3 Gene

This gene is overexpressed in Nasal epithelium (17.8) and Tlymphocyte (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPCS3 Gene



Protein tissue co-expression partners for SPCS3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPCS3

SOURCE GeneReport for Unigene cluster for SPCS3 Gene:

Hs.42194

Evidence on tissue expression from TISSUES for SPCS3 Gene

  • Nervous system(4.5)
  • Pancreas(4.3)
  • Liver(4.3)
  • Intestine(4.3)
  • Stomach(2)
genes like me logo Genes that share expression patterns with SPCS3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPCS3 Gene

Orthologs for SPCS3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPCS3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SPCS3 29 30
  • 99.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SPCS3 29 30
  • 96.11 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SPCS3 30
  • 96 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SPCS3 29 30
  • 95.74 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Spcs3 29
  • 93.52 (n)
Mouse
(Mus musculus)
Mammalia Spcs3 29 16 30
  • 93.33 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SPCS3 30
  • 91 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SPCS3 29 30
  • 85.56 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SPCS3 30
  • 89 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia spcs3 29
  • 78.15 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.25776 29
Zebrafish
(Danio rerio)
Actinopterygii spcs3 29 30
  • 76.11 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8388 29
Fruit Fly
(Drosophila melanogaster)
Insecta Spase22-23 29 30
  • 56.12 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea K12H4.4 29 30
  • 55.81 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SPC3 30
  • 23 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G05230 29
  • 51.35 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0131800 29
  • 50.56 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.5835 30
  • 53 (a)
OneToOne
Species where no ortholog for SPCS3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SPCS3 Gene

ENSEMBL:
Gene Tree for SPCS3 (if available)
TreeFam:
Gene Tree for SPCS3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPCS3: view image
Alliance of Genome Resources:
Additional Orthologs for SPCS3

Paralogs for SPCS3 Gene

Pseudogenes.org Pseudogenes for SPCS3 Gene

genes like me logo Genes that share paralogs with SPCS3: view

No data available for Paralogs for SPCS3 Gene

Variants for SPCS3 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPCS3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SPCS3 Gene

Variant ID Type Subtype PubMed ID
esv2728772 CNV deletion 23290073
esv34137 CNV loss 18971310
esv3603274 CNV gain 21293372
esv3894072 CNV loss 25118596

Variation tolerance for SPCS3 Gene

Residual Variation Intolerance Score: 55.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.07; 1.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPCS3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPCS3
Leiden Open Variation Database (LOVD)
SPCS3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPCS3 Gene

Disorders for SPCS3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SPCS3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
omsk hemorrhagic fever
  • ohf
retinitis pigmentosa 29
  • rp29
yellow fever
  • jungle yellow fever
- elite association - COSMIC cancer census association via MalaCards
Search SPCS3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPCS3

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SPCS3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPCS3 Gene

Publications for SPCS3 Gene

  1. Inverting the Topology of a Transmembrane Protein by Regulating the Translocation of the First Transmembrane Helix. (PMID: 27499293) Chen Q … Ye J (Molecular cell 2016) 3 4
  2. A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. (PMID: 27383988) Zhang R … Diamond MS (Nature 2016) 3 4
  3. Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency. (PMID: 24480542) Argente J … Pérez-Jurado LA (EMBO molecular medicine 2014) 2 3
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for SPCS3 Gene

Sources for SPCS3 Gene