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Aliases for APCS Gene

Aliases for APCS Gene

  • Amyloid P Component, Serum 2 3 5
  • 9.5S Alpha-1-Glycoprotein 2 3 4
  • Pentraxin-Related 2 3
  • Pentraxin-2 2 3
  • PTX2 3 4
  • SAP 3 4
  • Epididymis Secretory Sperm Binding Protein Li 92n 3
  • Serum Amyloid P-Component 3
  • Pentaxin-Related 3
  • HEL-S-92n 3

External Ids for APCS Gene

Previous GeneCards Identifiers for APCS Gene

  • GC01P157349
  • GC01P155289
  • GC01P156335
  • GC01P156774
  • GC01P156370
  • GC01P157824
  • GC01P130914

Summaries for APCS Gene

Entrez Gene Summary for APCS Gene

  • The protein encoded by this gene is a glycoprotein, belonging to the pentraxin family of proteins, which has a characteristic pentameric organization. These family members have considerable sequence homology which is thought to be the result of gene duplication. The binding of the encoded protein to proteins in the pathological amyloid cross-beta fold suggests its possible role as a chaperone. This protein is also thought to control the degradation of chromatin. It has been demonstrated that this protein binds to apoptotic cells at an early stage, which raises the possibility that it is involved in dealing with apoptotic cells in vivo. [provided by RefSeq, Sep 2008]

GeneCards Summary for APCS Gene

APCS (Amyloid P Component, Serum) is a Protein Coding gene. Diseases associated with APCS include Candidiasis and Carotenemia. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include calcium ion binding and unfolded protein binding. An important paralog of this gene is CRP.

UniProtKB/Swiss-Prot for APCS Gene

  • Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.

Gene Wiki entry for APCS Gene

Additional gene information for APCS Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APCS Gene

Genomics for APCS Gene

GeneHancer (GH) Regulatory Elements for APCS Gene

Promoters and enhancers for APCS 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
GH01I159587 Promoter 0.9 EPDnew 550.8 0.0 -18 0.1 FOXA2 RXRA TAF1 MAX REST RAD21 FOXA1 NR2F2 YY1 JUND APCS GC01M159580 GC01P159502
GH01I159596 Enhancer 0.9 Ensembl ENCODE 0.4 +10.1 10149 2.7 FOXA2 JUN MAX RAD21 YY1 GATA3 FOSL2 RXRA CEBPB EP300 OR10J6P OR10J5 OR10J3 DUSP23 SLAMF9 APCS GC01P159502
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around APCS on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the APCS gene promoter:

Genomic Locations for APCS Gene

Genomic Locations for APCS Gene
chr1:159,587,825-159,588,871
(GRCh38/hg38)
Size:
1,047 bases
Orientation:
Plus strand
chr1:159,557,615-159,558,661
(GRCh37/hg19)

Genomic View for APCS Gene

Genes around APCS on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for APCS Gene

Proteins for APCS Gene

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

    Protein Symbol:
    P02743-SAMP_HUMAN
    Recommended name:
    Serum amyloid P-component
    Protein Accession:
    P02743

    Protein attributes for APCS Gene

    Size:
    223 amino acids
    Molecular mass:
    25387 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    • Homopentamer. Pentraxin (or pentaxin) have a discoid arrangement of 5 non-covalently bound subunits.

    Three dimensional structures from OCA and Proteopedia for APCS Gene

neXtProt entry for APCS Gene

Post-translational modifications for APCS Gene

  • N-glycosylated with a complex biantennary oligosaccharide chain with a sialic acid at the end (disialo-SAP). Monosialo-SAP as well as asioalo-SAP are also detected (PubMed:15174148).
  • Glycosylation at posLast=5151
  • Modification sites at PhosphoSitePlus

Other Protein References for APCS Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for APCS Gene

Domains & Families for APCS Gene

Gene Families for APCS Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Potential drug targets
  • Predicted secreted proteins
  • Transporters

Protein Domains for APCS Gene

Suggested Antigen Peptide Sequences for APCS Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P02743

UniProtKB/Swiss-Prot:

SAMP_HUMAN :
  • Belongs to the pentraxin family.
Family:
  • Belongs to the pentraxin family.
genes like me logo Genes that share domains with APCS: view

Function for APCS Gene

Molecular function for APCS Gene

GENATLAS Biochemistry:
amyloid P component,serum,pentaxin (pentraxin) family
UniProtKB/Swiss-Prot Function:
Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.

Phenotypes From GWAS Catalog for APCS Gene

Gene Ontology (GO) - Molecular Function for APCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001849 complement component C1q binding IDA 23544079
GO:0005509 calcium ion binding IDA 23544079
GO:0030246 carbohydrate binding IEA --
GO:0042802 identical protein binding IPI 19372378
GO:0046790 virion binding IDA 23544079
genes like me logo Genes that share ontologies with APCS: view
genes like me logo Genes that share phenotypes with APCS: view

Animal Models for APCS Gene

MGI Knock Outs for APCS:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for APCS

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for APCS Gene

Localization for APCS Gene

Subcellular locations from UniProtKB/Swiss-Prot for APCS Gene

Secreted.

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 APCS gene
Compartment Confidence
extracellular 5
nucleus 5
plasma membrane 1
cytoskeleton 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for APCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS,IDA --
GO:0005615 extracellular space TAS,IDA 14607961
GO:0005634 nucleus HDA,IDA 21630459
GO:0031012 colocalizes_with extracellular matrix IDA 20551380
GO:0070062 extracellular exosome HDA,IDA 19056867
genes like me logo Genes that share ontologies with APCS: view

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

Pathways & Interactions for APCS Gene

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

Pathways by source for APCS Gene

2 Reactome pathways for APCS Gene

Gene Ontology (GO) - Biological Process for APCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002674 negative regulation of acute inflammatory response IC 14607961
GO:0006457 protein folding TAS 10812074
GO:0006953 acute-phase response TAS 2987268
GO:0044267 cellular protein metabolic process TAS --
GO:0044869 negative regulation by host of viral exo-alpha-sialidase activity IDA 23544079
genes like me logo Genes that share ontologies with APCS: view

No data available for SIGNOR curated interactions for APCS Gene

Drugs & Compounds for APCS Gene

(10) Drugs for APCS Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved, Investigational Pharma Target 202
Zinc Approved, Investigational Pharma Target 2430
calcium Approved Nutra 0
BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE Experimental Pharma Target 0
BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE Experimental Pharma Target 0

(4) Additional Compounds for APCS Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with APCS: view

Transcripts for APCS Gene

mRNA/cDNA for APCS Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(177) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for APCS Gene

Amyloid P component, serum:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for APCS

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

No ASD Table

Relevant External Links for APCS Gene

GeneLoc Exon Structure for
APCS
ECgene alternative splicing isoforms for
APCS

Expression for APCS Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for APCS Gene

This gene is overexpressed in Liver (x52.5).

Protein differential expression in normal tissues from HIPED for APCS Gene

This gene is overexpressed in Lung (6.3).

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



Protein tissue co-expression partners for APCS Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of APCS Gene:

APCS

SOURCE GeneReport for Unigene cluster for APCS Gene:

Hs.507080

mRNA Expression by UniProt/SwissProt for APCS Gene:

P02743-SAMP_HUMAN
Tissue specificity: Found in serum and urine.

Evidence on tissue expression from TISSUES for APCS Gene

  • Liver(4.9)
  • Bone marrow(4.3)
  • Muscle(4.2)
  • Blood(2.6)
  • Spleen(2.1)
  • Heart(2)
  • Kidney(2)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with APCS: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for APCS Gene

Orthologs for APCS Gene

This gene was present in the common ancestor of chordates.

Orthologs for APCS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia APCS 33 34
  • 99.1 (n)
cow
(Bos Taurus)
Mammalia APCS 33 34
  • 81.08 (n)
rat
(Rattus norvegicus)
Mammalia Apcs 33
  • 76.13 (n)
mouse
(Mus musculus)
Mammalia Apcs 33 16 34
  • 74.02 (n)
oppossum
(Monodelphis domestica)
Mammalia APCS 34
  • 60 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 50 (a)
OneToMany
chicken
(Gallus gallus)
Aves CRP 34
  • 45 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 43 (a)
ManyToMany
-- 34
  • 42 (a)
ManyToMany
-- 34
  • 41 (a)
ManyToMany
-- 34
  • 38 (a)
ManyToMany
-- 34
  • 37 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii crp2 34
  • 35 (a)
ManyToMany
crp3 34
  • 32 (a)
ManyToMany
crp7 34
  • 32 (a)
ManyToMany
crp 34
  • 31 (a)
ManyToMany
crp1 34
  • 31 (a)
ManyToMany
crp6 34
  • 30 (a)
ManyToMany
si:ch211-234p6.9 34
  • 27 (a)
ManyToMany
Species where no ortholog for APCS was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for APCS Gene

ENSEMBL:
Gene Tree for APCS (if available)
TreeFam:
Gene Tree for APCS (if available)

Paralogs for APCS Gene

Paralogs for APCS Gene

(2) SIMAP similar genes for APCS Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for APCS Gene

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

Variants for APCS Gene

Sequence variations from dbSNP and Humsavar for APCS Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
VAR_035814 A breast cancer sample p.Gly141Ser
rs1000102078 -- 159,588,417(+) G/T coding_sequence_variant, missense_variant
rs1002441835 -- 159,586,909(+) G/C upstream_transcript_variant
rs1002494109 -- 159,587,322(+) T/C upstream_transcript_variant
rs1003344971 -- 159,588,226(+) C/T coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv3578214 CNV loss 25503493
nsv1005195 CNV gain 25217958

Variation tolerance for APCS Gene

Residual Variation Intolerance Score: 42.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.51; 11.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for APCS Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
APCS

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APCS Gene

Disorders for APCS Gene

MalaCards: The human disease database

(6) MalaCards diseases for APCS Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
candidiasis
  • disseminated candidiasis
carotenemia
  • hypercarotinemia
candida glabrata
human immunodeficiency virus type 1
  • human immunodeficiency virus type 1, susceptibility to
splenic artery aneurysm
  • aneurysm of splenic artery
- elite association - COSMIC cancer census association via MalaCards
Search APCS in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SAMP_HUMAN
  • Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with amyloid deposits.

Additional Disease Information for APCS

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with APCS: view

No data available for Genatlas for APCS Gene

Publications for APCS Gene

  1. Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene disease. (PMID: 15649951) Soares ML … Buxbaum JN (Human molecular genetics 2005) 3 22 44 58
  2. Human serum amyloid P component. cDNA isolation, complete sequence of pre-serum amyloid P component, and localization of the gene to chromosome 1. (PMID: 2987268) Mantzouranis EC … Colten HR (The Journal of biological chemistry 1985) 2 3 4 58
  3. Integrative predictive model of coronary artery calcification in atherosclerosis. (PMID: 19948975) McGeachie M … Ramoni MF (Circulation 2009) 3 44 58
  4. Association of polymorphisms in complement component C3 gene with susceptibility to systemic lupus erythematosus. (PMID: 18174230) Miyagawa H … Horiuchi T (Rheumatology (Oxford, England) 2008) 3 44 58
  5. Serum amyloid P and cardiovascular disease in older men and women: results from the Cardiovascular Health Study. (PMID: 17138933) Jenny NS … Psaty BM (Arteriosclerosis, thrombosis, and vascular biology 2007) 3 22 58

Products for APCS Gene

  • Addgene plasmids for APCS

Sources for APCS Gene

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