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Aliases for APCS Gene

Aliases for APCS Gene

  • Amyloid P Component, Serum 2 3
  • 9.5S Alpha-1-Glycoprotein 2 3 4
  • SAP 3 4 6
  • Pentaxin-Related 2 3
  • PTX2 3 4
  • Epididymis Secretory Sperm Binding Protein Li 92n 3
  • Serum Amyloid P-Component 3
  • HEL-S-92n 3

External Ids for APCS Gene

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 candida glabrata and burns. Among its related pathways are Disease and RNA Polymerase I Promoter Opening. GO annotations related to this gene include unfolded protein binding. An important paralog of this gene is PTX3.

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

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

Genomics for APCS Gene

Genomic Location for APCS Gene

Start:
159,587,825 bp from pter
End:
159,588,871 bp from pter
Size:
1,047 bases
Orientation:
Plus strand

Genomic View for APCS Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for APCS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APCS Gene

Regulatory Elements 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
    Secondary Accessions:

    Protein attributes for APCS Gene

    Size:
    223 amino acids
    Molecular mass:
    25387 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Note=Binds 2 calcium ions per subunit.;
    Quaternary structure:
    • Homopentamer. Pentaxin (or pentraxin) 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

Proteomics data for APCS Gene at MOPED

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).
  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn51

Other Protein References for APCS Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for APCS Gene

Domains for APCS Gene

Protein Domains for APCS Gene

InterPro:
Blocks:
ProtoNet:

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
Domain:
  • Contains 1 pentaxin domain.:
    • P02743
Family:
  • Belongs to the pentaxin family.:
    • P02743
genes like me logo Genes that share domains with APCS: view

No data available for Gene Families for APCS Gene

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

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:0046790 virion binding IDA 23544079
GO:0051082 unfolded protein binding TAS 10812074
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:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for APCS Gene

Localization for APCS Gene

Subcellular locations from UniProtKB/Swiss-Prot for APCS Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for APCS Gene COMPARTMENTS Subcellular localization image for APCS gene
Compartment Confidence
extracellular 5
nucleus 2
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 --
GO:0005615 extracellular space IDA 14607961
GO:0005634 nucleus IDA 21630459
GO:0031012 colocalizes_with extracellular matrix IDA 20551380
GO:0043234 protein complex IEA --
genes like me logo Genes that share ontologies with APCS: view

Pathways for APCS Gene

SuperPathways for APCS Gene

Superpath Contained pathways
1 Disease
2 RNA Polymerase I Promoter Opening
.68
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:0006461 protein complex assembly --
GO:0006953 acute-phase response TAS 2987268
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

Compounds for APCS Gene

(1) HMDB Compounds for APCS Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2

(8) Novoseek inferred chemical compound relationships for APCS Gene

Compound -log(P) Hits PubMed IDs
saquinavir 67.7 1
indinavir 64.1 2
ganglioside 29.7 1
phosphatidylethanolamine 26 4
ceramide 25.2 1
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:

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 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 (52.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for APCS Gene

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.
genes like me logo Genes that share expressions with APCS: view

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 35
  • 99.1 (n)
  • 98.21 (a)
APCS 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia APCS 35
  • 81.08 (n)
  • 74.32 (a)
APCS 36
  • 74 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Apcs 35
  • 74.02 (n)
  • 69.37 (a)
Apcs 16
Apcs 36
  • 69 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia APCS 36
  • 60 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 50 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Apcs 35
  • 76.13 (n)
  • 72.07 (a)
chicken
(Gallus gallus)
Aves CRP 36
  • 45 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 38 (a)
ManyToMany
-- 36
  • 41 (a)
ManyToMany
-- 36
  • 42 (a)
ManyToMany
-- 36
  • 43 (a)
ManyToMany
-- 36
  • 37 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii crp 36
  • 31 (a)
ManyToMany
crp1 36
  • 31 (a)
ManyToMany
crp2 36
  • 35 (a)
ManyToMany
crp3 36
  • 32 (a)
ManyToMany
crp6 36
  • 30 (a)
ManyToMany
crp7 36
  • 32 (a)
ManyToMany
si:ch211-234p6.9 36
  • 27 (a)
ManyToMany
Species with no ortholog for APCS:
  • 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

Selected 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 Sequence Context AA Info Type MAF
rs2592882 -- 159,587,521(+) AGAGA(A/G)GGGGC upstream-variant-2KB
rs2808646 -- 159,586,134(+) GGATA(A/T)TAGAA upstream-variant-2KB
rs2808655 -- 159,587,565(+) CAGCC(C/T)AGCGC upstream-variant-2KB
rs2808661 -- 159,588,468(+) TTTGT(A/G)GAAGC reference, synonymous-codon
rs2808662 -- 159,589,031(+) ATATC(A/G)CAAAG downstream-variant-500B

Relevant External Links for APCS Gene

HapMap Linkage Disequilibrium report
APCS

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for APCS Gene

Disorders for APCS Gene

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.

(3) University of Copenhagen DISEASES for APCS Gene

(6) Novoseek inferred disease relationships for APCS Gene

Disease -log(P) Hits PubMed IDs
candidiasis 69.4 3
oropharyngeal 51.2 1
response acute phase 42.7 1
immunodeficiency 19.8 4
inflammation 19.3 1

Relevant External Links for APCS

Genetic Association Database (GAD)
APCS
Human Genome Epidemiology (HuGE) Navigator
APCS
genes like me logo Genes that share disorders with APCS: view

Publications for APCS Gene

  1. Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene disease. (PMID: 15649951) Soares M.L. … Buxbaum J.N. (Hum. Mol. Genet. 2005) 3 23 48
  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 E.C. … Colten H.R. (J. Biol. Chem. 1985) 2 3 4
  3. Isolation and characterization of the complete complementary and genomic DNA sequences of human serum amyloid P component. (PMID: 3029048) Ohnishi S. … Arao T. (J. Biochem. 1986) 3 4
  4. Protective molecules--C-reactive protein (CRP), serum amyloid P (SAP), pentraxin3 (PTX3), mannose-binding lectin (MBL), and apolipoprotein A1 (Apo A1), and their autoantibodies: prevalence and clinical significance in autoimmunity. (PMID: 16380821) Kravitz M.S. … Shoenfeld Y. (J. Clin. Immunol. 2005) 3 23
  5. Human plasma P component: isolation and characterization. (PMID: 81686) Thompson A.R. … Enfield D.L. (Biochemistry 1978) 3 4

Products for APCS Gene

Sources for APCS Gene

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