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Aliases for SDC1 Gene

Aliases for SDC1 Gene

  • Syndecan 1 2 3
  • Syndecan Proteoglycan 1 2 3
  • CD138 Antigen 3 4
  • SYND1 3 4
  • SDC 3 4
  • Heparan Sulfate Proteoglycan Fibroblast Growth Factor Receptor 3
  • Syndecan-1 3
  • Syndecan 3
  • CD138 3

External Ids for SDC1 Gene

Previous HGNC Symbols for SDC1 Gene

  • SDC

Previous GeneCards Identifiers for SDC1 Gene

  • GC02M020292
  • GC02M020469
  • GC02M020368
  • GC02M020385
  • GC02M020322
  • GC02M020264
  • GC02M020400
  • GC02M020158

Summaries for SDC1 Gene

Entrez Gene Summary for SDC1 Gene

  • The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for SDC1 Gene

SDC1 (Syndecan 1) is a Protein Coding gene. Diseases associated with SDC1 include monoclonal gammopathy of uncertain significance and breast carcinoma in situ. Among its related pathways are Signaling by GPCR and Proteoglycans in cancer. GO annotations related to this gene include protein C-terminus binding and glycoprotein binding. An important paralog of this gene is SDC4.

UniProtKB/Swiss-Prot for SDC1 Gene

  • Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix

Gene Wiki entry for SDC1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDC1 Gene

Genomics for SDC1 Gene

Regulatory Elements for SDC1 Gene

Transcription factor binding sites by QIAGEN in the SDC1 gene promoter:

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SDC1 Gene

Start:
20,200,797 bp from pter
End:
20,225,433 bp from pter
Size:
24,637 bases
Orientation:
Minus strand

Genomic View for SDC1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDC1 Gene

Proteins for SDC1 Gene

  • Protein details for SDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P18827-SDC1_HUMAN
    Recommended name:
    Syndecan-1
    Protein Accession:
    P18827
    Secondary Accessions:
    • D6W523
    • Q53QV0
    • Q546D3
    • Q96HB7

    Protein attributes for SDC1 Gene

    Size:
    310 amino acids
    Molecular mass:
    32462 Da
    Quaternary structure:
    • Interacts with CDCP1. Interacts (via C-terminus) with TIAM1 (via PDZ domain).

    Three dimensional structures from OCA and Proteopedia for SDC1 Gene

neXtProt entry for SDC1 Gene

Proteomics data for SDC1 Gene at MOPED

Post-translational modifications for SDC1 Gene

  • Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3
  • Glycosylation at Ser37, Asn43, Ser45, Ser47, Thr61, Thr72, Thr76, Ser77, Thr81, Thr122, Thr164, Ser165, Thr166, Ser171, Thr177, Thr180, Ser186, Thr188, Ser206, Ser216, and Thr240
  • Modification sites at PhosphoSitePlus

Other Protein References for SDC1 Gene

Antibody Products

  • R&D Systems Antibodies for SDC1 (Syndecan-1/CD138)
  • Cell Signaling Technology (CST) Antibodies for SDC1 (syndecan-1)

Protein Products

No data available for DME Specific Peptides for SDC1 Gene

Domains for SDC1 Gene

Gene Families for SDC1 Gene

HGNC:
  • CD :CD molecules
  • SDC :Proteoglycans / Cell Surface : Syndecans

Protein Domains for SDC1 Gene

Suggested Antigen Peptide Sequences for SDC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P18827

UniProtKB/Swiss-Prot:

SDC1_HUMAN :
  • P18827
Family:
  • Belongs to the syndecan proteoglycan family.
genes like me logo Genes that share domains with SDC1: view

Function for SDC1 Gene

Molecular function for SDC1 Gene

GENATLAS Biochemistry: syndecan,integral membrane heparan sulfate proteoglycan,matrix receptor,expressed in distinct stages of differentiation of normal lymphoid cells (pre-B) and in B chronic lymphoblastic leukemia (BCLL) in plamocytoid lymphomas and myelomas,underexpressed in squamous cell carcinoma of the head and neck
UniProtKB/Swiss-Prot Function: Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix

Gene Ontology (GO) - Molecular Function for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001948 glycoprotein binding IEA --
GO:0005515 protein binding IPI 15292202
GO:0008022 protein C-terminus binding IPI 16982797
GO:0008092 cytoskeletal protein binding --
genes like me logo Genes that share ontologies with SDC1: view
genes like me logo Genes that share phenotypes with SDC1: view

Animal Models for SDC1 Gene

MGI Knock Outs for SDC1:

Animal Model Products

miRNA for SDC1 Gene

miRNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for SDC1 Gene

Localization for SDC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDC1 Gene

Membrane; Single-pass type I membrane protein. Secreted. Note=Shedding of the ectodomain produces a soluble form.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SDC1 Gene COMPARTMENTS Subcellular localization image for SDC1 gene
Compartment Confidence
extracellular 5
golgi apparatus 4
lysosome 4
plasma membrane 4
vacuole 4
cytosol 3
cytoskeleton 2
endoplasmic reticulum 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
GO:0005796 Golgi lumen TAS --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 2324102
GO:0005925 focal adhesion IDA --
genes like me logo Genes that share ontologies with SDC1: view

Pathways for SDC1 Gene

genes like me logo Genes that share pathways with SDC1: view

Gene Ontology (GO) - Biological Process for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0001657 ureteric bud development IEA --
GO:0005975 carbohydrate metabolic process TAS --
GO:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
genes like me logo Genes that share ontologies with SDC1: view

Compounds for SDC1 Gene

(1) HMDB Compounds for SDC1 Gene

Compound Synonyms Cas Number PubMed IDs
Heparan sulfate
  • HHS 5
9050-30-0
genes like me logo Genes that share compounds with SDC1: view

Transcripts for SDC1 Gene

Unigene Clusters for SDC1 Gene

Syndecan 1:
Representative Sequences:

miRNA Products

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SDC1 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g ^ 7 ^ 8a · 8b
SP1: - - -
SP2: - - - - -
SP3: - - - - - - -
SP4: - -
SP5: - - - -
SP6: - -
SP7:

Relevant External Links for SDC1 Gene

GeneLoc Exon Structure for
SDC1
ECgene alternative splicing isoforms for
SDC1

Expression for SDC1 Gene

mRNA expression in normal human tissues for SDC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SDC1 Gene

This gene is overexpressed in Liver (8.6), Esophagus - Mucosa (8.2), Skin - Not Sun Exposed (Suprapubic) (7.8), and Skin - Sun Exposed (Lower leg) (7.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SDC1 Gene

SOURCE GeneReport for Unigene cluster for SDC1 Gene Hs.224607

genes like me logo Genes that share expressions with SDC1: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for SDC1 Gene

Orthologs for SDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SDC1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SDC1 35
  • 80.95 (n)
  • 74.68 (a)
SDC1 36
  • 74 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SDC1 35
  • 83.33 (n)
  • 80.65 (a)
SDC1 36
  • 81 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sdc1 35
  • 80.15 (n)
  • 77.02 (a)
Sdc1 16
Sdc1 36
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDC1 36
  • 40 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sdc1 35
  • 80.75 (n)
  • 77.74 (a)
chicken
(Gallus gallus)
Aves SDC1 35
  • 51.11 (n)
  • 46.67 (a)
SDC1 36
  • 33 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SDC1 36
  • 31 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Sdc 36
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sdn-1 36
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 36
  • 27 (a)
OneToMany
Species with no ortholog for SDC1:
  • 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • oppossum (Monodelphis domestica)
  • 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 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)
  • zebrafish (Danio rerio)

Evolution for SDC1 Gene

ENSEMBL:
Gene Tree for SDC1 (if available)
TreeFam:
Gene Tree for SDC1 (if available)

Paralogs for SDC1 Gene

Paralogs for SDC1 Gene

Pseudogenes.org Pseudogenes for SDC1 Gene

genes like me logo Genes that share paralogs with SDC1: view

Variants for SDC1 Gene

Sequence variations from dbSNP and Humsavar for SDC1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs9430 -- 20,201,851(-) AGCCC(A/G)TGTGA utr-variant-3-prime
rs1106111 -- 20,219,351(-) TGCCC(A/G)CCCTC intron-variant
rs1131351 -- 20,202,619(-) GAGTC(C/G)TGGGG utr-variant-3-prime
rs1131475 -- 20,201,000(-) GATCA(A/G)AGATG utr-variant-3-prime
rs1131478 -- 20,200,993(-) GATGC(A/C)CCACC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SDC1 Gene

Variant ID Type Subtype PubMed ID
esv29979 CNV Loss 17803354
nsv819169 CNV Gain 19587683
esv29269 CNV Loss 19812545

Relevant External Links for SDC1 Gene

HapMap Linkage Disequilibrium report
SDC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDC1 Gene

Disorders for SDC1 Gene

(2) University of Copenhagen DISEASES for SDC1 Gene

(3) Novoseek inferred disease relationships for SDC1 Gene

Disease -log(P) Hits PubMed IDs
carcinoma 26.6 6
tumors 2.02 2
breast cancer 0 1

Relevant External Links for SDC1

Genetic Association Database (GAD)
SDC1
Human Genome Epidemiology (HuGE) Navigator
SDC1
genes like me logo Genes that share disorders with SDC1: view

No data available for UniProtKB/Swiss-Prot for SDC1 Gene

Publications for SDC1 Gene

  1. Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. (PMID: 19107206) Dalmasso C. … Theodorou I. (PLoS ONE 2008) 3 48
  2. The mapping and visual ordering of the human syndecan-1 and N-myc genes near the telomeric region of chromosome 2p. (PMID: 9050911) Kaukonen J. … Palotie A. (Hum. Genet. 1997) 3 4
  3. Syndecan-1 expression is regulated in an isoform-specific manner by the farnesoid-X receptor. (PMID: 12660231) Anisfeld A.M. … Edwards P.A. (J. Biol. Chem. 2003) 3 23
  4. Induction of syndecan-1 expression in stromal fibroblasts promotes proliferation of human breast cancer cells. (PMID: 14744776) Maeda T. … Friedl A. (Cancer Res. 2004) 3 23
  5. Evaluation of the association with cervical cancer of polymorphisms in syndecan-1, a heparan sulfate proteoglycan involved with viral cell entry. (PMID: 18006945) Yu K.J. … Hildesheim A. (Cancer Epidemiol. Biomarkers Prev. 2007) 3 23

Products for SDC1 Gene

  • Addgene plasmids for SDC1

Sources for SDC1 Gene

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