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Aliases for SDC1 Gene

Aliases for SDC1 Gene

  • Syndecan 1 2 3 5
  • 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 Granulomatous Endometritis and Diverticulitis. Among its related pathways are Cell surface interactions at the vascular wall and Glycosaminoglycan metabolism. GO annotations related to this gene include protein C-terminus binding and glycoprotein binding. An important paralog of this gene is SDC3.

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. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).

Gene Wiki entry for SDC1 Gene

Additional gene information for SDC1 Gene

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

Genomics for SDC1 Gene

Regulatory Elements for SDC1 Gene

Enhancers for SDC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H020205 2 FANTOM5 Ensembl ENCODE dbSUPER 39.9 +9.5 9450 21 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B SDC1 PUM2 RNU7-113P RNU6-961P LAPTM4A ENSG00000228950 RHOB GC02M020197
GH02H020181 2 FANTOM5 Ensembl ENCODE dbSUPER 21.5 +40.8 40821 5 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A ZBTB7B YY1 SLC30A9 ZNF766 SDC1 MATN3 TTC32 PUM2 RNU7-113P HS1BP3 RNU6-961P GC02M020197
GH02H020177 1.5 FANTOM5 ENCODE dbSUPER 25.6 +46.0 46007 3 ELF3 PKNOX1 FOXA2 SIN3A DMAP1 ZSCAN9 RAD21 YY1 ZNF143 FOS SDC1 RNU7-113P MATN3 RNU6-961P GC02M020197
GH02H020230 1.7 FANTOM5 Ensembl ENCODE dbSUPER 19.5 -8.8 -8770 7 ELF3 TBP PKNOX1 SIN3A RAD21 RFX5 ZNF366 SCRT2 ZNF143 FOS SDC1 RNU6-961P ENSG00000269976 GC02M020239
GH02H020135 1.5 Ensembl ENCODE dbSUPER 18.9 +89.2 89174 1 PKNOX1 ARID4B SIN3A DMAP1 YBX1 ZNF2 ZNF143 RUNX3 MXD4 REST SDC1 RNU6-961P MATN3 GC02P020141 ENSG00000234378
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SDC1 on UCSC Golden Path with GeneCards custom track

Promoters for SDC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000113757 833 2401 MLX ARID4B SIN3A DMAP1 ZNF2 SLC30A9 GLIS2 ZNF143 SP3 SP5

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

Genomic Location for SDC1 Gene

Chromosome:
2
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

Genes around SDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

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, isoforms=77, isoforms=122, isoforms=188, Ser206, Ser216, and Thr240
  • Modification sites at PhosphoSitePlus

Protein Products

No data available for DME Specific Peptides for SDC1 Gene

Domains & Families for SDC1 Gene

Gene Families for SDC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • CD markers
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins
  • Transporters

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 :
  • Belongs to the syndecan proteoglycan family.
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. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).

Phenotypes From GWAS Catalog for SDC1 Gene

Gene Ontology (GO) - Molecular Function for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15292202
GO:0008022 protein C-terminus binding IPI 16982797
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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SDC1
  • Applied Biological Materials Clones for SDC1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets 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. Secreted, exosome. Note=Shedding of the ectodomain produces a soluble form. {ECO:0000269 PubMed:9169435}.

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 SDC1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
lysosome 5
golgi apparatus 5
cytosol 3
cytoskeleton 2
nucleus 2
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Focal adhesion sites (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005796 Golgi lumen TAS --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 2324102
GO:0009897 external side of plasma membrane IEA --
genes like me logo Genes that share ontologies with SDC1: view

Pathways & Interactions 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:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
GO:0006954 inflammatory response IEA --
genes like me logo Genes that share ontologies with SDC1: view

No data available for SIGNOR curated interactions for SDC1 Gene

Drugs & Compounds for SDC1 Gene

(1) Additional Compounds for SDC1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
heparan sulfate
  • alpha-Idosane
  • Heparan N-sulfate
  • Heparan N-sulphate
  • Heparan sulfate
  • Heparan sulphate
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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SDC1
  • Applied Biological Materials Clones for SDC1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x8.6), Esophagus - Mucosa (x8.2), Skin - Not Sun Exposed (Suprapubic) (x7.8), and Skin - Sun Exposed (Lower leg) (x7.1).

Protein differential expression in normal tissues from HIPED for SDC1 Gene

This gene is overexpressed in Hair follicle (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SDC1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SDC1 Gene:

SDC1

SOURCE GeneReport for Unigene cluster for SDC1 Gene:

Hs.224607

Evidence on tissue expression from TISSUES for SDC1 Gene

  • Kidney(4.6)
  • Liver(4.6)
  • Lung(3.7)
  • Bone marrow(3.3)
  • Skin(3.1)
  • Intestine(3)
  • Blood(2.7)
  • Lymph node(2.6)
  • Spleen(2.2)
  • Stomach(2.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with SDC1: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
dog
(Canis familiaris)
Mammalia SDC1 33 34
  • 83.33 (n)
cow
(Bos Taurus)
Mammalia SDC1 33 34
  • 80.95 (n)
rat
(Rattus norvegicus)
Mammalia Sdc1 33
  • 80.75 (n)
mouse
(Mus musculus)
Mammalia Sdc1 33 16 34
  • 80.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SDC1 34
  • 40 (a)
OneToOne
chicken
(Gallus gallus)
Aves SDC1 33 34
  • 51.11 (n)
lizard
(Anolis carolinensis)
Reptilia SDC1 34
  • 31 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Sdc 34
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sdn-1 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 34
  • 27 (a)
OneToMany
Species where no ortholog for SDC1 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)
  • 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

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
rs777304384 Likely benign 20,204,252(+) AAGTG(A/G)AGGGG reference, missense
rs1000022786 -- 20,200,915(+) ACCCC(C/T)GAGTC utr-variant-3-prime
rs1000024390 -- 20,207,701(+) ACTCC(A/G)TCTCA intron-variant, upstream-variant-2KB
rs1000269171 -- 20,210,140(+) AATTC(C/T)AAACC intron-variant
rs1000615386 -- 20,202,159(+) GGGAA(C/G)CAAGA utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
dgv3737n100 CNV gain 25217958
dgv6731n54 CNV gain 21841781
esv29269 CNV loss 19812545
esv29979 CNV loss 17803354
esv3402038 CNV duplication 20981092
nsv1072400 CNV deletion 25765185
nsv581157 CNV loss 21841781
nsv581160 CNV gain+loss 21841781
nsv581161 CNV loss 21841781
nsv581162 CNV gain+loss 21841781
nsv581163 CNV gain 21841781
nsv581164 CNV loss 21841781
nsv819169 CNV gain 19587683

Variation tolerance for SDC1 Gene

Residual Variation Intolerance Score: 60.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.37; 53.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SDC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDC1

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

Disorders for SDC1 Gene

MalaCards: The human disease database

(19) MalaCards diseases for SDC1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
granulomatous endometritis
diverticulitis
multiple myeloma
  • plasma cell neoplasm
mucinous bronchioloalveolar adenocarcinoma
  • bronchiolo-alveolar carcinoma, mucinous
diffuse large b-cell lymphoma
  • dlbcl
- elite association - COSMIC cancer census association via MalaCards
Search SDC1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SDC1

Genetic Association Database (GAD)
SDC1
Human Genome Epidemiology (HuGE) Navigator
SDC1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SDC1
genes like me logo Genes that share disorders with SDC1: view

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

Publications for SDC1 Gene

  1. The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. (PMID: 23395182) Liu X … Fuentes EJ (Structure (London, England : 1993) 2013) 3 4 60
  2. Syndecan-syntenin-ALIX regulates the biogenesis of exosomes. (PMID: 22660413) Baietti MF … David G (Nature cell biology 2012) 3 4 60
  3. Bone marrow stromal cell interaction reduces syndecan-1 expression and induces kinomic changes in myeloma cells. (PMID: 20307537) Fuhler GM … Bos NA (Experimental cell research 2010) 3 22 60
  4. Syndecan-1 regulates alphavbeta3 and alphavbeta5 integrin activation during angiogenesis and is blocked by synstatin, a novel peptide inhibitor. (PMID: 19255147) Beauvais DM … Rapraeger AC (The Journal of experimental medicine 2009) 3 22 60
  5. 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 … ANRS Genome Wide Association 01 (PloS one 2008) 3 45 60

Products for SDC1 Gene

  • Addgene plasmids for SDC1

Sources for SDC1 Gene

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