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SDC1 syndecan 1 [ Homo sapiens (human) ]

Gene ID: 6382, updated on 21-Apr-2019

Summary

Official Symbol
SDC1provided by HGNC
Official Full Name
syndecan 1provided by HGNC
Primary source
HGNC:HGNC:10658
See related
Ensembl:ENSG00000115884 MIM:186355
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SDC; CD138; SYND1; syndecan
Summary
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]
Expression
Broad expression in esophagus (RPKM 110.6), skin (RPKM 101.9) and 14 other tissues See more
Orthologs

Genomic context

See SDC1 in Genome Data Viewer
Location:
2p24.1
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (20200797..20225433, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (20400558..20425194, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 140, pseudogene Neighboring gene RNA, U6 small nuclear 961, pseudogene Neighboring gene developmentally regulated GTP binding protein 1 pseudogene Neighboring gene RNA, U7 small nuclear 113 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of syndecan 1 (SDC1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env The V3 region (amino acids 298-329) of HIV-1 gp120 contains the syndecan-binding site for HIV-1 via 6-O sulfated motifs; a single conserved arginine (Arg-298) in the V3 region of gp120 governs HIV-1 binding to syndecans PubMed
Tat tat HIV-1 Tat tethered to the surface of syndecan-1 expression B-lymphoid cells or of peripheral blood monocytes promotes their transendothelial migration in vitro in response to CXCL12 or CCL5, respectively PubMed
tat Binding of HIV-1 Tat to heparan sulfate proteoglycans is competed out by the heparin-binding factor bFGF PubMed
tat Cell membrane heparin sulfate proteoglycans bind to the basic region of HIV-1 Tat (amino acids 49-57) and act as receptors for extracellular Tat uptake, an effect that may contribute to the angiogenic properties of Tat in promoting Kaposi's sarcoma PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystem (from REACTOME)
    A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystemThe biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence to the core protein. The ...
  • Arf6 trafficking events, organism-specific biosystem (from Pathway Interaction Database)
    Arf6 trafficking events, organism-specific biosystem
    Arf6 trafficking events
  • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
    Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
    Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell surface interactions at the vascular wall, organism-specific biosystem (from REACTOME)
    Cell surface interactions at the vascular wall, organism-specific biosystemLeukocyte extravasation is a rigorously controlled process that guides white cell movement from the vascular lumen to sites of tissue inflammation. The powerful adhesive interactions that are require...
  • Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystem (from REACTOME)
    Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystemChondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG). CS chains are unbranched polysaccharides of varying length containing two alternating monosaccharides: D-glucuronic acid (GlcA) and N-a...
  • Defective B3GALT6 causes EDSP2 and SEMDJL1, organism-specific biosystem (from REACTOME)
    Defective B3GALT6 causes EDSP2 and SEMDJL1, organism-specific biosystemThe biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence attached to the core prot...
  • Defective B3GAT3 causes JDSSDHD, organism-specific biosystem (from REACTOME)
    Defective B3GAT3 causes JDSSDHD, organism-specific biosystemGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferases1, 2 and 3 (B3GAT1-3) are involved in forming the linker tetrasaccharide present in heparan sulfate and chondroitin sulfate. Defects ...
  • Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystem (from REACTOME)
    Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystemEhlers?Danlos syndrome (EDS) is a group of inherited connective tissue disorders, caused by a defect in the synthesis of collagen types I or III. Abnormal collagen renders connective tissues more ela...
  • Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystem (from REACTOME)
    Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Ex...
  • Defective EXT2 causes exostoses 2, organism-specific biosystem (from REACTOME)
    Defective EXT2 causes exostoses 2, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 ...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases associated with glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
    Diseases associated with glycosaminoglycan metabolism, organism-specific biosystemA number of genetic disorders are caused by mutations in the genes encoding glycosyltransferases and sulfotransferases, enzymes responsible for the synthesis of glycosaminoglycans (GAGs) as well as ...
  • Diseases of glycosylation, organism-specific biosystem (from REACTOME)
    Diseases of glycosylation, organism-specific biosystemDiseases of glycosylation, usually referred to as congenital disorders of glycosylation (CDG), are rare inherited disorders ascribing defects of nucleotide-sugar biosynthesis and transport, glycosylt...
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Fluid shear stress and atherosclerosis, organism-specific biosystem (from KEGG)
    Fluid shear stress and atherosclerosis, organism-specific biosystemShear stress represents the frictional force that the flow of blood exerts at the endothelial surface of the vessel wall and plays a central role in vascular biology and contributes to the progress o...
  • Fluid shear stress and atherosclerosis, conserved biosystem (from KEGG)
    Fluid shear stress and atherosclerosis, conserved biosystemShear stress represents the frictional force that the flow of blood exerts at the endothelial surface of the vessel wall and plays a central role in vascular biology and contributes to the progress o...
  • Glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
    Glycosaminoglycan metabolism, organism-specific biosystemGlycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)...
  • HS-GAG biosynthesis, organism-specific biosystem (from REACTOME)
    HS-GAG biosynthesis, organism-specific biosystemHeparan sulfate (HS) and heparin (sometimes collectively called HS-GAG) consist of the disaccharide unit GlcNAc-GlcA (N-acetylglucosamine-glucuronic acid) connected by a beta1,4 linkage. Heparin is e...
  • HS-GAG degradation, organism-specific biosystem (from REACTOME)
    HS-GAG degradation, organism-specific biosystemLysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of heparan sulfate/heparin. Complete d...
  • Hemostasis, organism-specific biosystem (from REACTOME)
    Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
  • Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystem (from REACTOME)
    Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystemThe acronym HS-GAG is used to describe both heparin and heparan sulfate. HS-GAG is a member of the glycosaminoglycan family and consists of a variably sulfated repeating disaccharide unit, the most ...
  • Integrins in angiogenesis, organism-specific biosystem (from Pathway Interaction Database)
    Integrins in angiogenesis, organism-specific biosystem
    Integrins in angiogenesis
  • Malaria, organism-specific biosystem (from KEGG)
    Malaria, organism-specific biosystemPlasmodium protozoa are parasites that account for malaria infection. Sporozoite forms of the parasite are injected by mosquito bites under the skin and are carried to the liver where they develop in...
  • Malaria, conserved biosystem (from KEGG)
    Malaria, conserved biosystemPlasmodium protozoa are parasites that account for malaria infection. Sporozoite forms of the parasite are injected by mosquito bites under the skin and are carried to the liver where they develop in...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of carbohydrates, organism-specific biosystem (from REACTOME)
    Metabolism of carbohydrates, organism-specific biosystemThese pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the b...
  • Metabolism of fat-soluble vitamins, organism-specific biosystem (from REACTOME)
    Metabolism of fat-soluble vitamins, organism-specific biosystemVitamins A, D, E, and K are classified as fat-soluble. Metabolic pathways by which dietary precursors of vitamins A (Harrison 2005) and K(Shearer et al. 2012) are converted to active forms, and by wh...
  • Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, classified according to their solubility, either fat-soluble or water-soluble, that are either not synthesized or synthesized only in limited amount...
  • Non-integrin membrane-ECM interactions, organism-specific biosystem (from REACTOME)
    Non-integrin membrane-ECM interactions, organism-specific biosystemSeveral non-integrin membrane proteins interact with extracellular matrix proteins. Transmembrane proteoglycans may associate with integrins and growth factor receptors to influence their function, o...
  • Proteoglycans in cancer, organism-specific biosystem (from KEGG)
    Proteoglycans in cancer, organism-specific biosystemMany proteoglycans (PGs) in the tumor microenvironment have been shown to be key macromolecules that contribute to biology of various types of cancer including proliferation, adhesion, angiogenesis a...
  • Proteoglycans in cancer, conserved biosystem (from KEGG)
    Proteoglycans in cancer, conserved biosystemMany proteoglycans (PGs) in the tumor microenvironment have been shown to be key macromolecules that contribute to biology of various types of cancer including proliferation, adhesion, angiogenesis a...
  • Proteogylcan syndecan-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
    Proteogylcan syndecan-mediated signaling events, organism-specific biosystem
    Proteogylcan syndecan-mediated signaling events
  • Retinoid metabolism and transport, organism-specific biosystem (from REACTOME)
    Retinoid metabolism and transport, organism-specific biosystemVitamin A (all-trans-retinol) must be taken up, either as carotenes from plants, or as retinyl esters from animal food. The most prominent carotenes are alpha-carotene, lycopene, lutein, beta-cryptox...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Syndecan interactions, organism-specific biosystem (from REACTOME)
    Syndecan interactions, organism-specific biosystemSyndecans are type I transmembrane proteins, with an N-terminal ectodomain that contains several consensus sequences for glycosaminoglycan (GAG) attachment and a short C-terminal cytoplasmic domain. ...
  • Syndecan-1-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
    Syndecan-1-mediated signaling events, organism-specific biosystem
    Syndecan-1-mediated signaling events
  • Visual phototransduction, organism-specific biosystem (from REACTOME)
    Visual phototransduction, organism-specific biosystemVisual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are p...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Sertoli cell development IEA
Inferred from Electronic Annotation
more info
 
canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
glycosaminoglycan biosynthetic process TAS
Traceable Author Statement
more info
 
glycosaminoglycan catabolic process TAS
Traceable Author Statement
more info
 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
leukocyte migration TAS
Traceable Author Statement
more info
 
myoblast development ISS
Inferred from Sequence or Structural Similarity
more info
 
odontogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of exosomal secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of extracellular exosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to cAMP IEA
Inferred from Electronic Annotation
more info
 
response to calcium ion IEA
Inferred from Electronic Annotation
more info
 
response to glucocorticoid IEA
Inferred from Electronic Annotation
more info
 
response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
retinoid metabolic process TAS
Traceable Author Statement
more info
 
striated muscle cell development IEP
Inferred from Expression Pattern
more info
PubMed 
ureteric bud development IEA
Inferred from Electronic Annotation
more info
 
wound healing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi lumen TAS
Traceable Author Statement
more info
 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
lysosomal lumen TAS
Traceable Author Statement
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
protein-containing complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
syndecan-1
Names
CD138 antigen
heparan sulfate proteoglycan fibroblast growth factor receptor
syndecan proteoglycan 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_050639.1 RefSeqGene

    Range
    5001..29637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001006946.1NP_001006947.1  syndecan-1 precursor

    See identical proteins and their annotated locations for NP_001006947.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AJ551176, BC008765, BM785035, CB321970, X60306
    Consensus CDS
    CCDS1697.1
    UniProtKB/Swiss-Prot
    P18827
    Related
    ENSP00000370542.1, ENST00000381150.5
    Conserved Domains (1) summary
    pfam01034
    Location:245308
    Syndecan; Syndecan domain
  2. NM_002997.5NP_002988.4  syndecan-1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC104792
    Consensus CDS
    CCDS1697.1
    Related
    ENSP00000254351.4, ENST00000254351.9
    Conserved Domains (1) summary
    pfam01034
    Location:245308
    Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    20200797..20225433 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005262622.2XP_005262679.1  syndecan-1 isoform X3

    Conserved Domains (1) summary
    pfam01034
    Location:227290
    Syndecan; Syndecan domain
  2. XM_005262620.4XP_005262677.1  syndecan-1 isoform X1

    Conserved Domains (1) summary
    pfam01034
    Location:269332
    Syndecan; Syndecan domain
  3. XM_005262621.3XP_005262678.3  syndecan-1 isoform X2

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