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SDC1 syndecan 1 [ Homo sapiens (human) ]

Gene ID: 6382, updated on 13-Mar-2020

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
109.20200228 current GRCh38.p13 (GCF_000001405.39) 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 DRG1 pseudogene 1 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 Functions

What'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 PubChem

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
 
cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 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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