SDC1 syndecan 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SDC1provided by HGNC
Official Full Name: syndecan 1provided by HGNC
Primary source: HGNC:HGNC:10658
See related: Ensembl:ENSG00000115884 MIM:186355; AllianceGenome:HGNC:10658
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: mouse all
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Genomic context

Location:: 2p24.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (20200797..20225475, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (20234345..20259019, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (20400558..20425236, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Serum syndecan1 has the potential to reflect activity at diagnosis and predict death during follow-up in patients with ANCA-associated vasculitis.
Title: Serum syndecan1 has the potential to reflect activity at diagnosis and predict death during follow-up in patients with ANCA-associated vasculitis.
Sirt7/HIC1 complex participates in hyperglycaemia-mediated EndMT via modulation of SDC1 expression in diabetic kidney disease and metabolic memory.
Title: Sirt7/HIC1 complex participates in hyperglycaemia-mediated EndMT via modulation of SDC1 expression in diabetic kidney disease and metabolic memory.
The significance of Syndecan 1, a new marker for endothelial dysfunction, in cases of fetal growth retardation.
Title: The significance of Syndecan 1, a new marker for endothelial dysfunction, in cases of fetal growth retardation.
Soluble Endoglin and Syndecan-1 levels predicts the clinical outcome in COVID-19 patients.
Title: Soluble Endoglin and Syndecan-1 levels predicts the clinical outcome in COVID-19 patients.
CD9 co-operation with syndecan-1 is required for a major staphylococcal adhesion pathway.
Title: CD9 co-operation with syndecan-1 is required for a major staphylococcal adhesion pathway.
CLINICAL VALUE OF SYNDECAN-1 LEVELS IN TRAUMA BRAIN INJURY: A META-ANALYSIS.
Title: CLINICAL VALUE OF SYNDECAN-1 LEVELS IN TRAUMA BRAIN INJURY: A META-ANALYSIS.
Syndecan-1: A Novel Diagnostic and Therapeutic Target in Liver Diseases.
Title: Syndecan-1: A Novel Diagnostic and Therapeutic Target in Liver Diseases.
Neutrophil Extracellular Traps Are Induced by Coronavirus 2019 Disease-Positive Patient Plasma and Persist Longitudinally: A Possible Link to Endothelial Dysfunction as Measured by Syndecan-1.
Title: Neutrophil Extracellular Traps Are Induced by Coronavirus 2019 Disease-Positive Patient Plasma and Persist Longitudinally: A Possible Link to Endothelial Dysfunction as Measured by Syndecan-1.
SDC1 and ITGA2 as novel prognostic biomarkers for PDAC related to IPMN.
Title: SDC1 and ITGA2 as novel prognostic biomarkers for PDAC related to IPMN.
Binding of Trichinella spiralis C-type lectin with syndecan-1 on intestinal epithelial cells mediates larval invasion of intestinal epithelium.
Title: Binding of Trichinella spiralis C-type lectin with syndecan-1 on intestinal epithelial cells mediates larval invasion of intestinal epithelium.

Submit: New GeneRIF Correction See all GeneRIFs (360)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH16622 (e-PCR)
- UniSTS:41891

RH17406 (e-PCR)
- UniSTS:54750

RH67771 (e-PCR)
- UniSTS:30189

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cargo receptor activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Sertoli cell development	IEA Inferred from Electronic Annotation more info
involved_in canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in myoblast development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of extracellular exosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor-mediated endocytosis	IEA Inferred from Electronic Annotation more info
involved_in response to cAMP	IEA Inferred from Electronic Annotation more info
involved_in response to calcium ion	IEA Inferred from Electronic Annotation more info
involved_in response to glucocorticoid	IEA Inferred from Electronic Annotation more info
involved_in response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info
involved_in striated muscle cell development	IEP Inferred from Expression Pattern more info	PubMed
involved_in ureteric bud development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in external side of plasma membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in lysosomal lumen	TAS Traceable Author Statement more info
located_in plasma membrane	TAS Traceable Author Statement more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: syndecan-1

Names: CD138 antigen; heparan sulfate proteoglycan fibroblast growth factor receptor; syndecan proteoglycan 1

NCBI Reference Sequences (RefSeq)

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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

NG_050639.2 RefSeqGene

Range

5345..29678

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001006946.2 → NP_001006947.2 syndecan-1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AC104792

Consensus CDS

CCDS1697.1

UniProtKB/Swiss-Prot

D6W523, P18827, Q53QV0, Q546D3, Q96HB7

Related

ENSP00000370542.1, ENST00000381150.5

Conserved Domains (1) summary

pfam01034
Location:245 → 308

Syndecan; Syndecan domain
NM_002997.5 → NP_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

UniProtKB/Swiss-Prot

D6W523, P18827, Q53QV0, Q546D3, Q96HB7

Related

ENSP00000254351.4, ENST00000254351.9

Conserved Domains (1) summary

pfam01034
Location:245 → 308

Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

20200797..20225475 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005262622.3 → XP_005262679.1 syndecan-1 isoform X3

Conserved Domains (1) summary

pfam01034
Location:227 → 290

Syndecan; Syndecan domain
XM_005262620.5 → XP_005262677.1 syndecan-1 isoform X1

Conserved Domains (1) summary

pfam01034
Location:269 → 332

Syndecan; Syndecan domain
XM_005262621.3 → XP_005262678.3 syndecan-1 isoform X2