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VCAM1 vascular cell adhesion molecule 1 [ Homo sapiens (human) ]

Gene ID: 7412, updated on 22-Jan-2023

Summary

Official Symbol
VCAM1provided by HGNC
Official Full Name
vascular cell adhesion molecule 1provided by HGNC
Primary source
HGNC:HGNC:12663
See related
Ensembl:ENSG00000162692 MIM:192225; AllianceGenome:HGNC:12663
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
CD106; INCAM-100
Summary
This gene is a member of the Ig superfamily and encodes a cell surface sialoglycoprotein expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2010]
Expression
Biased expression in spleen (RPKM 208.8), lymph node (RPKM 52.3) and 7 other tissues See more
Orthologs
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Genomic context

See VCAM1 in Genome Data Viewer
Location:
1p21.2
Exon count:
9
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100719742..100739045)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (100568139..100587438)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (101185298..101204601)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904231 Neighboring gene ribosomal protein L36a pseudogene 12 Neighboring gene Sharpr-MPRA regulatory region 5467 Neighboring gene exostosin like glycosyltransferase 2 Neighboring gene solute carrier family 30 member 7 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 68

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

EBI GWAS Catalog

Description
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1/HCV co-infection correlates with elevated ICAM1 and VCAM1 serum levels, which relates to disease progression PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 activates human brain micro vascular endothelial cells (HBMEC) via CD4 in upregulating ICAM-1 and VCAM-1 expression, IL-6 secretion and increased monocyte transmigration across monolayers PubMed
Tat tat HIV-1 Tat upregulates VCAM1 protein expression in hCMEC/D3 cells PubMed
tat HIV-1 Tat upregulates VCAM1 mRNA and protein expression in CRT-MG human astroglioma cells PubMed
tat HIV-1 Tat upregulates the expression of VCAM-1 in endothelial cells and astrocytes, an effect that is in part regulated by NF-kappa B and may be associated with AIDS-related Kaposi's sarcoma PubMed
tat Cell-permeable SOD inhibits the activation of MAP kinases including ERK, JNK and p38 and the upregulation of ICAM-1 and VCAM-1 by HIV-1 Tat PubMed
tat HIV-1 Tat-induced upregulation of VCAM-1/ICAM-1 is blocked by NADPH oxidase inhibitor PubMed
Vpu vpu HIV-1 Vpu upregulates CD40 expression, which enhances efficient expression of VCAM-1 in endothelial cells 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

Clone Names

  • MGC99561, DKFZp779G2333

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell adhesion molecule binding IDA
Inferred from Direct Assay
more info
PubMed 
enables cell adhesion molecule binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables integrin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables integrin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables integrin binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables primary amine oxidase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in B cell differentiation IC
Inferred by Curator
more info
PubMed 
involved_in acute inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in aging IEA
Inferred from Electronic Annotation
more info
 
involved_in amine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in calcium-mediated signaling using intracellular calcium source IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cardiac neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell chemotaxis IEA
Inferred from Electronic Annotation
more info
 
involved_in cell-cell adhesion in response to extracellular stimulus IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cell-matrix adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to amyloid-beta IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cellular response to tumor necrosis factor IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to vascular endothelial growth factor stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in chronic inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IDA
Inferred from Direct Assay
more info
PubMed 
involved_in heterotypic cell-cell adhesion IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in innervation IEA
Inferred from Electronic Annotation
more info
 
involved_in leukocyte cell-cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in leukocyte tethering or rolling IDA
Inferred from Direct Assay
more info
PubMed 
involved_in leukocyte tethering or rolling IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in membrane to membrane docking IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in positive regulation of T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to ethanol IEA
Inferred from Electronic Annotation
more info
 
involved_in response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
involved_in response to ionizing radiation IEA
Inferred from Electronic Annotation
more info
 
involved_in response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
involved_in response to nicotine IEA
Inferred from Electronic Annotation
more info
 
involved_in response to nutrient IEA
Inferred from Electronic Annotation
more info
 
involved_in response to zinc ion IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
part_of alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in apical part of cell IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular exosome HDA PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
located_in filopodium IDA
Inferred from Direct Assay
more info
PubMed 
located_in microvillus IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in podosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in sarcolemma IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
vascular cell adhesion protein 1
Names
CD106 antigen

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_023034.2 RefSeqGene

    Range
    5002..24305
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001078.4NP_001069.1  vascular cell adhesion protein 1 isoform a precursor

    See identical proteins and their annotated locations for NP_001069.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the predominant, full-length isoform (a).
    Source sequence(s)
    BC017276, BF791565, DB096825
    Consensus CDS
    CCDS773.1
    UniProtKB/Swiss-Prot
    P19320, Q6NUP8
    Related
    ENSP00000294728.2, ENST00000294728.7
    Conserved Domains (5) summary
    cd07689
    Location:116214
    Ig_VCAM-1; Immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1, CD106) and intercellular cell adhesion molecule-1 (ICAM-1, CD54) and similar domains
    smart00408
    Location:238298
    IGc2; Immunoglobulin C-2 Type
    smart00409
    Location:33112
    IG; Immunoglobulin
    smart00410
    Location:519596
    IG_like; Immunoglobulin like
    cl28434
    Location:313399
    I-set; Immunoglobulin I-set domain
  2. NM_001199834.2NP_001186763.1  vascular cell adhesion protein 1 isoform c precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame segment in the CDS compared to transcript variant 1. The resulting isoform (c) lacks an internal segment compared to isoform a.
    Source sequence(s)
    AK296692, BC017276, BF968655
    Consensus CDS
    CCDS55617.1
    UniProtKB/Swiss-Prot
    P19320
    Related
    ENSP00000359137.3, ENST00000370119.8
    Conserved Domains (4) summary
    cd07689
    Location:54152
    Ig2_VCAM-1; Second immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1, CD106) and intercellular cell adhesion molecule-1 (ICAM-1, CD54) and similar proteins
    smart00408
    Location:176236
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:259337
    IG_like; Immunoglobulin like
    pfam13927
    Location:546610
    Ig_3; Immunoglobulin domain
  3. NM_080682.3NP_542413.1  vascular cell adhesion protein 1 isoform b precursor

    See identical proteins and their annotated locations for NP_542413.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the CDS compared to transcript variant 1. The resulting isoform (b) lacks an internal segment compared to isoform a.
    Source sequence(s)
    BC017276, BF791565, DB096825, M30257
    Consensus CDS
    CCDS774.1
    UniProtKB/Swiss-Prot
    P19320
    Related
    ENSP00000304611.2, ENST00000347652.6
    Conserved Domains (5) summary
    cd07689
    Location:116214
    Ig2_VCAM-1; Second immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1, CD106) and intercellular cell adhesion molecule-1 (ICAM-1, CD54) and similar proteins
    smart00408
    Location:238298
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:33112
    IG_like; Immunoglobulin like
    pfam00047
    Location:3597
    ig; Immunoglobulin domain
    pfam13927
    Location:516580
    Ig_3; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    100719742..100739045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    100568139..100587438
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)