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

    Gene ID: 7412, updated on 5-May-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VCAM1 in Genome Data Viewer
    Location:
    1p21.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100719742..100739045)
    RS_2023_10 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 ReSE screen-validated silencer GRCh37_chr1:101121642-101121817 Neighboring gene uncharacterized LOC124904231 Neighboring gene ribosomal protein L36a pseudogene 12 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:101177825-101179024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1386 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:101301135-101302334 Neighboring gene Sharpr-MPRA regulatory region 5467 Neighboring gene MPRA-validated peak338 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101359730-101360453 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101360454-101361176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1388 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

    Clone Names

    • MGC99561, DKFZp779G2333

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cell adhesion mediator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    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 amine metabolic process IDA
    Inferred from Direct Assay
    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
     
    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 mediated by integrin 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 inflammatory response IDA
    Inferred from Direct Assay
    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
     
    is_active_in plasma membrane IC
    Inferred by Curator
    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
      A8K6R7, B4DKS4, E9PDD1, P19320, Q6NUP8
      UniProtKB/TrEMBL
      Q53FL7
      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/TrEMBL
      Q53FL7
      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/TrEMBL
      Q53FL7
      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: GCF_000001405.40-RS_2023_10

    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)