VCAM1 Gene (Protein Coding)

Vascular Cell Adhesion Molecule 1

GC01P100719
GIFtS:
47
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 iso... See more...

Aliases for VCAM1 Gene

Aliases for VCAM1 Gene

  • Vascular Cell Adhesion Molecule 1 2 3 5
  • Vascular Cell Adhesion Protein 1 3 4
  • CD106 Antigen 3 4
  • INCAM-100 3 4
  • V-CAM 1 4
  • VCAM-1 4
  • CD106 3

External Ids for VCAM1 Gene

Previous GeneCards Identifiers for VCAM1 Gene

  • GC01P101976
  • GC01P100366
  • GC01P100476
  • GC01P100648
  • GC01P100897
  • GC01P101185
  • GC01P099309

Summaries for VCAM1 Gene

Entrez Gene Summary for VCAM1 Gene

  • 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]

GeneCards Summary for VCAM1 Gene

VCAM1 (Vascular Cell Adhesion Molecule 1) is a Protein Coding gene. Diseases associated with VCAM1 include Viral Encephalitis and Mooren's Ulcer. Among its related pathways are Interferon gamma signaling and p70S6K Signaling. Gene Ontology (GO) annotations related to this gene include integrin binding and primary amine oxidase activity. An important paralog of this gene is CNTN3.

UniProtKB/Swiss-Prot Summary for VCAM1 Gene

  • Important in cell-cell recognition. Appears to function in leukocyte-endothelial cell adhesion. Interacts with integrin alpha-4/beta-1 (ITGA4/ITGB1) on leukocytes, and mediates both adhesion and signal transduction. The VCAM1/ITGA4/ITGB1 interaction may play a pathophysiologic role both in immune responses and in leukocyte emigration to sites of inflammation.

Gene Wiki entry for VCAM1 Gene

Additional gene information for VCAM1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VCAM1 Gene

Genomics for VCAM1 Gene

GeneHancer (GH) Regulatory Elements for VCAM1 Gene

Promoters and enhancers for VCAM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J100719 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 771.5 +1.6 1581 3.6 RELA ZNF652 ZNF687 POLR2A IKZF1 CEBPA IKZF2 DPF2 EED RUNX3 VCAM1 ENSG00000228086 GPR88 HSALNG0005548
GH01J100621 Enhancer 1.1 Ensembl ENCODE dbSUPER 29.4 -92.9 -92939 11 ZBTB33 IKZF1 GLIS2 ZIC2 POLR2A PRDM10 IKZF2 PATZ1 CEBPB HDAC1 ENSG00000285525 VCAM1 GPR88 LINC01349 RTCA piR-32461-005
GH01J100712 Enhancer 0.8 Ensembl ENCODE dbSUPER 21.2 -5.8 -5840 2.8 MIXL1 ZNF316 CREB1 ATF2 ATF7 piR-38426-001 piR-59928-010 VCAM1
GH01J100643 Enhancer 0.8 Ensembl ENCODE dbSUPER 19.2 -76.1 -76123 1 SP1 YY1 GABPA RAD21 HNF4A RXRA TAF1 VCAM1 GPR88 LINC01349 piR-58308-013
GH01J100348 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 4.2 -367.5 -367450 7.2 SIN3A ZBTB40 CTCF ZBTB6 SMARCE1 POLR2A CTBP1 MYC CC2D1A NFYC CDC14A lnc-DBT-7 TRMT13 ENSG00000235795 SLC30A7 BRI3P1 MFSD14A HNRNPA1P68 EXTL2 LOC646970
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VCAM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VCAM1 gene promoter:
  • CREB
  • deltaCREB
  • IRF-1
  • PPAR-gamma2
  • STAT1

Genomic Locations for VCAM1 Gene

Genomic Locations for VCAM1 Gene
chr1:100,719,640-100,739,045
(GRCh38/hg38)
Size:
19,406 bases
Orientation:
Plus strand
chr1:101,185,196-101,204,601
(GRCh37/hg19)
Size:
19,406 bases
Orientation:
Plus strand

Genomic View for VCAM1 Gene

Genes around VCAM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCAM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCAM1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for VCAM1 Gene

Proteins for VCAM1 Gene

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  • Protein details for VCAM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P19320-VCAM1_HUMAN
    Recommended name:
    Vascular cell adhesion protein 1
    Protein Accession:
    P19320
    Secondary Accessions:
    • A8K6R7
    • B4DKS4
    • E9PDD1
    • Q6NUP8

    Protein attributes for VCAM1 Gene

    Size:
    739 amino acids
    Molecular mass:
    81276 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for VCAM1 Gene

    Alternative splice isoforms for VCAM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VCAM1 Gene

Protein Expression for VCAM1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for VCAM1 Gene

  • Sialoglycoprotein.
  • Glycosylation at Asn273, Asn365, Asn417, Asn463, Asn531, and Asn561
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • VCAM1_HUMAN (1984)

Other Protein References for VCAM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for VCAM1

Protein Products

  • Abcam proteins for VCAM1

Assay Products

  • Abcam assays for VCAM1

No data available for DME Specific Peptides for VCAM1 Gene

Domains & Families for VCAM1 Gene

Gene Families for VCAM1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • CD markers
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for VCAM1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VCAM1 Gene

GenScript: Design optimal peptide antigens:
  • Vascular cell adhesion molecule 1 (F2YYR6_HUMAN)
  • Vascular cell adhesion molecule 1 (F8UU18_HUMAN)
  • Vascular cell adhesion molecule 1 (F8UV74_HUMAN)
  • INCAM-100 (VCAM1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P19320

UniProtKB/Swiss-Prot:

VCAM1_HUMAN :
  • Either the first or the fourth Ig-like C2-type domain is required for VLA4-dependent cell adhesion.
Domain:
  • Either the first or the fourth Ig-like C2-type domain is required for VLA4-dependent cell adhesion.
genes like me logo Genes that share domains with VCAM1: view

Function for VCAM1 Gene

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Molecular function for VCAM1 Gene

UniProtKB/Swiss-Prot Function:
Important in cell-cell recognition. Appears to function in leukocyte-endothelial cell adhesion. Interacts with integrin alpha-4/beta-1 (ITGA4/ITGB1) on leukocytes, and mediates both adhesion and signal transduction. The VCAM1/ITGA4/ITGB1 interaction may play a pathophysiologic role both in immune responses and in leukocyte emigration to sites of inflammation.
UniProtKB/Swiss-Prot Induction:
By cytokines (e.g. IL-1, TNF-alpha).
GENATLAS Biochemistry:
cell adhesion molecule,vascular 1,with alternative splicing forms,ligand for ITGA4 (VLA4A),endothelial sialoglycoprotein

Phenotypes From GWAS Catalog for VCAM1 Gene

Gene Ontology (GO) - Molecular Function for VCAM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding IEA,IMP 19738201
GO:0008131 primary amine oxidase activity IDA 23474851
GO:0050839 cell adhesion molecule binding IPI 12082081
genes like me logo Genes that share ontologies with VCAM1: view
genes like me logo Genes that share phenotypes with VCAM1: view

Animal Models for VCAM1 Gene

MGI Knock Outs for VCAM1:

Animal Model Products

CRISPR Products

miRNA for VCAM1 Gene

miRTarBase miRNAs that target VCAM1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VCAM1 Gene

Localization for VCAM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VCAM1 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VCAM1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
endosome 5
golgi apparatus 5
cytoskeleton 4
nucleus 3
peroxisome 2
cytosol 2
mitochondrion 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VCAM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002102 podosome IDA 15220135
GO:0005615 extracellular space IEA,IDA 9290466
GO:0005769 early endosome IDA 23474851
GO:0005783 endoplasmic reticulum IDA 23474851
GO:0005794 Golgi apparatus IDA 23474851
genes like me logo Genes that share ontologies with VCAM1: view

Pathways & Interactions for VCAM1 Gene

genes like me logo Genes that share pathways with VCAM1: view

Pathways by source for VCAM1 Gene

3 Qiagen pathways for VCAM1 Gene
  • LDL Oxidation in Atherogenesis
  • Renin-Angiotensin Pathway
  • Transendothelial Migration of Leukocytes
2 Cell Signaling Technology pathways for VCAM1 Gene

Gene Ontology (GO) - Biological Process for VCAM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0002526 acute inflammatory response IEA --
GO:0002544 chronic inflammatory response IEA --
GO:0007155 cell adhesion IDA,IEA 16809613
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IDA 1715889
genes like me logo Genes that share ontologies with VCAM1: view

No data available for SIGNOR curated interactions for VCAM1 Gene

Drugs & Compounds for VCAM1 Gene

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  1. Drug

(87) Drugs for VCAM1 Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ethanol Approved Pharma Target 3120
Carvedilol Approved, Investigational Pharma Antagonist, Target, inhibitor 191
Clove oil Approved Nutra Target, antagonist 0
Succinobucol Investigational Pharma Target 0
AGI-1067, SUCCINOBUCOL Pharma 0

(73) Additional Compounds for VCAM1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
8-Hydroxycarvedilol
genes like me logo Genes that share compounds with VCAM1: view

Transcripts for VCAM1 Gene

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mRNA/cDNA for VCAM1 Gene

(3) REFSEQ mRNAs :
(14) Additional mRNA sequences :
(152) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VCAM1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b
SP1: -
SP2: - -
SP3: - -
SP4: - -
SP5: - -
SP6:

Relevant External Links for VCAM1 Gene

GeneLoc Exon Structure for
VCAM1
ECgene alternative splicing isoforms for
VCAM1

Expression for VCAM1 Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VCAM1 Gene

mRNA expression in normal human tissues for VCAM1 Gene
mRNA expression by GTEx for VCAM1 GenemRNA expression by BioGPS for VCAM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VCAM1 Gene

This gene is overexpressed in Spleen (x15.9), Adrenal Gland (x4.2), and Kidney - Cortex (x4.0).

Protein differential expression in normal tissues from HIPED for VCAM1 Gene

This gene is overexpressed in Serum (45.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VCAM1 Gene



NURSA nuclear receptor signaling pathways regulating expression of VCAM1 Gene:

VCAM1

SOURCE GeneReport for Unigene cluster for VCAM1 Gene:

Hs.109225

mRNA Expression by UniProt/SwissProt for VCAM1 Gene:

P19320-VCAM1_HUMAN
Tissue specificity: Expressed on inflamed vascular endothelium, as well as on macrophage-like and dendritic cell types in both normal and inflamed tissue.

Evidence on tissue expression from TISSUES for VCAM1 Gene

  • Heart(4.8)
  • Bone marrow(4.6)
  • Eye(4.4)
  • Spleen(3.7)
  • Blood(3.6)
  • Kidney(3.4)
  • Lung(3.2)
  • Lymph node(3.1)
  • Liver(3)
  • Nervous system(3)
  • Muscle(2.9)
  • Intestine(2.7)
  • Skin(2.3)
genes like me logo Genes that share expression patterns with VCAM1: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for VCAM1 Gene

Orthologs for VCAM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for VCAM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia VCAM1 33
  • 99 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia VCAM1 33 32
  • 84.21 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia LOC534578 32
  • 83.4 (n)
VCAM1 33 33
  • 77 (a)
 OneToMany
rat
(Rattus norvegicus)
 Mammalia Vcam1 32
  • 80.88 (n)
mouse
(Mus musculus)
 Mammalia Vcam1 17 33 32
  • 80.29 (n)
oppossum
(Monodelphis domestica)
 Mammalia VCAM1 33
  • 53 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia VCAM1 33
  • 42 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves VCAM1 33
  • 35 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia VCAM1 33
  • 39 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii vcam1 33 32
  • 44.53 (n)
 OneToOne
Species where no ortholog for VCAM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VCAM1 Gene

ENSEMBL:
Gene Tree for VCAM1 (if available)
TreeFam:
Gene Tree for VCAM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VCAM1: view image

Paralogs for VCAM1 Gene

Paralogs for VCAM1 Gene

(1) SIMAP similar genes for VCAM1 Gene using alignment to 7 proteins:

  • VCAM1_HUMAN
  • E9PDD2_HUMAN
  • F2YYR6_HUMAN
  • F8UU18_HUMAN
  • F8UV74_HUMAN
  • G0ZFQ0_HUMAN
  • G0ZI12_HUMAN
genes like me logo Genes that share paralogs with VCAM1: view

Variants for VCAM1 Gene

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Sequence variations from dbSNP and Humsavar for VCAM1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000371179 -- 100,724,810(+) T/A/C coding_sequence_variant, missense_variant
rs1000903747 -- 100,730,707(+) A/G intron_variant
rs1001093955 -- 100,739,000(+) G/A 3_prime_UTR_variant
rs1001199909 -- 100,730,806(+) T/G intron_variant
rs1001231059 -- 100,736,954(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VCAM1 Gene

Variant ID Type Subtype PubMed ID
nsv522064 CNV gain 19592680
nsv546889 CNV gain 21841781
nsv546890 CNV loss 21841781

Variation tolerance for VCAM1 Gene

Residual Variation Intolerance Score: 30.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.25; 62.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VCAM1 Gene

Human Gene Mutation Database (HGMD)
VCAM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VCAM1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCAM1 Gene

Disorders for VCAM1 Gene

MalaCards: The human disease database

(66) MalaCards diseases for VCAM1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search VCAM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VCAM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VCAM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VCAM1 Gene

Publications for VCAM1 Gene

  1. Genetic risk factors for cerebrovascular disease in children with sickle cell disease: design of a case-control association study and genomewide screen. (PMID: 12871600) Adams GT … Kutlar A (BMC medical genetics 2003) 3 23 43 56
  2. Alternative splicing of human VCAM-1 in activated vascular endothelium. (PMID: 1707234) Cybulsky MI … Collins T (The American journal of pathology 1991) 3 4 23 56
  3. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. (PMID: 21833088) International Multiple Sclerosis Genetics Consortium … Compston A (Nature 2011) 3 43 56
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 43 56
  5. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey LT … EPICURO/Spanish Bladder Cancer Study investigators (European urology 2010) 3 43 56

ExternalLinks

View latest publications for VCAM1 gene in Mastermind

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