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Aliases for VEGFB Gene

Aliases for VEGFB Gene

  • Vascular Endothelial Growth Factor B 2 3 5
  • VEGF-Related Factor 3 4
  • VRF 3 4
  • VEGF-B 4
  • VEGFL 3

External Ids for VEGFB Gene

Previous HGNC Symbols for VEGFB Gene

  • VRF

Previous GeneCards Identifiers for VEGFB Gene

  • GC11P066518
  • GC11P065683
  • GC11P064253
  • GC11P063777
  • GC11P063758
  • GC11P064002
  • GC11P060330

Summaries for VEGFB Gene

Entrez Gene Summary for VEGFB Gene

  • This gene encodes a member of the PDGF (platelet-derived growth factor)/VEGF (vascular endothelial growth factor) family. The VEGF family members regulate the formation of blood vessels and are involved in endothelial cell physiology. This member is a ligand for VEGFR-1 (vascular endothelial growth factor receptor 1) and NRP-1 (neuropilin-1). Studies in mice showed that this gene was co-expressed with nuclear-encoded mitochondrial genes and the encoded protein specifically controlled endothelial uptake of fatty acids. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Sep 2011]

GeneCards Summary for VEGFB Gene

VEGFB (Vascular Endothelial Growth Factor B) is a Protein Coding gene. Diseases associated with VEGFB include Macular Degeneration, Age-Related, 7 and Macular Degeneration, Age-Related, 1. Among its related pathways are Phospholipase-C Pathway and CREB Pathway. GO annotations related to this gene include protein homodimerization activity and growth factor activity. An important paralog of this gene is VEGFA.

UniProtKB/Swiss-Prot for VEGFB Gene

  • Growth factor for endothelial cells. VEGF-B167 binds heparin and neuropilin-1 whereas the binding to neuropilin-1 of VEGF-B186 is regulated by proteolysis.

Gene Wiki entry for VEGFB Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VEGFB Gene

Genomics for VEGFB Gene

Regulatory Elements for VEGFB Gene

Enhancers for VEGFB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G064237 1.4 ENCODE dbSUPER 19.7 +10.8 10781 16.6 CREB3L1 MLX AGO1 DMAP1 FEZF1 YY1 ZNF143 ZNF263 SP3 NFYC ENSG00000257086 TRMT112 TRPT1 ZFPL1 PPP1R14B LOC102723878 VEGFB KCNK4 PLCB3 FERMT3
GH11G064262 0.7 ENCODE 17.1 +28.7 28719 1.7 CTCF JUN KLF17 GATA3 ZFHX2 SCRT2 PATZ1 ZNF600 FOS EGR2 VEGFB GC11P064262 GPR137
GH11G064183 1.4 FANTOM5 ENCODE 8 -48.9 -48865 4.4 MLX CREB3L1 AGO1 ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC TBX21 TRPT1 C11orf84 ENSG00000269038 IMMP1LP1 FERMT3 C11orf95 ENSG00000257086 PLCB3 ENSG00000256341 SNX15
GH11G064093 1.5 Ensembl ENCODE dbSUPER 6.9 -140.0 -139989 2.4 PKNOX1 FOXA2 ATF1 MLX ZNF133 ARID4B DMAP1 ZNF48 YY1 GLIS2 PLCB3 ENSG00000256341 ZFPL1 TRPT1 VEGFB NRXN2 FKBP2 ENSG00000256481 PIR46997
GH11G064097 1.1 ENCODE dbSUPER 9.1 -136.0 -136035 1.5 PKNOX1 BMI1 NFXL1 FEZF1 ZBTB40 RARA ZNF121 ZSCAN5C ETV6 RELB TRMT112 VEGFB CCDC88B ENSG00000256481 PIR46997
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VEGFB on UCSC Golden Path with GeneCards custom track

Promoters for VEGFB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040635 162 1001 ARID4B SIN3A ZNF48 GLIS2 KLF13 SP3 SP5 MXD4 PPARG GLIS1

Genomic Location for VEGFB Gene

Chromosome:
11
Start:
64,234,538 bp from pter
End:
64,239,264 bp from pter
Size:
4,727 bases
Orientation:
Plus strand

Genomic View for VEGFB Gene

Genes around VEGFB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for VEGFB Gene

Proteins for VEGFB Gene

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

    Protein Symbol:
    P49765-VEGFB_HUMAN
    Recommended name:
    Vascular endothelial growth factor B
    Protein Accession:
    P49765
    Secondary Accessions:
    • Q16528

    Protein attributes for VEGFB Gene

    Size:
    207 amino acids
    Molecular mass:
    21602 Da
    Quaternary structure:
    • Homodimer; disulfide-linked. Can also form heterodimer with VEGF.

    Three dimensional structures from OCA and Proteopedia for VEGFB Gene

    Alternative splice isoforms for VEGFB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VEGFB Gene

Post-translational modifications for VEGFB Gene

Other Protein References for VEGFB Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for VEGFB (VEGFB)

Protein Products

No data available for DME Specific Peptides for VEGFB Gene

Domains & Families for VEGFB Gene

Gene Families for VEGFB Gene

Graphical View of Domain Structure for InterPro Entry

P49765

UniProtKB/Swiss-Prot:

VEGFB_HUMAN :
  • Belongs to the PDGF/VEGF growth factor family.
Family:
  • Belongs to the PDGF/VEGF growth factor family.
genes like me logo Genes that share domains with VEGFB: view

Function for VEGFB Gene

Molecular function for VEGFB Gene

GENATLAS Biochemistry:
vascular endothelial growth factor B,with two alternatively spliced forms differing at their C terminal,universally expressed,PDGF family,hypoxia-inducible,involved in vasculogenesis,downregulated by VHL
UniProtKB/Swiss-Prot Function:
Growth factor for endothelial cells. VEGF-B167 binds heparin and neuropilin-1 whereas the binding to neuropilin-1 of VEGF-B186 is regulated by proteolysis.

Gene Ontology (GO) - Molecular Function for VEGFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19483306
GO:0008083 growth factor activity IBA --
GO:0008201 heparin binding IEA --
GO:0042803 protein homodimerization activity IEA --
GO:0043183 vascular endothelial growth factor receptor 1 binding IBA --
genes like me logo Genes that share ontologies with VEGFB: view
genes like me logo Genes that share phenotypes with VEGFB: view

Animal Models for VEGFB Gene

MGI Knock Outs for VEGFB:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

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

Localization for VEGFB Gene

Subcellular locations from UniProtKB/Swiss-Prot for VEGFB Gene

Secreted. Note=Secreted but remains associated to cells or to the extracellular matrix unless released by heparin.

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 VEGFB gene
Compartment Confidence
extracellular 5
mitochondrion 1

Gene Ontology (GO) - Cellular Components for VEGFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IBA --
GO:0005622 intracellular IEA --
GO:0016020 membrane IEA --
GO:0031093 platelet alpha granule lumen TAS --
genes like me logo Genes that share ontologies with VEGFB: view

Pathways & Interactions for VEGFB Gene

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

Gene Ontology (GO) - Biological Process for VEGFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IBA --
GO:0001666 response to hypoxia IBA --
GO:0001938 positive regulation of endothelial cell proliferation IBA --
GO:0002576 platelet degranulation TAS --
GO:0006493 protein O-linked glycosylation IEA --
genes like me logo Genes that share ontologies with VEGFB: view

No data available for SIGNOR curated interactions for VEGFB Gene

Drugs & Compounds for VEGFB Gene

(14) Drugs for VEGFB Gene - From: DrugBank, ApexBio, DGIdb, FDA Approved Drugs, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Aflibercept Approved Pharma Target, binder Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors 0
Avastin Approved July 2009 Pharma inhibitor 0
Bevacizumab Approved, Investigational Pharma antagonist, antibody, inhibitor VEGF antagonist, Therapeutic Antibodies, Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors 2020
Lenalidomide Approved Pharma Anti-angiogenic., inhibitor Anti-angiogenic. 736
Zaltrap Approved August 2012 Pharma 0

(1) Additional Compounds for VEGFB Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(1) ApexBio Compounds for VEGFB Gene

Compound Action Cas Number
Nintedanib (BIBF 1120) VEGFR/PDGFR/FGFR inhibitor 928326-83-4
genes like me logo Genes that share compounds with VEGFB: view

Drug Products

Transcripts for VEGFB Gene

Unigene Clusters for VEGFB Gene

Vascular endothelial growth factor B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b
SP1:
SP2: -

Relevant External Links for VEGFB Gene

GeneLoc Exon Structure for
VEGFB
ECgene alternative splicing isoforms for
VEGFB

Expression for VEGFB Gene

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

Protein differential expression in normal tissues from HIPED for VEGFB Gene

This gene is overexpressed in Platelet (69.0).

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



Protein tissue co-expression partners for VEGFB Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VEGFB Gene:

VEGFB

SOURCE GeneReport for Unigene cluster for VEGFB Gene:

Hs.732095

mRNA Expression by UniProt/SwissProt for VEGFB Gene:

P49765-VEGFB_HUMAN
Tissue specificity: Expressed in all tissues except liver. Highest levels found in heart, skeletal muscle and pancreas.

Evidence on tissue expression from TISSUES for VEGFB Gene

  • Nervous system(4.6)
  • Heart(3.4)
  • Muscle(2.9)
  • Eye(2.3)
  • Kidney(2.3)
  • Lung(2.3)
  • Intestine(2.2)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with VEGFB: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VEGFB Gene

Orthologs for VEGFB Gene

This gene was present in the common ancestor of chordates.

Orthologs for VEGFB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VEGFB 35 34
  • 100 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VEGFB 34 35
  • 93.33 (n)
dog
(Canis familiaris)
Mammalia VEGFB 34 35
  • 92.7 (n)
rat
(Rattus norvegicus)
Mammalia Vegfb 34
  • 90 (n)
mouse
(Mus musculus)
Mammalia Vegfb 35 16 34
  • 89.96 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VEGFB 35
  • 41 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VEGFB 35
  • 39 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii vegfbb 35
  • 34 (a)
OneToMany
BX511266.1 35
  • 20 (a)
OneToMany
Species where no ortholog for VEGFB 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 VEGFB Gene

ENSEMBL:
Gene Tree for VEGFB (if available)
TreeFam:
Gene Tree for VEGFB (if available)

Paralogs for VEGFB Gene

Paralogs for VEGFB Gene

(2) SIMAP similar genes for VEGFB Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VEGFB: view

Variants for VEGFB Gene

Sequence variations from dbSNP and Humsavar for VEGFB Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000078381 -- 64,236,664(+) GTGAG(C/T)CAAGA intron-variant
rs1000475163 -- 64,233,150(+) CAAAT(A/G)CAGCA intron-variant, upstream-variant-2KB
rs1000548533 -- 64,232,920(+) GAATT(C/T)CAGTG intron-variant, upstream-variant-2KB
rs1000579773 -- 64,232,714(+) GGACA(-/C)CCCCC upstream-variant-2KB, reference, frameshift-variant
rs1000845623 -- 64,238,529(+) GCTCT(C/T)CTGCC utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
dgv1963n54 CNV loss 21841781
dgv1964n54 CNV loss 21841781
esv24861 CNV gain 19812545
esv992196 CNV deletion 20482838
nsv1070041 CNV deletion 25765185
nsv1159904 CNV deletion 26073780
nsv469961 CNV loss 18288195
nsv555184 CNV loss 21841781
nsv555187 CNV loss 21841781
nsv555191 CNV loss 21841781
nsv832186 CNV loss 17160897
nsv951010 CNV deletion 24416366

Variation tolerance for VEGFB Gene

Residual Variation Intolerance Score: 90.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.72; 46.60% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VEGFB Gene

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

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

Disorders for VEGFB Gene

MalaCards: The human disease database

(3) MalaCards diseases for VEGFB Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
macular degeneration, age-related, 7
  • macular degeneration, age-related, neovascular type
macular degeneration, age-related, 1
  • macular degeneration, age-related, reduced risk of
kuhnt-junius degeneration
  • exudative senile macular degeneration of retina
- elite association - COSMIC cancer census association via MalaCards
Search VEGFB in MalaCards View complete list of genes associated with diseases

Relevant External Links for VEGFB

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

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

Publications for VEGFB Gene

  1. Vascular endothelial growth factor B, a novel growth factor for endothelial cells. (PMID: 8637916) Olofsson B. … Eriksson U. (Proc. Natl. Acad. Sci. U.S.A. 1996) 2 3 4 22 64
  2. Cloning and characterization of a novel human gene related to vascular endothelial growth factor. (PMID: 8919691) Grimmond S. … Weber G. (Genome Res. 1996) 2 3 4 22 64
  3. Crystal structure of human vascular endothelial growth factor-B: identification of amino acids important for receptor binding. (PMID: 16616187) Iyer S. … Ravi Acharya K. (J. Mol. Biol. 2006) 3 4 22 64
  4. Genomic organization of the mouse and human genes for vascular endothelial growth factor B (VEGF-B) and characterization of a second splice isoform. (PMID: 8702615) Olofsson B. … Eriksson U. (J. Biol. Chem. 1996) 3 4 22 64
  5. Allelic variations in angiogenic pathway genes are associated with preeclampsia. (PMID: 20223440) Srinivas S.K. … Elovitz M.A. (Am. J. Obstet. Gynecol. 2010) 3 46 64

Products for VEGFB Gene

Sources for VEGFB Gene

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