Human Gene VEGFD (ENST00000297904.4_7) from GENCODE V47lift37
  Description: vascular endothelial growth factor D (from RefSeq NM_004469.5)
Gencode Transcript: ENST00000297904.4_7
Gencode Gene: ENSG00000165197.5_12
Transcript (Including UTRs)
   Position: hg19 chrX:15,363,718-15,402,535 Size: 38,818 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chrX:15,364,255-15,402,068 Size: 37,814 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:15,363,718-15,402,535)mRNA (may differ from genome)Protein (354 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VEGFD_HUMAN
DESCRIPTION: RecName: Full=Vascular endothelial growth factor D; Short=VEGF-D; AltName: Full=c-Fos-induced growth factor; Short=FIGF; Flags: Precursor;
FUNCTION: Growth factor active in angiogenesis, lymphangiogenesis and endothelial cell growth, stimulating their proliferation and migration and also has effects on the permeability of blood vessels. May function in the formation of the venous and lymphatic vascular systems during embryogenesis, and also in the maintenance of differentiated lymphatic endothelium in adults. Binds and activates VEGFR-2 (KDR/FLK1) and VEGFR-3 (FLT4) receptors.
SUBUNIT: Homodimer; non-covalent and antiparallel.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Highly expressed in lung, heart, small intestine and fetal lung, and at lower levels in skeletal muscle, colon, and pancreas.
PTM: Undergoes a complex proteolytic maturation which generates a variety of processed secreted forms with increased activity toward VEGFR-3 and VEGFR-2. VEGF-D first form an antiparallel homodimer linked by disulfide bonds before secretion. The fully processed VEGF-D is composed mostly of two VEGF homology domains (VHDs) bound by non-covalent interactions.
SIMILARITY: Belongs to the PDGF/VEGF growth factor family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: VEGFD
Diseases sorted by gene-association score: breast cancer (7), breast ductal carcinoma (5), anal canal squamous cell carcinoma (4), lymphangioleiomyomatosis (4), congenital lymphedema (4), esophageal cancer (3), colorectal cancer (3), lung cancer (2), lung cancer susceptibility 3 (2), stomach cancer (2), differentiated thyroid carcinoma (1)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.45 RPKM in Lung
Total median expression: 134.87 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -109.90467-0.235 Picture PostScript Text
3' UTR -123.80537-0.231 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000072 - PD_growth_factor
IPR023581 - PD_growth_factor_CS

Pfam Domains:
PF00341 - PDGF/VEGF domain
PF03128 - CXCXC repeat

SCOP Domains:
57501 - Cystine-knot cytokines

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2XV7 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O43915
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005161 platelet-derived growth factor receptor binding
GO:0005172 vascular endothelial growth factor receptor binding
GO:0005515 protein binding
GO:0008083 growth factor activity
GO:0042056 chemoattractant activity
GO:0042803 protein homodimerization activity
GO:0043185 vascular endothelial growth factor receptor 3 binding

Biological Process:
GO:0001525 angiogenesis
GO:0001666 response to hypoxia
GO:0001938 positive regulation of endothelial cell proliferation
GO:0002576 platelet degranulation
GO:0007275 multicellular organism development
GO:0008283 cell proliferation
GO:0008284 positive regulation of cell proliferation
GO:0010469 regulation of receptor activity
GO:0030154 cell differentiation
GO:0045766 positive regulation of angiogenesis
GO:0048010 vascular endothelial growth factor receptor signaling pathway
GO:0050918 positive chemotaxis
GO:0050930 induction of positive chemotaxis
GO:0051781 positive regulation of cell division
GO:0060754 positive regulation of mast cell chemotaxis
GO:0071542 dopaminergic neuron differentiation

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0016020 membrane
GO:0031093 platelet alpha granule lumen


-  Descriptions from all associated GenBank mRNAs
  AX740234 - Sequence 1 from Patent EP1283268.
LF211724 - JP 2014500723-A/19227: Polycomb-Associated Non-Coding RNAs.
Y12863 - Homo sapiens mRNA for growth factor FIGF.
LQ270818 - Sequence 146 from Patent WO2016071350.
AK223160 - Homo sapiens mRNA for vascular endothelial growth factor D preproprotein variant, clone: LNG03255.
AJ000185 - Homo Sapiens mRNA for vascular endothelial growth factor-D.
AX740237 - Sequence 4 from Patent EP1283268.
BC027948 - Homo sapiens c-fos induced growth factor (vascular endothelial growth factor D), mRNA (cDNA clone MGC:34490 IMAGE:5207065), complete cds.
FW406921 - NUCLEIC ACID COMPOUNDS FOR INHIBITING VEGF FAMILY GENE EXPRESSION AND USES THEREOF.
JA810034 - Sequence 1167 from Patent EP2468864.
D89630 - Homo sapiens mRNA for VEGF-D, complete cds.
JD251311 - Sequence 232335 from Patent EP1572962.
JD518258 - Sequence 499282 from Patent EP1572962.
JD155322 - Sequence 136346 from Patent EP1572962.
JD182805 - Sequence 163829 from Patent EP1572962.
JD257443 - Sequence 238467 from Patent EP1572962.
JD060970 - Sequence 41994 from Patent EP1572962.
JD313945 - Sequence 294969 from Patent EP1572962.
JD423096 - Sequence 404120 from Patent EP1572962.
LF383120 - JP 2014500723-A/190623: Polycomb-Associated Non-Coding RNAs.
JD359237 - Sequence 340261 from Patent EP1572962.
LF383119 - JP 2014500723-A/190622: Polycomb-Associated Non-Coding RNAs.
AK313173 - Homo sapiens cDNA, FLJ93671, Homo sapiens c-fos induced growth factor (vascular endothelialgrowth factor D) (FIGF), mRNA.
KJ891176 - Synthetic construct Homo sapiens clone ccsbBroadEn_00570 FIGF gene, encodes complete protein.
AB590905 - Synthetic construct DNA, clone: pFN21AE1836, Homo sapiens FIGF gene for c-fos induced growth factor, without stop codon, in Flexi system.
LF383118 - JP 2014500723-A/190621: Polycomb-Associated Non-Coding RNAs.
LF383117 - JP 2014500723-A/190620: Polycomb-Associated Non-Coding RNAs.
LF383116 - JP 2014500723-A/190619: Polycomb-Associated Non-Coding RNAs.
LF383115 - JP 2014500723-A/190618: Polycomb-Associated Non-Coding RNAs.
LF383114 - JP 2014500723-A/190617: Polycomb-Associated Non-Coding RNAs.
LF383112 - JP 2014500723-A/190615: Polycomb-Associated Non-Coding RNAs.
LF383110 - JP 2014500723-A/190613: Polycomb-Associated Non-Coding RNAs.
JD096667 - Sequence 77691 from Patent EP1572962.
JD050113 - Sequence 31137 from Patent EP1572962.
JD300668 - Sequence 281692 from Patent EP1572962.
JD182730 - Sequence 163754 from Patent EP1572962.
LF383109 - JP 2014500723-A/190612: Polycomb-Associated Non-Coding RNAs.
JD312851 - Sequence 293875 from Patent EP1572962.
MA618697 - JP 2018138019-A/190623: Polycomb-Associated Non-Coding RNAs.
MA618696 - JP 2018138019-A/190622: Polycomb-Associated Non-Coding RNAs.
MA618695 - JP 2018138019-A/190621: Polycomb-Associated Non-Coding RNAs.
MA618694 - JP 2018138019-A/190620: Polycomb-Associated Non-Coding RNAs.
MA618693 - JP 2018138019-A/190619: Polycomb-Associated Non-Coding RNAs.
MA618692 - JP 2018138019-A/190618: Polycomb-Associated Non-Coding RNAs.
MA618691 - JP 2018138019-A/190617: Polycomb-Associated Non-Coding RNAs.
MA618689 - JP 2018138019-A/190615: Polycomb-Associated Non-Coding RNAs.
MA618687 - JP 2018138019-A/190613: Polycomb-Associated Non-Coding RNAs.
MA618686 - JP 2018138019-A/190612: Polycomb-Associated Non-Coding RNAs.
MA447301 - JP 2018138019-A/19227: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O43915 (Reactome details) participates in the following event(s):

R-HSA-195378 Homodimerization of VEGF proteins
R-HSA-481007 Exocytosis of platelet alpha granule contents
R-HSA-194308 VEGF-C,D bind to VEGFR3 leading to receptor dimerization
R-HSA-194310 VEGF-A,C,D bind to VEGFR2 leading to receptor dimerization
R-HSA-194313 VEGF ligand-receptor interactions
R-HSA-114608 Platelet degranulation
R-HSA-195399 VEGF binds to VEGFR leading to receptor dimerization
R-HSA-194138 Signaling by VEGF
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-162582 Signal Transduction
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: B2R7Z3, ENST00000297904.1, ENST00000297904.2, ENST00000297904.3, FIGF, NM_004469, O43915, uc317mcg.1, uc317mcg.2, VEGFD , VEGFD_HUMAN
UCSC ID: ENST00000297904.4_7
RefSeq Accession: NM_004469.5
Protein: O43915 (aka VEGFD_HUMAN or VEGD_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.