Human Gene WNT3A (ENST00000284523.2_4) from GENCODE V47lift37
  Description: Wnt family member 3A (from RefSeq NM_033131.4)
Gencode Transcript: ENST00000284523.2_4
Gencode Gene: ENSG00000154342.6_7
Transcript (Including UTRs)
   Position: hg19 chr1:228,194,699-228,248,972 Size: 54,274 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr1:228,194,830-228,247,166 Size: 52,337 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq 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 (chr1:228,194,699-228,248,972)mRNA (may differ from genome)Protein (352 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WNT3A_HUMAN
DESCRIPTION: RecName: Full=Protein Wnt-3a; Flags: Precursor;
FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Wnt-3 and Wnt-3a play distinct roles in cell-cell signaling during morphogenesis of the developing neural tube.
SUBUNIT: Homooligomer; disulfide-linked, leading to inactivation (By similarity). Interacts with PORCN. Interacts with APCDD1 and WLS. Component of the Wnt-Fzd-LRP5-LRP6 signaling complex that contains a WNT protein, a FZD protein and LRP5 or LRP6. Interacts directly in the complex with LRP6.
INTERACTION: Q9H461:FZD8; NbExp=2; IntAct=EBI-6173037, EBI-6254212;
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
TISSUE SPECIFICITY: Moderately expressed in placenta and at low levels in adult lung, spleen, and prostate.
PTM: Palmitoylation at Ser-209 is required for efficient binding to frizzled receptors. It is also required for subsequent palmitoylation at Cys-77. Palmitoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoylated WNT3A from WLS in secretory vesicles.
PTM: Proteolytic processing by TIKI1 and TIKI2 promotes oxidation and formation of large disulfide-bond oligomers, leading to inactivation of WNT3A.
SIMILARITY: Belongs to the Wnt 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: WNT3A
Diseases sorted by gene-association score: idiopathic juvenile osteoporosis* (12), diarrhea 4, malabsorptive, congenital (11), craniodiaphyseal dysplasia (7), hypotrichosis simplex (6), focal dermal hypoplasia (6), osteogenesis imperfecta, type vi (5), colorectal cancer (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D019256 Cadmium Chloride
  • D013749 Tetrachlorodibenzodioxin
  • C059514 resveratrol
  • C097949 1,25-dihydroxyvitamin D
  • C014024 2,4,5,2',4',5'-hexachlorobiphenyl
  • C472791 3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid
  • C493177 4-(4-(2,3-dihydrobenzo(1,4)dioxin-6-yl)-5-pyridin-2-yl-1H-imidazol-2-yl)benzamide
  • C552996 4-aminoethylamino-emodin
  • C060298 5,7-dimethoxyflavone
  • D001151 Arsenic
          more ... click here to view the complete list

+  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: 2.57 RPKM in Lung
Total median expression: 8.44 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -67.40131-0.515 Picture PostScript Text
3' UTR -870.901806-0.482 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
IPR005817 - Wnt
IPR009141 - Wnt3
IPR018161 - Wnt_CS

Pfam Domains:
PF00110 - wnt family

ModBase Predicted Comparative 3D Structure on P56704
FrontTopSide
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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0005102 receptor binding
GO:0005109 frizzled binding
GO:0005515 protein binding
GO:0019904 protein domain specific binding
GO:0039706 co-receptor binding
GO:0048018 receptor agonist activity

Biological Process:
GO:0001649 osteoblast differentiation
GO:0001701 in utero embryonic development
GO:0001756 somitogenesis
GO:0001819 positive regulation of cytokine production
GO:0001934 positive regulation of protein phosphorylation
GO:0001947 heart looping
GO:0002092 positive regulation of receptor internalization
GO:0003136 negative regulation of heart induction by canonical Wnt signaling pathway
GO:0007275 multicellular organism development
GO:0007368 determination of left/right symmetry
GO:0007409 axonogenesis
GO:0007411 axon guidance
GO:0007498 mesoderm development
GO:0008283 cell proliferation
GO:0008284 positive regulation of cell proliferation
GO:0009952 anterior/posterior pattern specification
GO:0010387 COP9 signalosome assembly
GO:0010469 regulation of receptor activity
GO:0010628 positive regulation of gene expression
GO:0010977 negative regulation of neuron projection development
GO:0016055 Wnt signaling pathway
GO:0021527 spinal cord association neuron differentiation
GO:0021766 hippocampus development
GO:0021846 cell proliferation in forebrain
GO:0021874 Wnt signaling pathway involved in forebrain neuroblast division
GO:0021904 dorsal/ventral neural tube patterning
GO:0022008 neurogenesis
GO:0030097 hemopoiesis
GO:0030168 platelet activation
GO:0030182 neuron differentiation
GO:0030198 extracellular matrix organization
GO:0030879 mammary gland development
GO:0030890 positive regulation of B cell proliferation
GO:0030901 midbrain development
GO:0032092 positive regulation of protein binding
GO:0033138 positive regulation of peptidyl-serine phosphorylation
GO:0033278 cell proliferation in midbrain
GO:0034613 cellular protein localization
GO:0035914 skeletal muscle cell differentiation
GO:0036342 post-anal tail morphogenesis
GO:0036465 synaptic vesicle recycling
GO:0042472 inner ear morphogenesis
GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0045595 regulation of cell differentiation
GO:0045599 negative regulation of fat cell differentiation
GO:0045860 positive regulation of protein kinase activity
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048103 somatic stem cell division
GO:0048337 positive regulation of mesodermal cell fate specification
GO:0048343 paraxial mesodermal cell fate commitment
GO:0048643 positive regulation of skeletal muscle tissue development
GO:0048697 positive regulation of collateral sprouting in absence of injury
GO:0048843 negative regulation of axon extension involved in axon guidance
GO:0050768 negative regulation of neurogenesis
GO:0050770 regulation of axonogenesis
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0060070 canonical Wnt signaling pathway
GO:0060923 cardiac muscle cell fate commitment
GO:0061098 positive regulation of protein tyrosine kinase activity
GO:0061184 positive regulation of dermatome development
GO:0061317 canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment
GO:0070507 regulation of microtubule cytoskeleton organization
GO:0070527 platelet aggregation
GO:0071300 cellular response to retinoic acid
GO:0090245 axis elongation involved in somitogenesis
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:0090676 calcium ion transmembrane transport via low voltage-gated calcium channel
GO:0099054 presynapse assembly
GO:1901215 negative regulation of neuron death
GO:1903078 positive regulation of protein localization to plasma membrane
GO:1904339 negative regulation of dopaminergic neuron differentiation
GO:1904798 positive regulation of core promoter binding
GO:1904886 beta-catenin destruction complex disassembly
GO:1904953 Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
GO:2000049 positive regulation of cell-cell adhesion mediated by cadherin
GO:2000081 positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation
GO:2000179 positive regulation of neural precursor cell proliferation
GO:2000347 positive regulation of hepatocyte proliferation
GO:2000727 positive regulation of cardiac muscle cell differentiation
GO:2001141 regulation of RNA biosynthetic process

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005788 endoplasmic reticulum lumen
GO:0005796 Golgi lumen
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0030666 endocytic vesicle membrane
GO:0031901 early endosome membrane
GO:0070062 extracellular exosome
GO:0098793 presynapse
GO:1990851 Wnt-Frizzled-LRP5/6 complex


-  Descriptions from all associated GenBank mRNAs
  AK056278 - Homo sapiens cDNA FLJ31716 fis, clone NT2RI2006565, highly similar to WNT-3A PROTEIN PRECURSOR.
FW415998 - NUCLEIC ACID COMPOUNDS FOR INHIBITING WNT GENE EXPRESSION AND USES THEREOF.
JA824506 - Sequence 1615 from Patent EP2471920.
BC103921 - Homo sapiens wingless-type MMTV integration site family, member 3A, mRNA (cDNA clone MGC:119418 IMAGE:40007188), complete cds.
BC103922 - Homo sapiens wingless-type MMTV integration site family, member 3A, mRNA (cDNA clone MGC:119419 IMAGE:40007189), complete cds.
BC103923 - Homo sapiens wingless-type MMTV integration site family, member 3A, mRNA (cDNA clone MGC:119420 IMAGE:40007191), complete cds.
AB060284 - Homo sapiens mRNA for WNT3A, complete cds.
KJ903528 - Synthetic construct Homo sapiens clone ccsbBroadEn_12922 WNT3A gene, encodes complete protein.
JD389357 - Sequence 370381 from Patent EP1572962.
JD300027 - Sequence 281051 from Patent EP1572962.
JD217667 - Sequence 198691 from Patent EP1572962.
JD254011 - Sequence 235035 from Patent EP1572962.
JD088353 - Sequence 69377 from Patent EP1572962.
JD473009 - Sequence 454033 from Patent EP1572962.
JD423348 - Sequence 404372 from Patent EP1572962.
JD397454 - Sequence 378478 from Patent EP1572962.
JD207097 - Sequence 188121 from Patent EP1572962.
JD342623 - Sequence 323647 from Patent EP1572962.
JD165182 - Sequence 146206 from Patent EP1572962.
JD163310 - Sequence 144334 from Patent EP1572962.
JD268856 - Sequence 249880 from Patent EP1572962.
JD160053 - Sequence 141077 from Patent EP1572962.
JD306622 - Sequence 287646 from Patent EP1572962.
JD357628 - Sequence 338652 from Patent EP1572962.
JD054915 - Sequence 35939 from Patent EP1572962.
JD076304 - Sequence 57328 from Patent EP1572962.
JD195080 - Sequence 176104 from Patent EP1572962.
JD136739 - Sequence 117763 from Patent EP1572962.
JD521312 - Sequence 502336 from Patent EP1572962.
JD478795 - Sequence 459819 from Patent EP1572962.
JD415316 - Sequence 396340 from Patent EP1572962.
JD325208 - Sequence 306232 from Patent EP1572962.
JD537947 - Sequence 518971 from Patent EP1572962.
JD402891 - Sequence 383915 from Patent EP1572962.
JD415782 - Sequence 396806 from Patent EP1572962.
JD185481 - Sequence 166505 from Patent EP1572962.
JD254028 - Sequence 235052 from Patent EP1572962.
JD161178 - Sequence 142202 from Patent EP1572962.
JD389283 - Sequence 370307 from Patent EP1572962.
JD127663 - Sequence 108687 from Patent EP1572962.
JD078629 - Sequence 59653 from Patent EP1572962.
JD115015 - Sequence 96039 from Patent EP1572962.
JD214770 - Sequence 195794 from Patent EP1572962.
JD336501 - Sequence 317525 from Patent EP1572962.
JD461512 - Sequence 442536 from Patent EP1572962.

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

Protein P56704 (Reactome details) participates in the following event(s):

R-HSA-3772441 sFRP binds WNT3A and inhibits WNT:FZD binding
R-HSA-201708 Frizzled receptors bind Wnts
R-HSA-3238694 PORCN palmitoleoylates N-glycosyl WNTs
R-HSA-4641249 ZNRF3,RNF43 binds the FZD:LRP5/6 receptor complex
R-HSA-4641236 USP8 deubiquitinates FZD to potentiate WNT signaling
R-HSA-4641253 ZNRF3 ubiquitinates FZD to promote its downregulation
R-HSA-1458875 WNT binds to FZD and LRP5/6
R-HSA-3247843 secretion of WNT ligands
R-HSA-3769370 WIF1 binds WNTs
R-HSA-5323545 Canonical WNT signaling through the atypical receptor RYK
R-HSA-3247840 WLS binds WNT ligands in the Golgi
R-HSA-1504188 FZD recruits DVL to the receptor complex
R-HSA-201691 Phosphorylation of LRP5/6 cytoplasmic domain by CSNKI
R-NUL-1458902 frog CK1gamma phosphorylates LRP5/6
R-HSA-201677 Phosphorylation of LRP5/6 cytoplasmic domain by membrane-associated GSK3beta
R-HSA-1504186 DVL recruits GSK3beta:AXIN1 to the receptor complex
R-HSA-3772470 Negative regulation of TCF-dependent signaling by WNT ligand antagonists
R-HSA-373080 Class B/2 (Secretin family receptors)
R-HSA-3238698 WNT ligand biogenesis and trafficking
R-HSA-4641263 Regulation of FZD by ubiquitination
R-HSA-5340588 RNF mutants show enhanced WNT signaling and proliferation
R-HSA-4641262 Disassembly of the destruction complex and recruitment of AXIN to the membrane
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-500792 GPCR ligand binding
R-HSA-195721 Signaling by WNT
R-HSA-4791275 Signaling by WNT in cancer
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000284523.1, NM_033131, P56704, Q3SY79, Q3SY80, Q969P2, uc317kfh.1, uc317kfh.2, WNT3A_HUMAN
UCSC ID: ENST00000284523.2_4
RefSeq Accession: NM_033131.4
Protein: P56704 (aka WNT3A_HUMAN or WN3A_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.