Human Gene WNT3 (ENST00000225512.6_7) from GENCODE V47lift37
  Description: Wnt family member 3 (from RefSeq NM_030753.5)
Gencode Transcript: ENST00000225512.6_7
Gencode Gene: ENSG00000108379.11_9
Transcript (Including UTRs)
   Position: hg19 chr17:44,839,872-44,896,058 Size: 56,187 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr17:44,845,686-44,895,963 Size: 50,278 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:44,839,872-44,896,058)mRNA (may differ from genome)Protein (355 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WNT3_HUMAN
DESCRIPTION: RecName: Full=Proto-oncogene Wnt-3; AltName: Full=Proto-oncogene Int-4 homolog; 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 (By similarity).
SUBUNIT: Interacts with PORCN (By similarity). Interacts with WLS (By similarity).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
PTM: Palmitoylation at Ser-212 is required for efficient binding to frizzled receptors. It is also required for subsequent palmitoylation at Cys-80. Palmitoylation is necessary for proper trafficking to cell surface (By similarity).
DISEASE: Defects in WNT3 are the cause of autosomal recessive tetra-amelia (ARTTRA) [MIM:273395]. Tetra-amelia is a rare human genetic disorder characterized by complete absence of all four limbs and other anomalies such as craniofacial, nervous system, pulmonary, skeletal and urogenital defects.
SIMILARITY: Belongs to the Wnt family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/WNT3";

-  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: WNT3
Diseases sorted by gene-association score: tetra-amelia syndrome* (1400), nodular basal cell carcinoma (16), bladder exstrophy-epispadias-cloacal exstrophy complex (6), klatskin's tumor (6), exstrophy of bladder (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 15.77 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 78.40 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 -22.9095-0.241 Picture PostScript Text
3' UTR -635.502124-0.299 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 P56703
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    
 RGDEnsembl   
      
      

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

Biological Process:
GO:0000902 cell morphogenesis
GO:0001707 mesoderm formation
GO:0007275 multicellular organism development
GO:0007276 gamete generation
GO:0007411 axon guidance
GO:0009948 anterior/posterior axis specification
GO:0009950 dorsal/ventral axis specification
GO:0009952 anterior/posterior pattern specification
GO:0010469 regulation of receptor activity
GO:0010628 positive regulation of gene expression
GO:0016055 Wnt signaling pathway
GO:0030177 positive regulation of Wnt signaling pathway
GO:0030182 neuron differentiation
GO:0035115 embryonic forelimb morphogenesis
GO:0035116 embryonic hindlimb morphogenesis
GO:0044338 canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation
GO:0044339 canonical Wnt signaling pathway involved in osteoblast differentiation
GO:0045165 cell fate commitment
GO:0048646 anatomical structure formation involved in morphogenesis
GO:0048697 positive regulation of collateral sprouting in absence of injury
GO:0048843 negative regulation of axon extension involved in axon guidance
GO:0050767 regulation of neurogenesis
GO:0060064 Spemann organizer formation at the anterior end of the primitive streak
GO:0060070 canonical Wnt signaling pathway
GO:0060173 limb development
GO:0060174 limb bud formation
GO:0060323 head morphogenesis
GO:0061180 mammary gland epithelium development
GO:0071300 cellular response to retinoic acid
GO:0072089 stem cell proliferation
GO:1904954 canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
GO:1905474 canonical Wnt signaling pathway involved in stem cell proliferation

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005788 endoplasmic reticulum lumen
GO:0005796 Golgi lumen
GO:0005886 plasma membrane
GO:0030666 endocytic vesicle membrane
GO:0070062 extracellular exosome
GO:1990909 Wnt signalosome


-  Descriptions from all associated GenBank mRNAs
  BC114219 - Homo sapiens wingless-type MMTV integration site family, member 3, mRNA (cDNA clone MGC:131950 IMAGE:5726751), complete cds.
LF213779 - JP 2014500723-A/21282: Polycomb-Associated Non-Coding RNAs.
JD563988 - Sequence 545012 from Patent EP1572962.
JD249323 - Sequence 230347 from Patent EP1572962.
JD525581 - Sequence 506605 from Patent EP1572962.
AB067628 - Homo sapiens WNT3 mRNA, complete cds.
JD321320 - Sequence 302344 from Patent EP1572962.
BC112118 - Homo sapiens wingless-type MMTV integration site family, member 3, mRNA (cDNA clone MGC:138323 IMAGE:8327586), complete cds.
JD312471 - Sequence 293495 from Patent EP1572962.
BC112116 - Homo sapiens wingless-type MMTV integration site family, member 3, mRNA (cDNA clone MGC:138321 IMAGE:8327584), complete cds.
AY009397 - Homo sapiens WNT3 precursor (WNT3) mRNA, complete cds.
BC111600 - Synthetic construct Homo sapiens clone IMAGE:40080563, MGC:133426 WNT3 protein (WNT3) mRNA, encodes complete protein.
AB464356 - Synthetic construct DNA, clone: pF1KB7181, Homo sapiens WNT3 gene for wingless-type MMTV integration site family, member 3, without stop codon, in Flexi system.
MA449356 - JP 2018138019-A/21282: Polycomb-Associated Non-Coding RNAs.

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

Protein P56703 (Reactome details) participates in the following event(s):

R-HSA-201708 Frizzled receptors bind Wnts
R-HSA-3238694 PORCN palmitoleoylates N-glycosyl WNTs
R-HSA-3247843 secretion of WNT ligands
R-HSA-5323545 Canonical WNT signaling through the atypical receptor RYK
R-HSA-3247840 WLS binds WNT ligands in the Golgi
R-HSA-373080 Class B/2 (Secretin family receptors)
R-HSA-3238698 WNT ligand biogenesis and trafficking
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-500792 GPCR ligand binding
R-HSA-195721 Signaling by WNT
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000225512.1, ENST00000225512.2, ENST00000225512.3, ENST00000225512.4, ENST00000225512.5, INT4, NM_030753, P56703, Q2M237, Q9H1J9, uc317djc.1, uc317djc.2, WNT3_HUMAN
UCSC ID: ENST00000225512.6_7
RefSeq Accession: NM_030753.5
Protein: P56703 (aka WNT3_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.