Human Gene WNT1 (ENST00000293549.4_4) from GENCODE V47lift37
  Description: Wnt family member 1 (from RefSeq NM_005430.4)
Gencode Transcript: ENST00000293549.4_4
Gencode Gene: ENSG00000125084.13_8
Transcript (Including UTRs)
   Position: hg19 chr12:49,372,105-49,376,403 Size: 4,299 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr12:49,372,434-49,375,423 Size: 2,990 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 (chr12:49,372,105-49,376,403)mRNA (may differ from genome)Protein (370 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WNT1_HUMAN
DESCRIPTION: RecName: Full=Proto-oncogene Wnt-1; AltName: Full=Proto-oncogene Int-1 homolog; Flags: Precursor;
FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. In some developmental processes, is also a ligand for the coreceptor RYK, thus triggering Wnt signaling. Probable developmental protein. May be a signaling molecule important in CNS development. Is likely to signal over only few cell diameters.
SUBUNIT: Interacts with PORCN. Interacts with RSPO1, RSPO2 and RSPO3 (By similarity). Interacts with WLS (By similarity).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
PTM: Palmitoylation at Ser-224 is required for efficient binding to frizzled receptors. It is also required for subsequent palmitoylation at Cys-93. Palmitoylation is necessary for proper trafficking to cell surface.
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: WNT1
Diseases sorted by gene-association score: osteogenesis imperfecta, type xv* (1325), osteoporosis, early-onset autosomal dominant* (575), wnt1-related osteogenesis imperfecta* (425), osteogenesis imperfecta, type iii* (182), osteoporosis* (140), osteogenesis imperfecta, type iv* (124), osteogenesis imperfecta (15), idiopathic juvenile osteoporosis* (11), craniodiaphyseal dysplasia (7), pancreatic mucinous cystadenoma (6), valproate embryopathy, susceptibility to (5), breast cancer (4), basal cell carcinoma (3), colorectal cancer (2), conotruncal heart malformations (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 2.82 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 11.10 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 -130.20329-0.396 Picture PostScript Text
3' UTR -285.80980-0.292 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
IPR009139 - Wnt1
IPR018161 - Wnt_CS

Pfam Domains:
PF00110 - wnt family

ModBase Predicted Comparative 3D Structure on P04628
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 Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005109 frizzled binding
GO:0005125 cytokine activity
GO:0016015 morphogen activity
GO:0019904 protein domain specific binding
GO:0044212 transcription regulatory region DNA binding
GO:0048018 receptor agonist activity

Biological Process:
GO:0000578 embryonic axis specification
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0001934 positive regulation of protein phosphorylation
GO:0007267 cell-cell signaling
GO:0007275 multicellular organism development
GO:0007520 myoblast fusion
GO:0008284 positive regulation of cell proliferation
GO:0009611 response to wounding
GO:0010469 regulation of receptor activity
GO:0010592 positive regulation of lamellipodium assembly
GO:0010812 negative regulation of cell-substrate adhesion
GO:0014902 myotube differentiation
GO:0016055 Wnt signaling pathway
GO:0021527 spinal cord association neuron differentiation
GO:0021536 diencephalon development
GO:0021549 cerebellum development
GO:0021551 central nervous system morphogenesis
GO:0021588 cerebellum formation
GO:0021797 forebrain anterior/posterior pattern specification
GO:0022004 midbrain-hindbrain boundary maturation during brain development
GO:0022008 neurogenesis
GO:0022037 metencephalon development
GO:0022408 negative regulation of cell-cell adhesion
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0030514 negative regulation of BMP signaling pathway
GO:0030579 ubiquitin-dependent SMAD protein catabolic process
GO:0030901 midbrain development
GO:0030917 midbrain-hindbrain boundary development
GO:0031100 animal organ regeneration
GO:0033077 T cell differentiation in thymus
GO:0033278 cell proliferation in midbrain
GO:0036520 astrocyte-dopaminergic neuron signaling
GO:0042472 inner ear morphogenesis
GO:0042770 signal transduction in response to DNA damage
GO:0043568 positive regulation of insulin-like growth factor receptor signaling pathway
GO:0044336 canonical Wnt signaling pathway involved in negative regulation of apoptotic process
GO:0045165 cell fate commitment
GO:0045596 negative regulation of cell differentiation
GO:0045599 negative regulation of fat cell differentiation
GO:0045747 positive regulation of Notch signaling pathway
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048146 positive regulation of fibroblast proliferation
GO:0048663 neuron fate commitment
GO:0048664 neuron fate determination
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0060061 Spemann organizer formation
GO:0060070 canonical Wnt signaling pathway
GO:0060071 Wnt signaling pathway, planar cell polarity pathway
GO:0060348 bone development
GO:0061184 positive regulation of dermatome development
GO:0070365 hepatocyte differentiation
GO:0071375 cellular response to peptide hormone stimulus
GO:0071425 hematopoietic stem cell proliferation
GO:0071542 dopaminergic neuron differentiation
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:0090344 negative regulation of cell aging
GO:1903204 negative regulation of oxidative stress-induced neuron death
GO:1904886 beta-catenin destruction complex disassembly
GO:1904948 midbrain dopaminergic neuron differentiation
GO:1904953 Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
GO:1904954 canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
GO:1990403 embryonic brain development
GO:2000059 negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process

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:0009986 cell surface
GO:0030666 endocytic vesicle membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF213374 - JP 2014500723-A/20877: Polycomb-Associated Non-Coding RNAs.
LF212638 - JP 2014500723-A/20141: Polycomb-Associated Non-Coding RNAs.
FW415541 - NUCLEIC ACID COMPOUNDS FOR INHIBITING WNT GENE EXPRESSION AND USES THEREOF.
JA824049 - Sequence 1158 from Patent EP2471920.
JD128746 - Sequence 109770 from Patent EP1572962.
BC074798 - Homo sapiens wingless-type MMTV integration site family, member 1, mRNA (cDNA clone MGC:104071 IMAGE:30915522), complete cds.
BC074799 - Homo sapiens wingless-type MMTV integration site family, member 1, mRNA (cDNA clone MGC:103919 IMAGE:30915309), complete cds.
JD535262 - Sequence 516286 from Patent EP1572962.
JD360913 - Sequence 341937 from Patent EP1572962.
JD209726 - Sequence 190750 from Patent EP1572962.
KJ892383 - Synthetic construct Homo sapiens clone ccsbBroadEn_01777 WNT1 gene, encodes complete protein.
BT019429 - Homo sapiens wingless-type MMTV integration site family, member 1 mRNA, complete cds.
JD522554 - Sequence 503578 from Patent EP1572962.
JD174250 - Sequence 155274 from Patent EP1572962.
JD121763 - Sequence 102787 from Patent EP1572962.
JD389583 - Sequence 370607 from Patent EP1572962.
JD254969 - Sequence 235993 from Patent EP1572962.
JD117381 - Sequence 98405 from Patent EP1572962.
JD311243 - Sequence 292267 from Patent EP1572962.
JD394042 - Sequence 375066 from Patent EP1572962.
JD535071 - Sequence 516095 from Patent EP1572962.
JD475559 - Sequence 456583 from Patent EP1572962.
JD515377 - Sequence 496401 from Patent EP1572962.
JD488854 - Sequence 469878 from Patent EP1572962.
JD102404 - Sequence 83428 from Patent EP1572962.
JD168785 - Sequence 149809 from Patent EP1572962.
JD372074 - Sequence 353098 from Patent EP1572962.
JD460266 - Sequence 441290 from Patent EP1572962.
JD307630 - Sequence 288654 from Patent EP1572962.
JD245016 - Sequence 226040 from Patent EP1572962.
JD363159 - Sequence 344183 from Patent EP1572962.
JD290315 - Sequence 271339 from Patent EP1572962.
JD433267 - Sequence 414291 from Patent EP1572962.
MA448951 - JP 2018138019-A/20877: Polycomb-Associated Non-Coding RNAs.
MA448215 - JP 2018138019-A/20141: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_hesPathway - Segmentation Clock
h_gsk3Pathway - Inactivation of Gsk3 by AKT causes accumulation of b-catenin in Alveolar Macrophages
h_ps1Pathway - Presenilin action in Notch and Wnt signaling
h_alkPathway - ALK in cardiac myocytes
h_pitx2Pathway - Multi-step Regulation of Transcription by Pitx2
h_wntPathway - WNT Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein P04628 (Reactome details) participates in the following event(s):

R-NUL-209104 Frog CKIgamma further phosphorylates Human LRP6 in the receptor complex
R-HSA-201708 Frizzled receptors bind Wnts
R-HSA-3238694 PORCN palmitoleoylates N-glycosyl WNTs
R-HSA-1458875 WNT binds to FZD and LRP5/6
R-HSA-3247843 secretion of WNT ligands
R-HSA-3858491 WNTs bind the FZD receptor to initiate PCP pathway
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-3858482 DVL is recruited to the receptor
R-HSA-3858480 WNT-dependent phosphorylation of DVL
R-HSA-1504186 DVL recruits GSK3beta:AXIN1 to the receptor complex
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-4086400 PCP/CE pathway
R-HSA-500792 GPCR ligand binding
R-HSA-195721 Signaling by WNT
R-HSA-4641262 Disassembly of the destruction complex and recruitment of AXIN to the membrane
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000293549.1, ENST00000293549.2, ENST00000293549.3, INT1, NM_005430, P04628, Q5U0N2, uc317lea.1, uc317lea.2, WNT1_HUMAN
UCSC ID: ENST00000293549.4_4
RefSeq Accession: NM_005430.4
Protein: P04628 (aka WNT1_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.