Human Gene WNT6 (ENST00000233948.4_4) from GENCODE V47lift37
  Description: Wnt family member 6 (from RefSeq NM_006522.4)
Gencode Transcript: ENST00000233948.4_4
Gencode Gene: ENSG00000115596.4_7
Transcript (Including UTRs)
   Position: hg19 chr2:219,724,528-219,738,955 Size: 14,428 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr2:219,724,761-219,738,567 Size: 13,807 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene 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 (chr2:219,724,528-219,738,955)mRNA (may differ from genome)Protein (365 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WNT6_HUMAN
DESCRIPTION: RecName: Full=Protein Wnt-6; Flags: Precursor;
FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters.
SUBUNIT: Interacts with PORCN (By similarity).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
PTM: Palmitoylation at Ser-228 is required for efficient binding to frizzled receptors. It is also required for subsequent palmitoylation at Cys-76. Palmitoylation is necessary for proper trafficking to cell surface (By similarity).
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


-  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: 22.48 RPKM in Nerve - Tibial
Total median expression: 99.26 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 -97.90233-0.420 Picture PostScript Text
3' UTR -170.70388-0.440 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
IPR009143 - Wnt6
IPR018161 - Wnt_CS

Pfam Domains:
PF00110 - wnt family

ModBase Predicted Comparative 3D Structure on Q9Y6F9
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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 Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005109 frizzled binding

Biological Process:
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0007275 multicellular organism development
GO:0009798 axis specification
GO:0010628 positive regulation of gene expression
GO:0016055 Wnt signaling pathway
GO:0030182 neuron differentiation
GO:0042475 odontogenesis of dentin-containing tooth
GO:0045165 cell fate commitment
GO:0045893 positive regulation of transcription, DNA-templated
GO:0060684 epithelial-mesenchymal cell signaling
GO:0061303 cornea development in camera-type eye
GO:0070172 positive regulation of tooth mineralization
GO:0071300 cellular response to retinoic acid
GO:0072079 nephron tubule formation
GO:0072080 nephron tubule development

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:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AY009401 - Homo sapiens WNT6 precursor (WNT6) mRNA, complete cds.
JD523262 - Sequence 504286 from Patent EP1572962.
AK075522 - Homo sapiens cDNA PSEC0220 fis, clone HEMBA1005301, highly similar to Wnt-6 protein precursor.
AB059570 - Homo sapiens mRNA for WNT6, complete cds.
DQ890770 - Synthetic construct clone IMAGE:100003400; FLH165806.01X; RZPDo839G12160D wingless-type MMTV integration site family, member 6 (WNT6) gene, encodes complete protein.
BC004329 - Homo sapiens wingless-type MMTV integration site family, member 6, mRNA (cDNA clone MGC:10938 IMAGE:3630498), complete cds.
AB590154 - Synthetic construct DNA, clone: pFN21AE1502, Homo sapiens WNT6 gene for wingless-type MMTV integration site family, member 6, without stop codon, in Flexi system.
BT007456 - Homo sapiens wingless-type MMTV integration site family, member 6 mRNA, complete cds.
JD543522 - Sequence 524546 from Patent EP1572962.
JD129767 - Sequence 110791 from Patent EP1572962.
JD522546 - Sequence 503570 from Patent EP1572962.
JD442873 - Sequence 423897 from Patent EP1572962.
JD383800 - Sequence 364824 from Patent EP1572962.
JD525603 - Sequence 506627 from Patent EP1572962.
JD456424 - Sequence 437448 from Patent EP1572962.
JD077448 - Sequence 58472 from Patent EP1572962.
JD100200 - Sequence 81224 from Patent EP1572962.
JD505528 - Sequence 486552 from Patent EP1572962.
JD502808 - Sequence 483832 from Patent EP1572962.
MP389274 - Sequence 1 from Patent WO2019207512.

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

Protein Q9Y6F9 (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-3247840 WLS binds WNT ligands in the Golgi
R-HSA-3247843 secretion of WNT ligands
R-HSA-373080 Class B/2 (Secretin family receptors)
R-HSA-3238698 WNT ligand biogenesis and trafficking
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: ENST00000233948.1, ENST00000233948.2, ENST00000233948.3, NM_006522, Q9H1J6, Q9H238, Q9Y6F9, uc317dye.1, uc317dye.2, WNT6_HUMAN
UCSC ID: ENST00000233948.4_4
RefSeq Accession: NM_006522.4
Protein: Q9Y6F9 (aka WNT6_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.