Human Gene WNT2 (ENST00000265441.8) from GENCODE V44
  Description: Homo sapiens Wnt family member 2 (WNT2), transcript variant 2, non-coding RNA. (from RefSeq NR_024047)
RefSeq Summary (NM_003391): This gene is a member of the WNT gene family. The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000265441.8
Gencode Gene: ENSG00000105989.10
Transcript (Including UTRs)
   Position: hg38 chr7:117,275,451-117,323,058 Size: 47,608 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr7:117,278,155-117,322,989 Size: 44,835 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:117,275,451-117,323,058)mRNA (may differ from genome)Protein (360 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WNT2_HUMAN
DESCRIPTION: RecName: Full=Protein Wnt-2; AltName: Full=Int-1-like protein 1; AltName: Full=Int-1-related protein; Short=IRP; 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.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
TISSUE SPECIFICITY: Expressed in brain in the thalamus, in fetal and adult lung and in placenta.
PTM: Palmitoylation at Ser-212 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


-  MalaCards Disease Associations
  MalaCards Gene Search: WNT2
Diseases sorted by gene-association score: autistic disorder (4), hyperferritinemia-cataract syndrome (3), colorectal cancer (2), autism spectrum disorder (1), proximal symphalangism (1), multiple synostoses syndrome (1), dementia, frontotemporal (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.96 RPKM in Lung
Total median expression: 24.15 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 -21.2069-0.307 Picture PostScript Text
3' UTR -773.802704-0.286 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
IPR009140 - Wnt2
IPR018161 - Wnt_CS

Pfam Domains:
PF00110 - wnt family

ModBase Predicted Comparative 3D Structure on P09544
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005109 frizzled binding
GO:0005125 cytokine activity
GO:0005515 protein binding
GO:0048018 receptor agonist activity

Biological Process:
GO:0001938 positive regulation of endothelial cell proliferation
GO:0002053 positive regulation of mesenchymal cell proliferation
GO:0002088 lens development in camera-type eye
GO:0007267 cell-cell signaling
GO:0007275 multicellular organism development
GO:0008284 positive regulation of cell proliferation
GO:0010469 regulation of receptor activity
GO:0016055 Wnt signaling pathway
GO:0022008 neurogenesis
GO:0030182 neuron differentiation
GO:0030324 lung development
GO:0033278 cell proliferation in midbrain
GO:0045165 cell fate commitment
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048146 positive regulation of fibroblast proliferation
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0055009 atrial cardiac muscle tissue morphogenesis
GO:0060045 positive regulation of cardiac muscle cell proliferation
GO:0060070 canonical Wnt signaling pathway
GO:0060317 cardiac epithelial to mesenchymal transition
GO:0060492 lung induction
GO:0060501 positive regulation of epithelial cell proliferation involved in lung morphogenesis
GO:0060716 labyrinthine layer blood vessel development
GO:0061072 iris morphogenesis
GO:0061180 mammary gland epithelium development
GO:0071300 cellular response to retinoic acid
GO:0071560 cellular response to transforming growth factor beta stimulus
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:1904948 midbrain dopaminergic neuron differentiation
GO:1904954 canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0031012 extracellular matrix
GO:1990909 Wnt signalosome
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  KJ892384 - Synthetic construct Homo sapiens clone ccsbBroadEn_01778 WNT2 gene, encodes complete protein.
BC029854 - Homo sapiens wingless-type MMTV integration site family member 2, mRNA (cDNA clone IMAGE:5177611), complete cds.
BC078170 - Homo sapiens wingless-type MMTV integration site family member 2, mRNA (cDNA clone MGC:90326 IMAGE:5761421), complete cds.
GQ900909 - Homo sapiens clone HEL-T-21 epididymis secretory sperm binding protein mRNA, complete cds.
FW415773 - NUCLEIC ACID COMPOUNDS FOR INHIBITING WNT GENE EXPRESSION AND USES THEREOF.
JA824281 - Sequence 1390 from Patent EP2471920.
X07876 - Human mRNA for irp protein (int-1 related protein).
AK056742 - Homo sapiens cDNA FLJ32180 fis, clone PLACE6001557, highly similar to Protein Wnt-2 precursor.
BT019608 - Homo sapiens wingless-type MMTV integration site family member 2 mRNA, complete cds.
DQ892457 - Synthetic construct clone IMAGE:100005087; FLH186497.01X; RZPDo839F0271D wingless-type MMTV integration site family member 2 (WNT2) gene, encodes complete protein.
DQ895669 - Synthetic construct Homo sapiens clone IMAGE:100010129; FLH186493.01L; RZPDo839F0261D wingless-type MMTV integration site family member 2 (WNT2) gene, encodes complete protein.
AB590430 - Synthetic construct DNA, clone: pFN21AE1395, Homo sapiens WNT2 gene for wingless-type MMTV integration site family member 2, without stop codon, in Flexi system.
CU688768 - Synthetic construct Homo sapiens gateway clone IMAGE:100019083 5' read WNT2 mRNA.
JD313291 - Sequence 294315 from Patent EP1572962.
JD294843 - Sequence 275867 from Patent EP1572962.
JD228346 - Sequence 209370 from Patent EP1572962.
JD209913 - Sequence 190937 from Patent EP1572962.
JD549989 - Sequence 531013 from Patent EP1572962.
JD427326 - Sequence 408350 from Patent EP1572962.
JD208392 - Sequence 189416 from Patent EP1572962.
JD491943 - Sequence 472967 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04310 - Wnt signaling pathway
hsa04340 - Hedgehog signaling pathway
hsa04916 - Melanogenesis
hsa05200 - Pathways in cancer
hsa05217 - Basal cell carcinoma

Reactome (by CSHL, EBI, and GO)

Protein P09544 (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: ENST00000265441.1, ENST00000265441.2, ENST00000265441.3, ENST00000265441.4, ENST00000265441.5, ENST00000265441.6, ENST00000265441.7, INT1L1, IRP, NR_024047, P09544, Q75N05, Q9UDP9, uc003viz.1, uc003viz.2, uc003viz.3, uc003viz.4, uc003viz.5, WNT2_HUMAN
UCSC ID: ENST00000265441.8
RefSeq Accession: NM_003391
Protein: P09544 (aka WNT2_HUMAN)
CCDS: CCDS5771.1

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