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WNT5B Wnt family member 5B [ Homo sapiens (human) ]

Gene ID: 81029, updated on 2-Nov-2024

Summary

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Official Symbol
WNT5Bprovided by HGNC
Official Full Name
Wnt family member 5Bprovided by HGNC
Primary source
HGNC:HGNC:16265
See related
Ensembl:ENSG00000111186 MIM:606361; AllianceGenome:HGNC:16265
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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. This gene is a member of the WNT gene family. It encodes a protein which shows 94% and 80% amino acid identity to the mouse Wnt5b protein and the human WNT5A protein, respectively. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]
Expression
Broad expression in prostate (RPKM 12.1), esophagus (RPKM 5.6) and 21 other tissues See more
Orthologs
mouse all
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Genomic context

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See WNT5B in Genome Data Viewer
Location:
12p13.33
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (1617056..1647212)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (1612578..1643573)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (1726222..1756378)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5803 Neighboring gene F-box and leucine rich repeat protein 14 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:1697008-1697667 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1701701-1702304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1715019-1715538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1714497-1715018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4116 Neighboring gene Sharpr-MPRA regulatory region 3814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1755758-1756258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1756259-1756759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4118 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5809 Neighboring gene microRNA 3649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5811 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:1800052-1800630 Neighboring gene SDA1 domain containing 1 pseudogene Neighboring gene adiponectin receptor 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. WNT5B drives osteosarcoma stemness, chemoresistance and metastasis. Perkins RS, et al. Clin Transl Med, 2024 May. PMID 38689429, Free PMC Article
  2. Molecular cloning and characterization of human WNT5B on chromosome 12p13.3 region. Saitoh T, et al. Int J Oncol, 2001 Aug. PMID 11445850
  3. Association of the gene encoding wingless-type mammary tumor virus integration-site family member 5B (WNT5B) with type 2 diabetes. Kanazawa A, et al. Am J Hum Genet, 2004 Nov. PMID 15386214, Free PMC Article
  4. Association of common gene variants in the WNT/β-catenin pathway with colon cancer recurrence. Páez D, et al. Pharmacogenomics J, 2014 Apr. PMID 23817222
  5. Wnt pathway in atypical teratoid rhabdoid tumors. Chakravadhanula M, et al. Neuro Oncol, 2015 Apr. PMID 25246426, Free PMC Article

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. WNT5B promotes the malignant phenotype of non-small cell lung cancer via the FZD3-DVL3-RAC1-PCP-JNK pathway.
    Title: WNT5B promotes the malignant phenotype of non-small cell lung cancer via the FZD3-DVL3-RAC1-PCP-JNK pathway.
  2. Role of Wnt5b-Ror1 signaling in the proliferation of pancreatic ductal adenocarcinoma cells.
    Title: Role of Wnt5b-Ror1 signaling in the proliferation of pancreatic ductal adenocarcinoma cells.
  3. WNT5B drives osteosarcoma stemness, chemoresistance and metastasis.
    Title: WNT5B drives osteosarcoma stemness, chemoresistance and metastasis.
  4. DLL4/Notch3/WNT5B axis mediates bidirectional prometastatic crosstalk between melanoma and lymphatic endothelial cells.
    Title: DLL4/Notch3/WNT5B axis mediates bidirectional prometastatic crosstalk between melanoma and lymphatic endothelial cells.
  5. Estrogen receptor alpha and NFATc1 bind to a bone mineral density-associated SNP to repress WNT5B in osteoblasts.
    Title: Estrogen receptor alpha and NFATc1 bind to a bone mineral density-associated SNP to repress WNT5B in osteoblasts.
  6. Exosome-mediated circ_0001846 participates in IL-1beta-induced chondrocyte cell damage by miR-149-5p-dependent regulation of WNT5B.
    Title: Exosome-mediated circ_0001846 participates in IL-1β-induced chondrocyte cell damage by miR-149-5p-dependent regulation of WNT5B.
  7. Up-regulated miR-374a-3p relieves lipopolysaccharides induced injury in CHON-001 cells via regulating Wingless-type MMTV integration site family member 5B.
    Title: Up-regulated miR-374a-3p relieves lipopolysaccharides induced injury in CHON-001 cells via regulating Wingless-type MMTV integration site family member 5B.
  8. The lncRNA RP11-142A22.4 promotes adipogenesis by sponging miR-587 to modulate Wnt5beta expression.
    Title: The lncRNA RP11-142A22.4 promotes adipogenesis by sponging miR-587 to modulate Wnt5β expression.
  9. WNT5B exerts oncogenic effects and is negatively regulated by miR-5587-3p in lung adenocarcinoma progression.
    Title: WNT5B exerts oncogenic effects and is negatively regulated by miR-5587-3p in lung adenocarcinoma progression.
  10. IMP3 also facilitates the transcription of SLUG, which is necessary for TAZ nuclear localization and activation, by a mechanism that is also mediated by WNT5B.
    Title: IMP3 Stabilization of WNT5B mRNA Facilitates TAZ Activation in Breast Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (38)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC2648

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables frizzled binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables signaling receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in canonical Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to retinoic acid ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chondrocyte differentiation IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in fat cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in lens fiber cell development ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of convergent extension involved in gastrulation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of non-canonical Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in Golgi lumen TAS
Traceable Author Statement
more info
  
colocalizes_with collagen-containing extracellular matrix HDA PubMed 
located_in endocytic vesicle membrane TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular exosome TAS
Traceable Author Statement
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space NAS
Non-traceable Author Statement
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
protein Wnt-5b
Names
WNT-5B protein
wingless-type MMTV integration site family, member 5B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_030775.2 → NP_110402.2  protein Wnt-5b precursor

    See identical proteins and their annotated locations for NP_110402.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs from variant 1 in the 5' UTR, which results from an alternate exon. Both variants encode the same protein.
    Source sequence(s)
    AY009399
    Consensus CDS
    CCDS8510.1
    UniProtKB/Swiss-Prot
    A8K315, D3DUP9, Q96S49, Q9BV04, Q9H1J7
    Related
    ENSP00000308887.3, ENST00000310594.7
    Conserved Domains (1) summary
    pfam00110
    Location:50 → 359
    wnt; wnt family

  2. NM_032642.3 → NP_116031.1  protein Wnt-5b precursor

    See identical proteins and their annotated locations for NP_116031.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs from variant 2 in the 5' UTR, which results from an alternate exon. Both variants encode the same protein.
    Source sequence(s)
    AC005182
    Consensus CDS
    CCDS8510.1
    UniProtKB/Swiss-Prot
    A8K315, D3DUP9, Q96S49, Q9BV04, Q9H1J7
    Related
    ENSP00000380379.2, ENST00000397196.7
    Conserved Domains (1) summary
    pfam00110
    Location:50 → 359
    wnt; wnt family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    1617056..1647212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    1612578..1643573
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H1J7.2 GenPept UniProtKB/Swiss-Prot:Q9H1J7

Gene LinkOut

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