CleftGeneDB-Search

Gene: Wnt3a

Basic information

Tag	Content
Uniprot ID	P27467
Entrez ID	22416
Genbank protein ID	CAA40173.1
Genbank nucleotide ID	NM_009522.2
Ensembl protein ID	ENSMUSP00000010044
Ensembl nucleotide ID	ENSMUSG00000009900
Gene name	Protein Wnt-3a
Gene symbol	Wnt3a
Organism	Mus musculus
NCBI taxa ID	10090
Cleft type	CPO
Developmental stage	E14.5
Data sources	Manually collected
Reference	23095888
Functional description	Ligand for members of the frizzled family of seven transmembrane receptors (Probable). Functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family (PubMed:26902720). Required for normal embryonic mesoderm development and formation of caudal somites (PubMed:8299937). Required for normal morphogenesis of the developing neural tube (PubMed:8299937). Mediates self-renewal of the stem cells at the bottom on intestinal crypts (in vitro) (PubMed:26902720).
Sequence	MAPLGYLLVL CSLKQALGSY PIWWSLAVGP QYSSLSTQPI LCASIPGLVP KQLRFCRNYV 60 EIMPSVAEGV KAGIQECQHQ FRGRRWNCTT VSNSLAIFGP VLDKATRESA FVHAIASAGV 120 AFAVTRSCAE GSAAICGCSS RLQGSPGEGW KWGGCSEDIE FGGMVSREFA DARENRPDAR 180 SAMNRHNNEA GRQAIASHMH LKCKCHGLSG SCEVKTCWWS QPDFRTIGDF LKDKYDSASE 240 MVVEKHRESR GWVETLRPRY TYFKVPTERD LVYYEASPNF CEPNPETGSF GTRDRTCNVS 300 SHGIDGCDLL CCGRGHNART ERRREKCHCV FHWCCYVSCQ ECTRVYDVHT CK 352

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation	Gene symbol	Entrez ID	UniProt ID	Cleft type	Developmental stage	Species	Evidence	Details
1:1 ortholog	WNT3A		A0A452ETX2			Capra hircus	Prediction	More>>
1:1 ortholog	WNT3A	89780	P56704			Homo sapiens	Publication	More>>
1:1 ortholog	Wnt3a	22416	P27467	CPO	E14.5	Mus musculus	Publication	More>>
1:1 ortholog	WNT3A	100615247	H2R817			Pan troglodytes	Prediction	More>>
1:1 ortholog		100514950	A0A480RFN3			Sus scrofa	Prediction	More>>
1:1 ortholog	WNT3A	100354583	G1SKY6			Oryctolagus cuniculus	Prediction	More>>
1:1 ortholog	Wnt3a	303181	F1M077			Rattus norvegicus	Prediction	More>>

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
WNT3A	rs1745420	Genotyping; PDT; and APL	18413325

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs26942846	p.Asp270His	missense variant	-	NC_000077.6:g.59249881C>G	UniProt

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0003713	transcription coactivator activity	IDA
GO:0005102	signaling receptor binding	ISO
GO:0005102	signaling receptor binding	TAS
GO:0005109	frizzled binding	IPI
GO:0005109	frizzled binding	IDA
GO:0005109	frizzled binding	IBA
GO:0005515	protein binding	IPI
GO:0019904	protein domain specific binding	IPI
GO:0039706	co-receptor binding	ISO
GO:0048018	receptor ligand activity	ISO
GO:0048018	receptor ligand activity	IDA

GO:Biological Process

GO ID	GO Term	Evidence
GO:0001649	osteoblast differentiation	IGI
GO:0001701	in utero embryonic development	IMP
GO:0001756	somitogenesis	IMP
GO:0001819	positive regulation of cytokine production	IDA
GO:0001934	positive regulation of protein phosphorylation	ISO
GO:0001934	positive regulation of protein phosphorylation	IDA
GO:0001947	heart looping	IMP
GO:0002092	positive regulation of receptor internalization	ISO
GO:0003136	negative regulation of heart induction by canonical Wnt signaling pathway	ISO
GO:0007165	signal transduction	TAS
GO:0007267	cell-cell signaling	TAS
GO:0007368	determination of left/right symmetry	IMP
GO:0007409	axonogenesis	IDA
GO:0007409	axonogenesis	IGI
GO:0007411	axon guidance	IDA
GO:0007498	mesoderm development	IMP
GO:0008283	cell population proliferation	ISO
GO:0008284	positive regulation of cell population proliferation	IDA
GO:0009887	animal organ morphogenesis	TAS
GO:0009952	anterior/posterior pattern specification	IDA
GO:0010387	COP9 signalosome assembly	IDA
GO:0010628	positive regulation of gene expression	ISO
GO:0010977	negative regulation of neuron projection development	IDA
GO:0016055	Wnt signaling pathway	IGI
GO:0016055	Wnt signaling pathway	IBA
GO:0021527	spinal cord association neuron differentiation	IDA
GO:0021527	spinal cord association neuron differentiation	IGI
GO:0021766	hippocampus development	IMP
GO:0021846	cell proliferation in forebrain	IDA
GO:0021874	Wnt signaling pathway involved in forebrain neuroblast division	IMP
GO:0021904	dorsal/ventral neural tube patterning	IMP
GO:0022008	neurogenesis	IDA
GO:0030097	hemopoiesis	IDA
GO:0030168	platelet activation	IDA
GO:0030182	neuron differentiation	IBA
GO:0030198	extracellular matrix organization	IDA
GO:0030509	BMP signaling pathway	ISO
GO:0030879	mammary gland development	IDA
GO:0030890	positive regulation of B cell proliferation	IDA
GO:0030901	midbrain development	IDA
GO:0032092	positive regulation of protein binding	ISO
GO:0033138	positive regulation of peptidyl-serine phosphorylation	ISO
GO:0033278	cell proliferation in midbrain	IDA
GO:0034613	cellular protein localization	IDA
GO:0035914	skeletal muscle cell differentiation	IGI
GO:0036342	post-anal tail morphogenesis	IMP
GO:0042472	inner ear morphogenesis	IGI
GO:0043280	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	IDA
GO:0045165	cell fate commitment	IBA
GO:0045595	regulation of cell differentiation	IDA
GO:0045599	negative regulation of fat cell differentiation	IDA
GO:0045599	negative regulation of fat cell differentiation	IGI
GO:0045860	positive regulation of protein kinase activity	IDA
GO:0045893	positive regulation of transcription, DNA-templated	IDA
GO:0045944	positive regulation of transcription by RNA polymerase II	ISO
GO:0045944	positive regulation of transcription by RNA polymerase II	IGI
GO:0045944	positive regulation of transcription by RNA polymerase II	IDA
GO:0045944	positive regulation of transcription by RNA polymerase II	NAS
GO:0048103	somatic stem cell division	IDA
GO:0048337	positive regulation of mesodermal cell fate specification	ISO
GO:0048343	paraxial mesodermal cell fate commitment	IMP
GO:0048643	positive regulation of skeletal muscle tissue development	IMP
GO:0048697	positive regulation of collateral sprouting in absence of injury	IDA
GO:0048843	negative regulation of axon extension involved in axon guidance	IDA
GO:0050768	negative regulation of neurogenesis	IDA
GO:0050770	regulation of axonogenesis	IGI
GO:0050804	modulation of chemical synaptic transmission	EXP
GO:0050804	modulation of chemical synaptic transmission	IDA
GO:0050804	modulation of chemical synaptic transmission	IMP
GO:0050807	regulation of synapse organization	ISO
GO:0051091	positive regulation of DNA-binding transcription factor activity	IDA
GO:0060070	canonical Wnt signaling pathway	ISO
GO:0060070	canonical Wnt signaling pathway	IGI
GO:0060070	canonical Wnt signaling pathway	IDA
GO:0060070	canonical Wnt signaling pathway	IMP
GO:0060923	cardiac muscle cell fate commitment	IGI
GO:0061098	positive regulation of protein tyrosine kinase activity	IGI
GO:0061184	positive regulation of dermatome development	ISO
GO:0061317	canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment	ISO
GO:0062009	secondary palate development	ISO
GO:0070507	regulation of microtubule cytoskeleton organization	IGI
GO:0070527	platelet aggregation	IDA
GO:0071542	dopaminergic neuron differentiation	TAS
GO:0090245	axis elongation involved in somitogenesis	IGI
GO:0090263	positive regulation of canonical Wnt signaling pathway	ISO
GO:0090263	positive regulation of canonical Wnt signaling pathway	IDA
GO:0090676	calcium ion transmembrane transport via low voltage-gated calcium channel	IDA
GO:0099527	postsynapse to nucleus signaling pathway	EXP
GO:0099527	postsynapse to nucleus signaling pathway	IDA
GO:1901215	negative regulation of neuron death	IGI
GO:1903078	positive regulation of protein localization to plasma membrane	IDA
GO:1904339	negative regulation of dopaminergic neuron differentiation	IDA
GO:1904798	positive regulation of core promoter binding	IMP
GO:1905606	regulation of presynapse assembly	ISO
GO:2000049	positive regulation of cell-cell adhesion mediated by cadherin	IDA
GO:2000081	positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation	IDA
GO:2000179	positive regulation of neural precursor cell proliferation	IDA
GO:2000347	positive regulation of hepatocyte proliferation	IDA
GO:2000727	positive regulation of cardiac muscle cell differentiation	ISO
GO:2001141	regulation of RNA biosynthetic process	IDA

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0005576	extracellular region	TAS
GO:0005615	extracellular space	ISO
GO:0005615	extracellular space	IDA
GO:0005615	extracellular space	IBA
GO:0005788	endoplasmic reticulum lumen	TAS
GO:0009986	cell surface	IDA
GO:0045202	synapse	IDA
GO:0098978	glutamatergic synapse	ISO
GO:0098978	glutamatergic synapse	EXP
GO:0098978	glutamatergic synapse	IDA
GO:0098978	glutamatergic synapse	IMP
GO:1990851	Wnt-Frizzled-LRP5/6 complex	ISO
GO:1990909	Wnt signalosome	IC
GO:1990909	Wnt signalosome	NAS

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-MMU-162582	Signal Transduction	IEA
R-MMU-195721	Signaling by WNT	IEA
R-MMU-201681	TCF dependent signaling in response to WNT	IEA
R-MMU-3238698	WNT ligand biogenesis and trafficking	IEA
R-MMU-4641262	Disassembly of the destruction complex and recruitment of AXIN to the membrane	IEA
R-MMU-4641263	Regulation of FZD by ubiquitination	IEA

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0217	Developmental protein
KW-1015	Disulfide bond
KW-0272	Extracellular matrix
KW-0325	Glycoprotein
KW-0449	Lipoprotein
KW-1185	Reference proteome
KW-0964	Secreted
KW-0732	Signal
KW-0879	Wnt signaling pathway

Interpro

InterPro ID	InterPro Term
IPR005817	Wnt
IPR009141	Wnt3
IPR043158	Wnt_C
IPR018161	Wnt_CS

PROSITE

PROSITE ID	PROSITE Term
PS00246	WNT1

Pfam

Pfam ID	Pfam Term
PF00110	wnt

Gene: Wnt3a

Basic information

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction