This gene encodes a member of the membrane-spanning 4A gene family. Members of this protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. This family member likely plays a role in signal transduction and may function as a subunit associate... See more...

Aliases for MS4A3 Gene

Aliases for MS4A3 Gene

  • Membrane Spanning 4-Domains A3 2 3 5
  • HTM4 2 3 4
  • Membrane-Spanning 4-Domains, Subfamily A, Member 3 (Hematopoietic Cell-Specific) 2 3
  • Membrane-Spanning 4-Domains Subfamily A Member 3 3 4
  • Hematopoietic-Specific Transmembrane Protein 4 3 4
  • CD20 Antigen-Like Protein 3 4
  • CD20L 3 4
  • Hematopoietic Cell 4 Transmembrane Protein 3
  • IgE Receptor Beta Subunit 3
  • IgE Receptor Beta Chain 3
  • CD20 Antigen Homolog 3
  • MS4A3 5
  • HTm4 4

External Ids for MS4A3 Gene

Previous HGNC Symbols for MS4A3 Gene

  • CD20L

Previous GeneCards Identifiers for MS4A3 Gene

  • GC11P062218
  • GC11P061337
  • GC11P060074
  • GC11P059599
  • GC11P059580
  • GC11P059824
  • GC11P056172

Summaries for MS4A3 Gene

Entrez Gene Summary for MS4A3 Gene

  • This gene encodes a member of the membrane-spanning 4A gene family. Members of this protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. This family member likely plays a role in signal transduction and may function as a subunit associated with receptor complexes. The gene encoding this protein is localized to 11q12, among a cluster of related family members. Alternative splicing may result in multiple transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]

GeneCards Summary for MS4A3 Gene

MS4A3 (Membrane Spanning 4-Domains A3) is a Protein Coding gene. Diseases associated with MS4A3 include Mental Retardation, Autosomal Dominant 22. Among its related pathways are Innate Immune System. An important paralog of this gene is MS4A6A.

UniProtKB/Swiss-Prot Summary for MS4A3 Gene

  • Hematopoietic modulator for the G1-S cell cycle transition. Modulates the level of phosphorylation of cyclin-dependent kinase 2 (CDK2) through its direct binding to cyclin-dependent kinase inhibitor 3 (CDKN3/KAP).

Gene Wiki entry for MS4A3 Gene

Additional gene information for MS4A3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MS4A3 Gene

Genomics for MS4A3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for MS4A3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J060056 Promoter 1.3 EPDnew Ensembl 600.7 +0.5 514 1.4 IKZF1 JUND MTA2 MTA1 DPF2 HDAC1 SOX6 TCF12 EP300 CBX3 HSALNG0084439 MS4A3 RF00017-925 MN309358 MS4A2
GH11J059968 Enhancer 0.9 FANTOM5 11.1 -88.3 -88316 0.3 LEF1 IKZF1 JUND DDX20 PKNOX1 ZNF24 REST ZNF740 BRD9 DPF2 OOSP2 MS4A3 MS4A2 MRPL16 OOSP4A OOSP4B OOSP1 ENSG00000214788
GH11J060077 Enhancer 0.6 Ensembl 16.9 +21.8 21814 3.6 FOXA1 ZNF24 CBX3 ZNF316 TRIM28 TRIM24 CBX5 TAL1 MAFK TCF12 ENSG00000255331 YWHAZP9 MS4A3 OOSP2 MS4A14 MS4A6A MS4A2 piR-57460-090
GH11J060100 Enhancer 1.1 FANTOM5 Ensembl ENCODE 2.2 +43.6 43614 4 GATAD2A SOX13 RCOR2 FOXA1 RXRB GABPA CEBPA FOXK2 TCF7 FOXA2 HSALNG0084442 piR-56133-041 MS4A6A MS4A2 ENSG00000255355 MS4A3 MRPL16 piR-51999-003
GH11J060058 Promoter 0.4 Ensembl 4.9 +2.1 2114 0.2 ZNF384 HSALNG0084439 MS4A3 MN309358 MS4A2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MS4A3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for MS4A3

Top Transcription factor binding sites by QIAGEN in the MS4A3 gene promoter:
  • AML1a
  • C/EBPbeta
  • FOXL1
  • IRF-1
  • IRF-2
  • Nkx5-1
  • POU3F2
  • RORalpha2
  • TBP
  • Zic1

Genomic Locations for MS4A3 Gene

Genomic Locations for MS4A3 Gene
chr11:60,056,587-60,071,116
(GRCh38/hg38)
Size:
14,530 bases
Orientation:
Plus strand
chr11:59,824,060-59,838,601
(GRCh37/hg19)
Size:
14,542 bases
Orientation:
Plus strand

Genomic View for MS4A3 Gene

Genes around MS4A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MS4A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MS4A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MS4A3 Gene

Proteins for MS4A3 Gene

  • Protein details for MS4A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96HJ5-MS4A3_HUMAN
    Recommended name:
    Membrane-spanning 4-domains subfamily A member 3
    Protein Accession:
    Q96HJ5
    Secondary Accessions:
    • A8MTP8
    • Q8NHW2

    Protein attributes for MS4A3 Gene

    Size:
    214 amino acids
    Molecular mass:
    22933 Da
    Quaternary structure:
    • Interacts with CDKN3. Interacts with CDKN3-CDK2 complexes through its binding to CDKN3; this interaction facilitates dissociation of cyclin A from CDKN3-CDK2 complexes.

    Alternative splice isoforms for MS4A3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MS4A3 Gene

Post-translational modifications for MS4A3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for MS4A3 Gene

Domains & Families for MS4A3 Gene

Gene Families for MS4A3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for MS4A3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for MS4A3 Gene

GenScript: Design optimal peptide antigens:
  • Hematopoietic-specific transmembrane protein 4 (MS4A3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96HJ5

UniProtKB/Swiss-Prot:

MS4A3_HUMAN :
  • The C-terminal region is required for binding to CDKN3-CDK2 complexes and the modulation of CDKN3 activity.
  • Belongs to the MS4A family.
Domain:
  • The C-terminal region is required for binding to CDKN3-CDK2 complexes and the modulation of CDKN3 activity.
Family:
  • Belongs to the MS4A family.
genes like me logo Genes that share domains with MS4A3: view

Function for MS4A3 Gene

Molecular function for MS4A3 Gene

UniProtKB/Swiss-Prot Function:
Hematopoietic modulator for the G1-S cell cycle transition. Modulates the level of phosphorylation of cyclin-dependent kinase 2 (CDK2) through its direct binding to cyclin-dependent kinase inhibitor 3 (CDKN3/KAP).
GENATLAS Biochemistry:
membrane-spanning 4-domains,subfamily A,member 3,hematopoietic cell-specific

Phenotypes From GWAS Catalog for MS4A3 Gene

Gene Ontology (GO) - Molecular Function for MS4A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15671017
genes like me logo Genes that share ontologies with MS4A3: view
genes like me logo Genes that share phenotypes with MS4A3: view

Animal Model Products

CRISPR Products

miRNA for MS4A3 Gene

miRTarBase miRNAs that target MS4A3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MS4A3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for MS4A3 Gene

Localization for MS4A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MS4A3 Gene

Endomembrane system. Multi-pass membrane protein. Cytoplasm, perinuclear region. Note=Located in the perinuclear area.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MS4A3 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
peroxisome 1
nucleus 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MS4A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane TAS --
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with MS4A3: view

Pathways & Interactions for MS4A3 Gene

PathCards logo

SuperPathways for MS4A3 Gene

genes like me logo Genes that share pathways with MS4A3: view

Pathways by source for MS4A3 Gene

3 Reactome pathways for MS4A3 Gene

Gene Ontology (GO) - Biological Process for MS4A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043312 neutrophil degranulation TAS --
GO:0051726 regulation of cell cycle IEA --
genes like me logo Genes that share ontologies with MS4A3: view

No data available for SIGNOR curated interactions for MS4A3 Gene

Drugs & Compounds for MS4A3 Gene

No Compound Related Data Available

Transcripts for MS4A3 Gene

mRNA/cDNA for MS4A3 Gene

3 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MS4A3

Alternative Splicing Database (ASD) splice patterns (SP) for MS4A3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c
SP1: - -
SP2: - -
SP3: - - - - -
SP4: - - - -
SP5: - - - -
SP6: - - -
SP7: -

Relevant External Links for MS4A3 Gene

GeneLoc Exon Structure for
MS4A3

Expression for MS4A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MS4A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MS4A3 Gene

This gene is overexpressed in Whole Blood (x45.8).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for MS4A3

SOURCE GeneReport for Unigene cluster for MS4A3 Gene:

Hs.99960

mRNA Expression by UniProt/SwissProt for MS4A3 Gene:

Q96HJ5-MS4A3_HUMAN
Tissue specificity: Expressed specifically in hematopoietic cells and tissues.

Evidence on tissue expression from TISSUES for MS4A3 Gene

  • Bone marrow(4.6)
  • Blood(4.6)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with MS4A3: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for MS4A3 Gene

Orthologs for MS4A3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for MS4A3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia MS4A3 30 31
  • 95.17 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ms4a3 30 17 31
  • 73.94 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ms4a3 30
  • 72.12 (n)
Cow
(Bos Taurus)
Mammalia MS4A3 30 31
  • 63.48 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia MS4A3 31
  • 45 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 31
  • 23 (a)
ManyToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 21 (a)
OneToMany
Species where no ortholog for MS4A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for MS4A3 Gene

ENSEMBL:
Gene Tree for MS4A3 (if available)
TreeFam:
Gene Tree for MS4A3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MS4A3: view image

Paralogs for MS4A3 Gene

(1) SIMAP similar genes for MS4A3 Gene using alignment to 2 proteins:

  • MS4A3_HUMAN
  • E9PRW8_HUMAN
genes like me logo Genes that share paralogs with MS4A3: view

Variants for MS4A3 Gene

Additional dbSNP identifiers (rs#s) for MS4A3 Gene

Structural Variations from Database of Genomic Variants (DGV) for MS4A3 Gene

Variant ID Type Subtype PubMed ID
nsv336 CNV insertion 18451855
nsv468579 CNV gain 19166990
nsv509411 CNV insertion 20534489
nsv555150 CNV gain 21841781
nsv832173 CNV gain 17160897

Variation tolerance for MS4A3 Gene

Residual Variation Intolerance Score: 78.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.67; 14.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MS4A3 Gene

Human Gene Mutation Database (HGMD)
MS4A3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MS4A3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MS4A3 Gene

Disorders for MS4A3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for MS4A3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
mental retardation, autosomal dominant 22
  • mrd22
- elite association - COSMIC cancer census association via MalaCards
Search MS4A3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MS4A3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with MS4A3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MS4A3 Gene

Publications for MS4A3 Gene

  1. Cloning of the cDNA for a hematopoietic cell-specific protein related to CD20 and the beta subunit of the high-affinity IgE receptor: evidence for a family of proteins with four membrane-spanning regions. (PMID: 7524084) Adra CN … Lim B (Proceedings of the National Academy of Sciences of the United States of America 1994) 2 3 4 23
  2. Binding of HTm4 to cyclin-dependent kinase (Cdk)-associated phosphatase (KAP).Cdk2.cyclin A complex enhances the phosphatase activity of KAP, dissociates cyclin A, and facilitates KAP dephosphorylation of Cdk2. (PMID: 15671017) Chinami M … Adra CN (The Journal of biological chemistry 2005) 3 4 23
  3. Human HTm4 is a hematopoietic cell cycle regulator. (PMID: 11781350) Donato JL … Adra CN (The Journal of clinical investigation 2002) 3 4 23
  4. Genome-wide association study identifies novel loci associated with serum level of vitamin B12 in Chinese men. (PMID: 22367966) Lin X … Sun J (Human molecular genetics 2012) 3 41
  5. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 41

Products for MS4A3 Gene

Sources for MS4A3 Gene