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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for MS4A4A |
 Gene summary |
| Gene information | Gene symbol | MS4A4A | Gene ID | 51338 |
| Gene name | membrane spanning 4-domains A4A | |
| Synonyms | 4SPAN1|CD20-L1|CD20L1|HDCME31P|MS4A4|MS4A7 | |
| Cytomap | 11q12.2 | |
| Type of gene | protein-coding | |
| Description | membrane-spanning 4-domains subfamily A member 4ACD20 antigen-like 1Fc epsilon receptor beta subunit homologepididymis secretory sperm binding proteinfour-span transmembrane protein 1membrane-spanning 4-domains, subfamily A, member 4 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 31413141(The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer's disease risk) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for MS4A4A |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000110079
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for MS4A4A |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_103651 | chr11 | 60280669:60280716:60282594:60282739:60292225:60292384 | 60282594:60282739 |
| exon_skip_10810 | chr11 | 60280685:60280716:60282594:60282739:60292225:60292384 | 60282594:60282739 |
| exon_skip_189639 | chr11 | 60280685:60280716:60292225:60292384:60297197:60297325 | 60292225:60292384 |
| exon_skip_192443 | chr11 | 60301001:60301057:60302559:60302717:60306100:60306201 | 60302559:60302717 |
| exon_skip_49072 | chr11 | 60292225:60292384:60297197:60297325:60301001:60301057 | 60297197:60297325 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for MS4A4A |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000337908 | 60292225 | 60292384 | Frame-shift |
| ENST00000337908 | 60297197 | 60297325 | In-frame |
| ENST00000337908 | 60302559 | 60302717 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000337908 | 60302559 | 60302717 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000337908 | 60292225 | 60292384 | Frame-shift |
| ENST00000337908 | 60297197 | 60297325 | In-frame |
| ENST00000337908 | 60302559 | 60302717 | In-frame |
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Infer the effects of exon skipping event on protein functional features for MS4A4A |
p-ENSG00000110079_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000337908 | 1621 | 239 | 60297197 | 60297325 | 293 | 420 | 67 | 110 |
| ENST00000337908 | 1621 | 239 | 60302559 | 60302717 | 479 | 636 | 129 | 182 |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000337908 | 1621 | 239 | 60302559 | 60302717 | 479 | 636 | 129 | 182 |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000337908 | 1621 | 239 | 60297197 | 60297325 | 293 | 420 | 67 | 110 |
| ENST00000337908 | 1621 | 239 | 60302559 | 60302717 | 479 | 636 | 129 | 182 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q96JQ5 | 67 | 110 | 1 | 239 | Chain | ID=PRO_0000158634;Note=Membrane-spanning 4-domains subfamily A member 4A |
| Q96JQ5 | 67 | 110 | 100 | 100 | Sequence conflict | Note=Y->H;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96JQ5 | 67 | 110 | 86 | 98 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 67 | 110 | 65 | 85 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 67 | 110 | 99 | 119 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 130 | 182 | Alternative sequence | ID=VSP_007380;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11486273;Dbxref=PMID:11486273 |
| Q96JQ5 | 129 | 182 | 1 | 239 | Chain | ID=PRO_0000158634;Note=Membrane-spanning 4-domains subfamily A member 4A |
| Q96JQ5 | 129 | 182 | 178 | 178 | Natural variant | ID=VAR_024540;Note=M->V;Dbxref=dbSNP:rs6591561 |
| Q96JQ5 | 129 | 182 | 120 | 137 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 159 | 179 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 138 | 158 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 180 | 200 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q96JQ5 | 129 | 182 | 130 | 182 | Alternative sequence | ID=VSP_007380;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11486273;Dbxref=PMID:11486273 |
| Q96JQ5 | 129 | 182 | 1 | 239 | Chain | ID=PRO_0000158634;Note=Membrane-spanning 4-domains subfamily A member 4A |
| Q96JQ5 | 129 | 182 | 178 | 178 | Natural variant | ID=VAR_024540;Note=M->V;Dbxref=dbSNP:rs6591561 |
| Q96JQ5 | 129 | 182 | 120 | 137 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 159 | 179 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 138 | 158 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 180 | 200 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q96JQ5 | 67 | 110 | 1 | 239 | Chain | ID=PRO_0000158634;Note=Membrane-spanning 4-domains subfamily A member 4A |
| Q96JQ5 | 67 | 110 | 100 | 100 | Sequence conflict | Note=Y->H;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96JQ5 | 67 | 110 | 86 | 98 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 67 | 110 | 65 | 85 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 67 | 110 | 99 | 119 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 130 | 182 | Alternative sequence | ID=VSP_007380;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11486273;Dbxref=PMID:11486273 |
| Q96JQ5 | 129 | 182 | 1 | 239 | Chain | ID=PRO_0000158634;Note=Membrane-spanning 4-domains subfamily A member 4A |
| Q96JQ5 | 129 | 182 | 178 | 178 | Natural variant | ID=VAR_024540;Note=M->V;Dbxref=dbSNP:rs6591561 |
| Q96JQ5 | 129 | 182 | 120 | 137 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 159 | 179 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 138 | 158 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96JQ5 | 129 | 182 | 180 | 200 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in MS4A4A |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for MS4A4A |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for MS4A4A |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MS4A4A |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for MS4A4A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for MS4A4A |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for MS4A4A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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