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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 MS4A6A |
 Gene summary |
| Gene information | Gene symbol | MS4A6A | Gene ID | 64231 |
| Gene name | membrane spanning 4-domains A6A | |
| Synonyms | 4SPAN3|4SPAN3.2|CD20L3|CDA01|MS4A6|MST090|MSTP090 | |
| Cytomap | 11q12.2 | |
| Type of gene | protein-coding | |
| Description | membrane-spanning 4-domains subfamily A member 6ACD20 antigen-like 3CD20-like precusorHAIRB-isoMS4A6A-polymorphfour-span transmembrane protein 3four-span transmembrane protein 3.1four-span transmembrane protein 3.2membrane-spanning 4-domains, subf | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 21460840(Common Variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP Are Associated With Alzheimer's Disease) |
| 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 MS4A6A |
| 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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ENSG00000110077
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000525549.5 | MS4A6A-204:retained_intron:MS4A6A | 4.681313e+00 | 9.873778e-01 | 1.193818e-05 | 5.753449e-04 |
| PG | UP | ENST00000529906.5 | MS4A6A-211:lncRNA:MS4A6A | 5.953244e+00 | 8.454662e-01 | 8.028612e-05 | 2.334699e-03 |
| PG | UP | ENST00000528851.5 | MS4A6A-208:protein_coding:MS4A6A | 3.382272e+01 | 8.477651e-01 | 1.846418e-04 | 4.304946e-03 |
| PG | UP | ENST00000412309.6 | MS4A6A-201:protein_coding:MS4A6A | 1.881750e+01 | 1.135015e+00 | 8.974169e-04 | 1.347226e-02 |
| PG | UP | ENST00000526697.1 | MS4A6A-206:retained_intron:MS4A6A | 2.283324e+00 | 8.266995e-01 | 5.420655e-03 | 4.832501e-02 |
| 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 MS4A6A |
| 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_112784 | chr11 | 60175506:60175611:60181581:60181741:60182978:60183030 | 60181581:60181741 |
| exon_skip_148169 | chr11 | 60178260:60178316:60181581:60181741:60182978:60183030 | 60181581:60181741 |
| exon_skip_247879 | chr11 | 60175506:60175611:60178260:60178316:60181581:60181666 | 60178260:60178316 |
| exon_skip_272729 | chr11 | 60179894:60179965:60181581:60181741:60182978:60183030 | 60181581:60181741 |
| exon_skip_276012 | chr11 | 60175506:60175611:60178260:60178316:60181581:60181741 | 60178260:60178316 |
| exon_skip_83460 | chr11 | 60178260:60178316:60179831:60179965:60181581:60181666 | 60179831:60179965 |
| exon_skip_95414 | chr11 | 60175506:60175611:60178260:60178316:60179831:60179965 | 60178260:60178316 |
| 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 MS4A6A |
| 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 |
| ENST00000530839 | 60179831 | 60179965 | 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 |
| ENST00000530839 | 60179831 | 60179965 | 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 |
| ENST00000530839 | 60181581 | 60181741 | 3UTR-3CDS |
| ENST00000530839 | 60178260 | 60178316 | In-frame |
| ENST00000530839 | 60179831 | 60179965 | In-frame |
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Infer the effects of exon skipping event on protein functional features for MS4A6A |
p-ENSG00000110077_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 |
| ENST00000530839 | 1400 | 248 | 60179831 | 60179965 | 641 | 774 | 49 | 93 |
| 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 |
| ENST00000530839 | 1400 | 248 | 60179831 | 60179965 | 641 | 774 | 49 | 93 |
| 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 |
| ENST00000530839 | 1400 | 248 | 60179831 | 60179965 | 641 | 774 | 49 | 93 |
| ENST00000530839 | 1400 | 248 | 60178260 | 60178316 | 776 | 831 | 94 | 112 |
| 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 |
| Q9H2W1 | 49 | 93 | 1 | 248 | Chain | ID=PRO_0000158638;Note=Membrane-spanning 4-domains subfamily A member 6A |
| Q9H2W1 | 49 | 93 | 68 | 84 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 49 | 93 | 47 | 67 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 49 | 93 | 85 | 105 | 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 |
| Q9H2W1 | 49 | 93 | 1 | 248 | Chain | ID=PRO_0000158638;Note=Membrane-spanning 4-domains subfamily A member 6A |
| Q9H2W1 | 49 | 93 | 68 | 84 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 49 | 93 | 47 | 67 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 49 | 93 | 85 | 105 | 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 |
| Q9H2W1 | 49 | 93 | 1 | 248 | Chain | ID=PRO_0000158638;Note=Membrane-spanning 4-domains subfamily A member 6A |
| Q9H2W1 | 49 | 93 | 68 | 84 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 49 | 93 | 47 | 67 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 49 | 93 | 85 | 105 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 94 | 112 | 95 | 141 | Alternative sequence | ID=VSP_041191;Note=In isoform 4. FIISGSLSIATEKRLTKLLVHSSLVGSILSALSALVGFIILSVKQAT->VSRVSEEGRMGQRGEEDANSLDFPPASLLCLICQEQGVNGESCSPVG;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.7 |
| Q9H2W1 | 94 | 112 | 1 | 248 | Chain | ID=PRO_0000158638;Note=Membrane-spanning 4-domains subfamily A member 6A |
| Q9H2W1 | 94 | 112 | 107 | 107 | Sequence conflict | Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9H2W1 | 94 | 112 | 107 | 107 | Sequence conflict | Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9H2W1 | 94 | 112 | 110 | 110 | Sequence conflict | Note=T->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9H2W1 | 94 | 112 | 110 | 110 | Sequence conflict | Note=T->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9H2W1 | 94 | 112 | 106 | 116 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H2W1 | 94 | 112 | 85 | 105 | 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 MS4A6A |
| 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 MS4A6A |
| - 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 MS4A6A |
| 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 MS4A6A |
| 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 MS4A6A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for MS4A6A |
| 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 MS4A6A |
| 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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