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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 CD47 |
 Gene summary |
| Gene information | Gene symbol | CD47 | Gene ID | 961 |
| Gene name | CD47 molecule | |
| Synonyms | IAP|MER6|OA3 | |
| Cytomap | 3q13.12 | |
| Type of gene | protein-coding | |
| Description | leukocyte surface antigen CD47CD47 antigen (Rh-related antigen, integrin-associated signal transducer)CD47 glycoproteinRh-related antigenantigen identified by monoclonal antibody 1D8antigenic surface determinant protein OA3integrin associated protei | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| CD47 | GO:0008284 | positive regulation of cell proliferation | 15383453 |
| CD47 | GO:0022409 | positive regulation of cell-cell adhesion | 15383453 |
| CD47 | GO:0050870 | positive regulation of T cell activation | 15383453 |
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Gene structures and expression levels for CD47 |
| 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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ENSG00000196776
| 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 |
| CB | DOWN | ENST00000398258.7 | CD47-203:protein_coding:CD47 | 4.770348e+01 | -1.771869e+00 | 6.681003e-09 | 2.146095e-07 |
| CB | UP | ENST00000361309.5 | CD47-202:protein_coding:CD47 | 5.817381e+02 | 9.182591e-01 | 1.725271e-07 | 3.366285e-06 |
| TC | DOWN | ENST00000398258.7 | CD47-203:protein_coding:CD47 | 1.510211e+01 | -1.279793e+00 | 4.367743e-04 | 5.164697e-03 |
| 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 CD47 |
| 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_117612 | chr3 | 108047138:108047292:108050578:108050602:108051939:108051970 | 108050578:108050602 |
| exon_skip_118033 | chr3 | 108060745:108060852:108071093:108071182:108079991:108080344 | 108071093:108071182 |
| exon_skip_127272 | chr3 | 108051939:108051970:108055520:108055566:108057477:108057533 | 108055520:108055566 |
| exon_skip_138988 | chr3 | 108047174:108047292:108051939:108051970:108057477:108057569 | 108051939:108051970 |
| exon_skip_145432 | chr3 | 108047081:108047292:108051939:108051970:108057477:108057569 | 108051939:108051970 |
| exon_skip_167944 | chr3 | 108047081:108047292:108050578:108050602:108051939:108051970 | 108050578:108050602 |
| exon_skip_180671 | chr3 | 108050578:108050602:108051939:108051970:108057477:108057569 | 108051939:108051970 |
| exon_skip_185247 | chr3 | 108047081:108047292:108049619:108049651:108050578:108050598 | 108049619:108049651 |
| exon_skip_224983 | chr3 | 108059457:108059544:108060745:108060852:108071093:108071182 | 108060745:108060852 |
| exon_skip_234110 | chr3 | 108047138:108047292:108049619:108049651:108050578:108050598 | 108049619:108049651 |
| exon_skip_235758 | chr3 | 108057477:108057569:108058337:108058429:108059452:108059532 | 108058337:108058429 |
| exon_skip_242237 | chr3 | 108047081:108047292:108050578:108050602:108051939:108051959 | 108050578:108050602 |
| exon_skip_277598 | chr3 | 108049619:108049651:108050578:108050602:108051939:108051970 | 108050578:108050602 |
| exon_skip_67559 | chr3 | 108047081:108047292:108051939:108051970:108057477:108057533 | 108051939:108051970 |
| exon_skip_67807 | chr3 | 108047223:108047292:108051939:108051970:108057477:108057569 | 108051939:108051970 |
| exon_skip_84425 | chr3 | 108051939:108051970:108055520:108055566:108057477:108057569 | 108055520:108055566 |
| exon_skip_8609 | chr3 | 108047081:108047292:108049619:108049651:108050578:108050602 | 108049619:108049651 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_131916 | MSBB_STG | 5.924242e-01 | 7.141667e-01 | -1.217424e-01 | 3.334116e-02 |
| exon_skip_131916 | MSBB_PG | 4.389583e-01 | 6.469643e-01 | -2.080060e-01 | 1.706321e-06 |
| exon_skip_103896 | Mayo_CB | 2.298780e-01 | 7.246753e-02 | 1.574105e-01 | 1.774864e-07 |
| exon_skip_277598 | Mayo_CB | 8.436585e-01 | 9.444737e-01 | -1.008151e-01 | 5.655614e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for CD47 |
| 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 |
| ENST00000361309 | 108050578 | 108050602 | Frame-shift |
| ENST00000361309 | 108049619 | 108049651 | In-frame |
| ENST00000361309 | 108058337 | 108058429 | In-frame |
| ENST00000361309 | 108060745 | 108060852 | In-frame |
| ENST00000361309 | 108071093 | 108071182 | 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 |
| ENST00000361309 | 108050578 | 108050602 | Frame-shift |
| ENST00000361309 | 108049619 | 108049651 | In-frame |
| ENST00000361309 | 108071093 | 108071182 | 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 |
| ENST00000361309 | 108050578 | 108050602 | Frame-shift |
| ENST00000361309 | 108051939 | 108051970 | Frame-shift |
| ENST00000361309 | 108049619 | 108049651 | In-frame |
| ENST00000361309 | 108071093 | 108071182 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CD47 |
p-ENSG00000196776_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 |
| ENST00000361309 | 1302 | 323 | 108071093 | 108071182 | 507 | 595 | 133 | 163 |
| ENST00000361309 | 1302 | 323 | 108060745 | 108060852 | 597 | 703 | 163 | 199 |
| ENST00000361309 | 1302 | 323 | 108058337 | 108058429 | 798 | 889 | 230 | 261 |
| ENST00000361309 | 1302 | 323 | 108049619 | 108049651 | 1041 | 1072 | 311 | 322 |
| 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 |
| ENST00000361309 | 1302 | 323 | 108071093 | 108071182 | 507 | 595 | 133 | 163 |
| ENST00000361309 | 1302 | 323 | 108049619 | 108049651 | 1041 | 1072 | 311 | 322 |
| 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 |
| ENST00000361309 | 1302 | 323 | 108071093 | 108071182 | 507 | 595 | 133 | 163 |
| ENST00000361309 | 1302 | 323 | 108049619 | 108049651 | 1041 | 1072 | 311 | 322 |
| 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 |
| Q08722 | 133 | 163 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 133 | 163 | 33 | 263 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11454874;Dbxref=PMID:11454874 |
| Q08722 | 133 | 163 | 19 | 141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 133 | 163 | 163 | 176 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 133 | 163 | 142 | 162 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 163 | 199 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 163 | 199 | 33 | 263 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11454874;Dbxref=PMID:11454874 |
| Q08722 | 163 | 199 | 163 | 176 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 163 | 199 | 198 | 207 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 163 | 199 | 177 | 197 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 230 | 261 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 230 | 261 | 33 | 263 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11454874;Dbxref=PMID:11454874 |
| Q08722 | 230 | 261 | 229 | 235 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 230 | 261 | 257 | 268 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 230 | 261 | 236 | 256 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 311 | 322 | 293 | 323 | Alternative sequence | ID=VSP_002535;Note=In isoform OA3-293. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q08722 | 311 | 322 | 306 | 323 | Alternative sequence | ID=VSP_002537;Note=In isoform OA3-305. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7691831,ECO:0000303|Ref.3;Dbxref=PMID:15489334,PMID:7691831 |
| Q08722 | 311 | 322 | 312 | 323 | Alternative sequence | ID=VSP_002538;Note=In isoform OA3-312. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q08722 | 311 | 322 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 311 | 322 | 290 | 323 | Topological domain | Note=Cytoplasmic;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 |
| Q08722 | 133 | 163 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 133 | 163 | 33 | 263 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11454874;Dbxref=PMID:11454874 |
| Q08722 | 133 | 163 | 19 | 141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 133 | 163 | 163 | 176 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 133 | 163 | 142 | 162 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 311 | 322 | 293 | 323 | Alternative sequence | ID=VSP_002535;Note=In isoform OA3-293. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q08722 | 311 | 322 | 306 | 323 | Alternative sequence | ID=VSP_002537;Note=In isoform OA3-305. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7691831,ECO:0000303|Ref.3;Dbxref=PMID:15489334,PMID:7691831 |
| Q08722 | 311 | 322 | 312 | 323 | Alternative sequence | ID=VSP_002538;Note=In isoform OA3-312. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q08722 | 311 | 322 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 311 | 322 | 290 | 323 | Topological domain | Note=Cytoplasmic;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 |
| Q08722 | 133 | 163 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 133 | 163 | 33 | 263 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11454874;Dbxref=PMID:11454874 |
| Q08722 | 133 | 163 | 19 | 141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 133 | 163 | 163 | 176 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 133 | 163 | 142 | 162 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q08722 | 311 | 322 | 293 | 323 | Alternative sequence | ID=VSP_002535;Note=In isoform OA3-293. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q08722 | 311 | 322 | 306 | 323 | Alternative sequence | ID=VSP_002537;Note=In isoform OA3-305. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7691831,ECO:0000303|Ref.3;Dbxref=PMID:15489334,PMID:7691831 |
| Q08722 | 311 | 322 | 312 | 323 | Alternative sequence | ID=VSP_002538;Note=In isoform OA3-312. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q08722 | 311 | 322 | 19 | 323 | Chain | ID=PRO_0000014880;Note=Leukocyte surface antigen CD47 |
| Q08722 | 311 | 322 | 290 | 323 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CD47 |
| 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 CD47 |
| - 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 CD47 |
| 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 CD47 |
| 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 CD47 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_103896 | 5.599424e-01 | 1.674506e-14 |
| CB | RBM5 | exon_skip_252431 | 4.190480e-01 | 3.853121e-08 |
| CB | NUP42 | exon_skip_252431 | 6.281207e-01 | 7.854393e-19 |
| CB | NOVA1 | exon_skip_252431 | 4.683206e-01 | 4.813599e-10 |
| CB | DAZAP1 | exon_skip_277598 | -4.449413e-01 | 4.705712e-09 |
| CB | NUP42 | exon_skip_277598 | 4.600108e-01 | 1.196788e-09 |
| FL | NOVA1 | exon_skip_131916 | 4.844080e-01 | 7.224979e-13 |
| HCC | DAZAP1 | exon_skip_131916 | -6.695926e-01 | 7.116534e-37 |
| HCC | TARDBP | exon_skip_131916 | -4.378511e-01 | 3.253539e-14 |
| HCC | RBM5 | exon_skip_131916 | -7.078928e-01 | 8.183021e-43 |
| HCC | RBM47 | exon_skip_131916 | -4.974904e-01 | 1.780128e-18 |
| HCC | DAZAP1 | exon_skip_195043 | -4.874065e-01 | 1.620788e-17 |
| HCC | RBM6 | exon_skip_195043 | -5.282231e-01 | 8.362361e-21 |
| HCC | RBM5 | exon_skip_195043 | -5.035427e-01 | 9.172840e-19 |
| PG | RBM47 | exon_skip_131916 | -4.086811e-01 | 1.880422e-09 |
| PG | NOVA1 | exon_skip_131916 | 5.263325e-01 | 1.200751e-15 |
| STG | NUP42 | exon_skip_131916 | 4.549222e-01 | 6.649295e-06 |
| STG | NOVA1 | exon_skip_131916 | 5.119243e-01 | 2.508057e-07 |
| TC | NUP42 | exon_skip_114905 | 7.382873e-01 | 8.113779e-29 |
| TC | NOVA1 | exon_skip_114905 | 6.965560e-01 | 1.500475e-24 |
| TC | NUP42 | exon_skip_195043 | 4.995069e-01 | 1.769877e-11 |
| TC | NOVA1 | exon_skip_195043 | 5.786780e-01 | 1.106523e-15 |
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RelatedDrugs for CD47 |
| 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 CD47 |
| 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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