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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 CD74 |
 Gene summary |
| Gene information | Gene symbol | CD74 | Gene ID | 972 |
| Gene name | CD74 molecule | |
| Synonyms | DHLAG|HLADG|II|Ia-GAMMA|p33 | |
| Cytomap | 5q33.1 | |
| Type of gene | protein-coding | |
| Description | HLA class II histocompatibility antigen gamma chainCD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)CD74 molecule, major histocompatibility complex, class II invariant chainHLA-DR antigens-associated | |
| 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 |
| CD74 | GO:0001516 | prostaglandin biosynthetic process | 12782713 |
| CD74 | GO:0001934 | positive regulation of protein phosphorylation | 24942581 |
| CD74 | GO:0002792 | negative regulation of peptide secretion | 19849849 |
| CD74 | GO:0033674 | positive regulation of kinase activity | 24942581 |
| CD74 | GO:0043066 | negative regulation of apoptotic process | 12782713 |
| CD74 | GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB signaling | 24942581 |
| CD74 | GO:0043410 | positive regulation of MAPK cascade | 24942581 |
| CD74 | GO:0043518 | negative regulation of DNA damage response, signal transduction by p53 class mediator | 17045821 |
| CD74 | GO:0045657 | positive regulation of monocyte differentiation | 24942581 |
| CD74 | GO:0045893 | positive regulation of transcription, DNA-templated | 24942581 |
| CD74 | GO:0046598 | positive regulation of viral entry into host cell | 24942581 |
| CD74 | GO:0050731 | positive regulation of peptidyl-tyrosine phosphorylation | 17045821 |
| CD74 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 17045821|24942581 |
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Gene structures and expression levels for CD74 |
| 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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ENSG00000019582
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| STG | UP | 1.125551e+03 | 8.723934e-01 | 4.776004e-05 | 3.925800e-03 |
| 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 |
| STG | UP | ENST00000377795.7 | CD74-203:protein_coding:CD74 | 1.890528e+02 | 1.395101e+00 | 8.383444e-05 | 9.924112e-03 |
| STG | UP | ENST00000353334.10 | CD74-202:protein_coding:CD74 | 5.876065e+02 | 9.882888e-01 | 1.470745e-04 | 1.386513e-02 |
| STG | UP | ENST00000518797.5 | CD74-206:protein_coding:CD74 | 1.005132e+02 | 9.953327e-01 | 1.863897e-04 | 1.587248e-02 |
| STG | UP | ENST00000523208.5 | CD74-209:nonsense_mediated_decay:CD74 | 5.176889e+01 | 1.302826e+00 | 2.065621e-04 | 1.681727e-02 |
| PG | UP | ENST00000523208.5 | CD74-209:nonsense_mediated_decay:CD74 | 6.813759e+01 | 8.102916e-01 | 8.127031e-05 | 2.356473e-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 CD74 |
| 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_131687 | chr5 | 150402563:150402625:150403121:150403312:150404680:150404767 | 150403121:150403312 |
| exon_skip_144024 | chr5 | 150402593:150402625:150403121:150403312:150404680:150404767 | 150403121:150403312 |
| exon_skip_158267 | chr5 | 150406259:150406321:150407152:150407324:150412625:150412751 | 150407152:150407324 |
| exon_skip_17636 | chr5 | 150402563:150402625:150404680:150404767:150405085:150405180 | 150404680:150404767 |
| exon_skip_189812 | chr5 | 150406259:150406321:150406881:150407324:150412625:150412751 | 150406881:150407324 |
| exon_skip_229432 | chr5 | 150406259:150406321:150406881:150406960:150407152:150407324 | 150406881:150406960 |
| exon_skip_232964 | chr5 | 150402563:150402625:150403121:150403312:150404680:150404712 | 150403121:150403312 |
| exon_skip_250552 | chr5 | 150402563:150402625:150403121:150403312:150406259:150406321 | 150403121:150403312 |
| exon_skip_276090 | chr5 | 150402574:150402625:150403121:150403312:150404680:150404767 | 150403121:150403312 |
| 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 CD74 |
| 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 |
| ENST00000009530 | 150406881 | 150406960 | Frame-shift |
| ENST00000009530 | 150403121 | 150403312 | 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 |
| ENST00000009530 | 150403121 | 150403312 | 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 |
| ENST00000009530 | 150406881 | 150406960 | Frame-shift |
| ENST00000009530 | 150403121 | 150403312 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CD74 |
p-ENSG00000019582_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 |
| ENST00000009530 | 998 | 296 | 150403121 | 150403312 | 628 | 818 | 208 | 272 |
| 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 |
| ENST00000009530 | 998 | 296 | 150403121 | 150403312 | 628 | 818 | 208 | 272 |
| 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 |
| ENST00000009530 | 998 | 296 | 150403121 | 150403312 | 628 | 818 | 208 | 272 |
| 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 |
| P04233 | 208 | 272 | 161 | 296 | Alternative sequence | ID=VSP_037870;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| P04233 | 208 | 272 | 209 | 272 | Alternative sequence | ID=VSP_005331;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:6324166,ECO:0000303|PubMed:6586420,ECO:0000303|Ref.5;Dbx |
| P04233 | 208 | 272 | 236 | 238 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L3H |
| P04233 | 208 | 272 | 240 | 244 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 249 | 253 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 265 | 267 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 1 | 296 | Chain | ID=PRO_0000067954;Note=HLA class II histocompatibility antigen gamma chain |
| P04233 | 208 | 272 | 213 | 232 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 243 | 250 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 252 | 271 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 210 | 271 | Domain | Note=Thyroglobulin type-1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00500 |
| P04233 | 208 | 272 | 256 | 256 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 212 | 217 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 208 | 209 | Site | Note=Breakpoint for translocation to form a CD74-ROS1 fusion protein |
| P04233 | 208 | 272 | 73 | 296 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P04233 | 208 | 272 | 245 | 248 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| 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 |
| P04233 | 208 | 272 | 161 | 296 | Alternative sequence | ID=VSP_037870;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| P04233 | 208 | 272 | 209 | 272 | Alternative sequence | ID=VSP_005331;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:6324166,ECO:0000303|PubMed:6586420,ECO:0000303|Ref.5;Dbx |
| P04233 | 208 | 272 | 236 | 238 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L3H |
| P04233 | 208 | 272 | 240 | 244 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 249 | 253 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 265 | 267 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 1 | 296 | Chain | ID=PRO_0000067954;Note=HLA class II histocompatibility antigen gamma chain |
| P04233 | 208 | 272 | 213 | 232 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 243 | 250 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 252 | 271 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 210 | 271 | Domain | Note=Thyroglobulin type-1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00500 |
| P04233 | 208 | 272 | 256 | 256 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 212 | 217 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 208 | 209 | Site | Note=Breakpoint for translocation to form a CD74-ROS1 fusion protein |
| P04233 | 208 | 272 | 73 | 296 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P04233 | 208 | 272 | 245 | 248 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| 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 |
| P04233 | 208 | 272 | 161 | 296 | Alternative sequence | ID=VSP_037870;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| P04233 | 208 | 272 | 209 | 272 | Alternative sequence | ID=VSP_005331;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:6324166,ECO:0000303|PubMed:6586420,ECO:0000303|Ref.5;Dbx |
| P04233 | 208 | 272 | 236 | 238 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L3H |
| P04233 | 208 | 272 | 240 | 244 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 249 | 253 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 265 | 267 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 1 | 296 | Chain | ID=PRO_0000067954;Note=HLA class II histocompatibility antigen gamma chain |
| P04233 | 208 | 272 | 213 | 232 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 243 | 250 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 252 | 271 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00500,ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 210 | 271 | Domain | Note=Thyroglobulin type-1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00500 |
| P04233 | 208 | 272 | 256 | 256 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10022822;Dbxref=PMID:10022822 |
| P04233 | 208 | 272 | 212 | 217 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
| P04233 | 208 | 272 | 208 | 209 | Site | Note=Breakpoint for translocation to form a CD74-ROS1 fusion protein |
| P04233 | 208 | 272 | 73 | 296 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P04233 | 208 | 272 | 245 | 248 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1ICF |
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3'-UTR located exon skipping events that lost miRNA binding sites in CD74 |
| 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 CD74 |
| - 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 CD74 |
| 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 CD74 |
| 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 CD74 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | RBM24 | exon_skip_131687 | 4.125078e-01 | 2.914945e-02 |
| IFG | EIF4G2 | exon_skip_131687 | 4.572145e-01 | 1.443990e-02 |
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RelatedDrugs for CD74 |
| 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 CD74 |
| 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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