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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 SREBF2 |
 Gene summary |
| Gene information | Gene symbol | SREBF2 | Gene ID | 6721 |
| Gene name | sterol regulatory element binding transcription factor 2 | |
| Synonyms | SREBP-2|SREBP2|bHLHd2 | |
| Cytomap | 22q13.2 | |
| Type of gene | protein-coding | |
| Description | sterol regulatory element-binding protein 2class D basic helix-loop-helix protein 2 | |
| Modification date | 20200329 | |
| UniProtAcc | ||
| Context | - 29503034(Alterations in cholesterol metabolism-related genes in sporadic 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 |
| SREBF2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 15358760|19098903 |
| SREBF2 | GO:0010886 | positive regulation of cholesterol storage | 15358760 |
| SREBF2 | GO:0032933 | SREBP signaling pathway | 27614840 |
| SREBF2 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 12242332|12446768 |
| SREBF2 | GO:0090370 | negative regulation of cholesterol efflux | 15358760 |
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Gene structures and expression levels for SREBF2 |
| 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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ENSG00000198911
| 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 |
| PCC | UP | ENST00000491541.1 | SREBF2-208:lncRNA:SREBF2 | 2.384247e+01 | 9.794422e-01 | 8.653634e-06 | 1.151501e-03 |
| CB | DOWN | ENST00000491541.1 | SREBF2-208:lncRNA:SREBF2 | 5.748205e+02 | -1.650694e+00 | 1.131847e-14 | 3.874769e-12 |
| CB | UP | ENST00000424354.5 | SREBF2-202:nonsense_mediated_decay:SREBF2 | 1.198636e+02 | 1.236921e+00 | 1.138755e-02 | 3.867497e-02 |
| TC | DOWN | ENST00000491541.1 | SREBF2-208:lncRNA:SREBF2 | 3.477377e+02 | -2.520393e+00 | 2.679091e-24 | 1.270776e-20 |
| 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 SREBF2 |
| 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_11191 | chr22 | 41903133:41903155:41904535:41904732:41904863:41904973 | 41904535:41904732 |
| exon_skip_115465 | chr22 | 41903084:41903155:41904535:41904732:41904863:41904973 | 41904535:41904732 |
| exon_skip_11676 | chr22 | 41886269:41886308:41891250:41891399:41893117:41893285 | 41891250:41891399 |
| exon_skip_162100 | chr22 | 41903076:41903155:41904535:41904732:41904863:41904973 | 41904535:41904732 |
| exon_skip_165551 | chr22 | 41893117:41893285:41894820:41894937:41897052:41897161 | 41894820:41894937 |
| exon_skip_17467 | chr22 | 41866831:41867280:41868611:41868792:41870889:41871035 | 41868611:41868792 |
| exon_skip_1936 | chr22 | 41877942:41878123:41878659:41878758:41880716:41880992 | 41878659:41878758 |
| exon_skip_212481 | chr22 | 41894820:41894937:41897052:41897161:41898649:41898781 | 41897052:41897161 |
| exon_skip_214063 | chr22 | 41902970:41903155:41904535:41904732:41904863:41904973 | 41904535:41904732 |
| exon_skip_219694 | chr22 | 41833164:41833358:41866831:41867280:41868611:41868792 | 41866831:41867280 |
| exon_skip_231318 | chr22 | 41898649:41898781:41899237:41899553:41900020:41900122 | 41899237:41899553 |
| exon_skip_250549 | chr22 | 41870889:41871035:41873798:41874019:41875337:41875451 | 41873798:41874019 |
| exon_skip_25702 | chr22 | 41868611:41868792:41870889:41871035:41873798:41874019 | 41870889:41871035 |
| exon_skip_294837 | chr22 | 41868619:41868792:41870889:41871035:41873798:41874019 | 41870889:41871035 |
| exon_skip_29601 | chr22 | 41877229:41877421:41877942:41878123:41880716:41880992 | 41877942:41878123 |
| exon_skip_61217 | chr22 | 41899237:41899553:41900020:41900122:41900330:41900498 | 41900020:41900122 |
| exon_skip_62571 | chr22 | 41833164:41833358:41866831:41867280:41868611:41868753 | 41866831:41867280 |
| exon_skip_99099 | chr22 | 41898676:41898781:41899237:41899553:41900020:41900122 | 41899237:41899553 |
| 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 SREBF2 |
| 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 |
| ENST00000361204 | 41877942 | 41878123 | Frame-shift |
| ENST00000361204 | 41894820 | 41894937 | Frame-shift |
| ENST00000361204 | 41897052 | 41897161 | Frame-shift |
| ENST00000361204 | 41866831 | 41867280 | In-frame |
| ENST00000361204 | 41870889 | 41871035 | In-frame |
| ENST00000361204 | 41873798 | 41874019 | 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 |
| ENST00000361204 | 41897052 | 41897161 | Frame-shift |
| ENST00000361204 | 41873798 | 41874019 | 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 |
| ENST00000361204 | 41868611 | 41868792 | Frame-shift |
| ENST00000361204 | 41877942 | 41878123 | Frame-shift |
| ENST00000361204 | 41897052 | 41897161 | Frame-shift |
| ENST00000361204 | 41866831 | 41867280 | In-frame |
| ENST00000361204 | 41870889 | 41871035 | In-frame |
| ENST00000361204 | 41873798 | 41874019 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SREBF2 |
p-ENSG00000198911_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 |
| ENST00000361204 | 5257 | 1141 | 41866831 | 41867280 | 256 | 704 | 30 | 179 |
| ENST00000361204 | 5257 | 1141 | 41870889 | 41871035 | 888 | 1033 | 240 | 289 |
| ENST00000361204 | 5257 | 1141 | 41873798 | 41874019 | 1035 | 1255 | 289 | 363 |
| 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 |
| ENST00000361204 | 5257 | 1141 | 41873798 | 41874019 | 1035 | 1255 | 289 | 363 |
| 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 |
| ENST00000361204 | 5257 | 1141 | 41866831 | 41867280 | 256 | 704 | 30 | 179 |
| ENST00000361204 | 5257 | 1141 | 41870889 | 41871035 | 888 | 1033 | 240 | 289 |
| ENST00000361204 | 5257 | 1141 | 41873798 | 41874019 | 1035 | 1255 | 289 | 363 |
| 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 |
| Q12772 | 30 | 179 | 1 | 1141 | Chain | ID=PRO_0000127452;Note=Sterol regulatory element-binding protein 2 |
| Q12772 | 30 | 179 | 1 | 484 | Chain | ID=PRO_0000314033;Note=Processed sterol regulatory element-binding protein 2 |
| Q12772 | 30 | 179 | 52 | 124 | Compositional bias | Note=Gly/Pro/Ser-rich |
| Q12772 | 30 | 179 | 125 | 244 | Compositional bias | Note=Gln-rich |
| Q12772 | 30 | 179 | 1 | 50 | Region | Note=Transcriptional activation (acidic) |
| Q12772 | 30 | 179 | 1 | 479 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q12772 | 240 | 289 | 273 | 275 | Alternative sequence | ID=VSP_054283;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q12772 | 240 | 289 | 1 | 1141 | Chain | ID=PRO_0000127452;Note=Sterol regulatory element-binding protein 2 |
| Q12772 | 240 | 289 | 1 | 484 | Chain | ID=PRO_0000314033;Note=Processed sterol regulatory element-binding protein 2 |
| Q12772 | 240 | 289 | 125 | 244 | Compositional bias | Note=Gln-rich |
| Q12772 | 240 | 289 | 273 | 273 | Natural variant | ID=VAR_036394;Note=In a breast cancer sample%3B somatic mutation. A->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q12772 | 240 | 289 | 237 | 491 | Region | Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q12772 | 240 | 289 | 1 | 479 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q12772 | 289 | 363 | 1 | 1141 | Chain | ID=PRO_0000127452;Note=Sterol regulatory element-binding protein 2 |
| Q12772 | 289 | 363 | 1 | 484 | Chain | ID=PRO_0000314033;Note=Processed sterol regulatory element-binding protein 2 |
| Q12772 | 289 | 363 | 330 | 380 | Domain | Note=bHLH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00981 |
| Q12772 | 289 | 363 | 346 | 357 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1UKL |
| Q12772 | 289 | 363 | 347 | 347 | Natural variant | ID=VAR_036395;Note=In a breast cancer sample%3B somatic mutation. N->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q12772 | 289 | 363 | 237 | 491 | Region | Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q12772 | 289 | 363 | 1 | 479 | 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 |
| Q12772 | 289 | 363 | 1 | 1141 | Chain | ID=PRO_0000127452;Note=Sterol regulatory element-binding protein 2 |
| Q12772 | 289 | 363 | 1 | 484 | Chain | ID=PRO_0000314033;Note=Processed sterol regulatory element-binding protein 2 |
| Q12772 | 289 | 363 | 330 | 380 | Domain | Note=bHLH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00981 |
| Q12772 | 289 | 363 | 346 | 357 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1UKL |
| Q12772 | 289 | 363 | 347 | 347 | Natural variant | ID=VAR_036395;Note=In a breast cancer sample%3B somatic mutation. N->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q12772 | 289 | 363 | 237 | 491 | Region | Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q12772 | 289 | 363 | 1 | 479 | 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 |
| Q12772 | 30 | 179 | 1 | 1141 | Chain | ID=PRO_0000127452;Note=Sterol regulatory element-binding protein 2 |
| Q12772 | 30 | 179 | 1 | 484 | Chain | ID=PRO_0000314033;Note=Processed sterol regulatory element-binding protein 2 |
| Q12772 | 30 | 179 | 52 | 124 | Compositional bias | Note=Gly/Pro/Ser-rich |
| Q12772 | 30 | 179 | 125 | 244 | Compositional bias | Note=Gln-rich |
| Q12772 | 30 | 179 | 1 | 50 | Region | Note=Transcriptional activation (acidic) |
| Q12772 | 30 | 179 | 1 | 479 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q12772 | 240 | 289 | 273 | 275 | Alternative sequence | ID=VSP_054283;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q12772 | 240 | 289 | 1 | 1141 | Chain | ID=PRO_0000127452;Note=Sterol regulatory element-binding protein 2 |
| Q12772 | 240 | 289 | 1 | 484 | Chain | ID=PRO_0000314033;Note=Processed sterol regulatory element-binding protein 2 |
| Q12772 | 240 | 289 | 125 | 244 | Compositional bias | Note=Gln-rich |
| Q12772 | 240 | 289 | 273 | 273 | Natural variant | ID=VAR_036394;Note=In a breast cancer sample%3B somatic mutation. A->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q12772 | 240 | 289 | 237 | 491 | Region | Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q12772 | 240 | 289 | 1 | 479 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q12772 | 289 | 363 | 1 | 1141 | Chain | ID=PRO_0000127452;Note=Sterol regulatory element-binding protein 2 |
| Q12772 | 289 | 363 | 1 | 484 | Chain | ID=PRO_0000314033;Note=Processed sterol regulatory element-binding protein 2 |
| Q12772 | 289 | 363 | 330 | 380 | Domain | Note=bHLH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00981 |
| Q12772 | 289 | 363 | 346 | 357 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1UKL |
| Q12772 | 289 | 363 | 347 | 347 | Natural variant | ID=VAR_036395;Note=In a breast cancer sample%3B somatic mutation. N->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q12772 | 289 | 363 | 237 | 491 | Region | Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q12772 | 289 | 363 | 1 | 479 | 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 SREBF2 |
| 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 SREBF2 |
| - 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 SREBF2 |
| 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 SREBF2 |
| 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 SREBF2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SREBF2 |
| 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 SREBF2 |
| 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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