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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 SREBF1 |
 Gene summary |
| Gene information | Gene symbol | SREBF1 | Gene ID | 6720 |
| Gene name | sterol regulatory element binding transcription factor 1 | |
| Synonyms | SREBP1|bHLHd1 | |
| Cytomap | 17p11.2 | |
| Type of gene | protein-coding | |
| Description | sterol regulatory element-binding protein 1class D basic helix-loop-helix protein 1 | |
| Modification date | 20200329 | |
| UniProtAcc | ||
| Context | - 18164103(Interactions Between the Products of the Herpes Simplex Genome and Alzheimer's Disease Susceptibility Genes: Relevance to Pathological-Signalling Cascades) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SREBF1 | GO:0032933 | SREBP signaling pathway | 27614840 |
| SREBF1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 26437365 |
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Gene structures and expression levels for SREBF1 |
| 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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ENSG00000072310
| 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 |
| STG | UP | ENST00000423161.3 | SREBF1-206:protein_coding:SREBF1 | 1.817359e+01 | 1.380411e+00 | 9.857649e-04 | 3.812144e-02 |
| PG | UP | ENST00000423161.3 | SREBF1-206:protein_coding:SREBF1 | 2.449302e+01 | 8.349808e-01 | 3.327769e-03 | 3.429624e-02 |
| CB | DOWN | ENST00000395756.5 | SREBF1-204:nonsense_mediated_decay:SREBF1 | 3.836843e+02 | -1.322199e+00 | 1.778133e-09 | 7.023767e-08 |
| CB | DOWN | ENST00000485080.6 | SREBF1-213:nonsense_mediated_decay:SREBF1 | 6.566212e+00 | -1.886716e+00 | 2.509937e-09 | 9.420377e-08 |
| TC | DOWN | ENST00000485080.6 | SREBF1-213:nonsense_mediated_decay:SREBF1 | 1.064832e+01 | -2.367079e+00 | 2.260840e-13 | 1.023000e-10 |
| TC | DOWN | ENST00000395756.5 | SREBF1-204:nonsense_mediated_decay:SREBF1 | 6.950893e+02 | -1.174354e+00 | 5.487068e-08 | 3.749523e-06 |
| TC | DOWN | ENST00000578469.1 | SREBF1-218:nonsense_mediated_decay:SREBF1 | 2.562480e+00 | -1.130735e+00 | 3.364833e-04 | 4.204314e-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 SREBF1 |
| 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_152250 | chr17 | 17814344:17814410:17814615:17814747:17814835:17814944 | 17814615:17814747 |
| exon_skip_170517 | chr17 | 17817256:17817457:17817548:17817591:17817696:17817900 | 17817548:17817591 |
| exon_skip_18344 | chr17 | 17816958:17817136:17817256:17817457:17817548:17817591 | 17817256:17817457 |
| exon_skip_186955 | chr17 | 17817696:17817916:17818260:17818374:17819013:17819234 | 17818260:17818374 |
| exon_skip_200043 | chr17 | 17820405:17820521:17823518:17823607:17836727:17836987 | 17823518:17823607 |
| exon_skip_209557 | chr17 | 17814835:17814944:17815221:17815329:17815860:17816028 | 17815221:17815329 |
| exon_skip_248831 | chr17 | 17812827:17812851:17813368:17813479:17813569:17813769 | 17813368:17813479 |
| exon_skip_274285 | chr17 | 17816958:17817136:17817256:17817457:17817696:17817900 | 17817256:17817457 |
| exon_skip_37651 | chr17 | 17819544:17819725:17820090:17820521:17836727:17836987 | 17820090:17820521 |
| exon_skip_59258 | chr17 | 17817256:17817457:17817548:17817591:17817696:17817727 | 17817548:17817591 |
| 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 SREBF1 |
| 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 |
| ENST00000261646 | 17814615 | 17814747 | Frame-shift |
| ENST00000261646 | 17817256 | 17817457 | Frame-shift |
| ENST00000261646 | 17818260 | 17818374 | Frame-shift |
| ENST00000261646 | 17820090 | 17820521 | 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 |
| ENST00000261646 | 17814615 | 17814747 | Frame-shift |
| ENST00000261646 | 17817256 | 17817457 | Frame-shift |
| 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 |
| ENST00000261646 | 17813368 | 17813479 | Frame-shift |
| ENST00000261646 | 17814615 | 17814747 | Frame-shift |
| ENST00000261646 | 17815221 | 17815329 | Frame-shift |
| ENST00000261646 | 17817256 | 17817457 | Frame-shift |
| ENST00000261646 | 17818260 | 17818374 | Frame-shift |
| ENST00000261646 | 17820090 | 17820521 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SREBF1 |
p-ENSG00000072310_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 |
| ENST00000261646 | 4195 | 1147 | 17820090 | 17820521 | 277 | 707 | 30 | 174 |
| 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 |
| 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 |
| ENST00000261646 | 4195 | 1147 | 17820090 | 17820521 | 277 | 707 | 30 | 174 |
| 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 |
| P36956 | 30 | 174 | 30 | 30 | Alternative sequence | ID=VSP_030859;Note=In isoform 4. E->EGEVGAGRGRANGLDAPRAGADRGAMDCTFE;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| P36956 | 30 | 174 | 1 | 1147 | Chain | ID=PRO_0000127447;Note=Sterol regulatory element-binding protein 1 |
| P36956 | 30 | 174 | 1 | 490 | Chain | ID=PRO_0000314029;Note=Processed sterol regulatory element-binding protein 1 |
| P36956 | 30 | 174 | 61 | 178 | Compositional bias | Note=Pro/Ser-rich |
| P36956 | 30 | 174 | 98 | 98 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P56720 |
| P36956 | 30 | 174 | 117 | 117 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| P36956 | 30 | 174 | 1 | 60 | Region | Note=Transcriptional activation (acidic) |
| P36956 | 30 | 174 | 1 | 487 | 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 |
| 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 |
| P36956 | 30 | 174 | 30 | 30 | Alternative sequence | ID=VSP_030859;Note=In isoform 4. E->EGEVGAGRGRANGLDAPRAGADRGAMDCTFE;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| P36956 | 30 | 174 | 1 | 1147 | Chain | ID=PRO_0000127447;Note=Sterol regulatory element-binding protein 1 |
| P36956 | 30 | 174 | 1 | 490 | Chain | ID=PRO_0000314029;Note=Processed sterol regulatory element-binding protein 1 |
| P36956 | 30 | 174 | 61 | 178 | Compositional bias | Note=Pro/Ser-rich |
| P36956 | 30 | 174 | 98 | 98 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P56720 |
| P36956 | 30 | 174 | 117 | 117 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| P36956 | 30 | 174 | 1 | 60 | Region | Note=Transcriptional activation (acidic) |
| P36956 | 30 | 174 | 1 | 487 | 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 SREBF1 |
| 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 SREBF1 |
| - 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 SREBF1 |
| 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 SREBF1 |
| 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 SREBF1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | NUP42 | exon_skip_170517 | -4.347126e-01 | 1.968685e-08 |
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RelatedDrugs for SREBF1 |
| 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 SREBF1 |
| 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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