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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for TNFRSF1A |
Gene summary |
Gene information | Gene symbol | TNFRSF1A | Gene ID | 7132 |
Gene name | TNF receptor superfamily member 1A | |
Synonyms | CD120a|FPF|TBP1|TNF-R|TNF-R-I|TNF-R55|TNFAR|TNFR1|TNFR55|TNFR60|p55|p55-R|p60 | |
Cytomap | 12p13.31 | |
Type of gene | protein-coding | |
Description | tumor necrosis factor receptor superfamily member 1ATNF-R1TNF-RITNFR-Itumor necrosis factor binding protein 1tumor necrosis factor receptor 1A isoform betatumor necrosis factor receptor type 1tumor necrosis factor-alpha receptor | |
Modification date | 20200322 | |
UniProtAcc | ||
Context | - 26621834(Genome-wide Haplotype Association Study Identify TNFRSF1A, CASP7, LRP1B, CDH1 and TG Genes Associated With Alzheimer's Disease in Caribbean Hispanic Individuals) |
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 TNFRSF1A |
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. |
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. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
PG | UP | ENST00000537842.5 | TNFRSF1A-210:lncRNA:TNFRSF1A | 3.984457e+00 | 2.319985e+00 | 2.309299e-05 | 9.295649e-04 |
CB | DOWN | ENST00000534885.5 | TNFRSF1A-205:nonsense_mediated_decay:TNFRSF1A | 2.128301e+01 | -2.386157e+00 | 8.210234e-03 | 2.956304e-02 |
TC | DOWN | ENST00000534885.5 | TNFRSF1A-205:nonsense_mediated_decay:TNFRSF1A | 3.490203e+01 | -3.292469e+00 | 1.671453e-06 | 6.106731e-05 |
TC | UP | ENST00000437813.7 | TNFRSF1A-203:lncRNA:TNFRSF1A | 4.604941e+00 | 1.402086e+00 | 4.640318e-03 | 3.167603e-02 |
TC | UP | ENST00000535958.1 | TNFRSF1A-207:lncRNA:TNFRSF1A | 1.831004e+00 | 1.240208e+00 | 4.921098e-03 | 3.311936e-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 TNFRSF1A |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_161527 | chr12 | 6330598:6330711:6330853:6330926:6333069:6333105 | 6330853:6330926 |
exon_skip_171427 | chr12 | 6333737:6333865:6334091:6334244:6341776:6342114 | 6334091:6334244 |
exon_skip_239332 | chr12 | 6329465:6329622:6329778:6330066:6330267:6330295 | 6329778:6330066 |
exon_skip_245437 | chr12 | 6329778:6330066:6330267:6330295:6330598:6330711 | 6330267:6330295 |
exon_skip_558 | chr12 | 6333845:6333865:6334091:6334244:6341776:6341848 | 6334091:6334244 |
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 TNFRSF1A |
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 |
ENST00000162749 | 6329778 | 6330066 | Frame-shift |
ENST00000162749 | 6330267 | 6330295 | Frame-shift |
ENST00000162749 | 6330853 | 6330926 | Frame-shift |
ENST00000162749 | 6334091 | 6334244 | Frame-shift |
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 |
ENST00000162749 | 6330267 | 6330295 | Frame-shift |
ENST00000162749 | 6330853 | 6330926 | Frame-shift |
ENST00000162749 | 6334091 | 6334244 | 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 |
ENST00000162749 | 6329778 | 6330066 | Frame-shift |
ENST00000162749 | 6330267 | 6330295 | Frame-shift |
ENST00000162749 | 6330853 | 6330926 | Frame-shift |
ENST00000162749 | 6334091 | 6334244 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for TNFRSF1A |
p-ENSG00000067182_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 |
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 |
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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in TNFRSF1A |
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 TNFRSF1A |
- 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 TNFRSF1A |
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 TNFRSF1A |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
CB | exon_skip_161527 | rs11064145 | chr12:6345932 | 3.009784e-11 | 3.421539e-08 |
CB | exon_skip_161527 | rs4149577 | chr12:6338356 | 3.774835e-06 | 1.120765e-03 |
DLPFC | exon_skip_161527 | rs11064145 | chr12:6345932 | 1.178405e-11 | 4.453490e-09 |
DLPFC | exon_skip_161527 | rs4149570 | chr12:6342424 | 9.963777e-06 | 1.127628e-03 |
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Correlation with RNA binding proteins (RBPs) for TNFRSF1A |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for TNFRSF1A |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
P19438 | approved | DB11626 | Tasonermin | biotech | P19438 |
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RelatedDiseases for TNFRSF1A |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |