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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 SEMA3F |
Gene summary |
Gene information | Gene symbol | SEMA3F | Gene ID | 6405 |
Gene name | semaphorin 3F | |
Synonyms | SEMA-IV|SEMA4|SEMAK | |
Cytomap | 3p21.31 | |
Type of gene | protein-coding | |
Description | semaphorin-3Fsema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fsema domain, immunoglobulin domain (Ig), short basic domain, secreted, 3Fsemaphorin III/Fsemaphorin IV | |
Modification date | 20200322 | |
UniProtAcc | ||
Context | - 30140277(Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SEMA3F | GO:0007411 | axon guidance | 15814794 |
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Gene structures and expression levels for SEMA3F |
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 | ENST00000426511.5 | SEMA3F-205:protein_coding:SEMA3F | 8.280305e-01 | 1.582455e+00 | 3.055553e-03 | 3.223441e-02 |
CB | UP | ENST00000450338.5 | SEMA3F-207:protein_coding:SEMA3F | 1.809207e+01 | 1.048148e+00 | 6.732067e-08 | 1.520373e-06 |
TC | UP | ENST00000450338.5 | SEMA3F-207:protein_coding:SEMA3F | 1.944546e+01 | 9.226653e-01 | 3.447056e-04 | 4.290682e-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 SEMA3F |
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_177867 | chr3 | 50185666:50185707:50185889:50186046:50186281:50186348 | 50185889:50186046 |
exon_skip_261939 | chr3 | 50174231:50174350:50175096:50175188:50176768:50176861 | 50175096:50175188 |
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 SEMA3F |
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 |
ENST00000002829 | 50185889 | 50186046 | Frame-shift |
ENST00000002829 | 50175096 | 50175188 | 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 |
ENST00000002829 | 50175096 | 50175188 | 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 |
ENST00000002829 | 50185889 | 50186046 | Frame-shift |
ENST00000002829 | 50175096 | 50175188 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SEMA3F |
p-ENSG00000001617_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 |
ENST00000002829 | 3819 | 785 | 50175096 | 50175188 | 942 | 1033 | 152 | 183 |
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 |
ENST00000002829 | 3819 | 785 | 50175096 | 50175188 | 942 | 1033 | 152 | 183 |
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 |
ENST00000002829 | 3819 | 785 | 50175096 | 50175188 | 942 | 1033 | 152 | 183 |
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 |
Q13275 | 152 | 183 | 153 | 183 | Alternative sequence | ID=VSP_053417;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8786119;Dbxref=PMID:8786119 |
Q13275 | 152 | 183 | 19 | 785 | Chain | ID=PRO_0000032320;Note=Semaphorin-3F |
Q13275 | 152 | 183 | 31 | 545 | Domain | Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00352 |
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 |
Q13275 | 152 | 183 | 153 | 183 | Alternative sequence | ID=VSP_053417;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8786119;Dbxref=PMID:8786119 |
Q13275 | 152 | 183 | 19 | 785 | Chain | ID=PRO_0000032320;Note=Semaphorin-3F |
Q13275 | 152 | 183 | 31 | 545 | Domain | Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00352 |
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 |
Q13275 | 152 | 183 | 153 | 183 | Alternative sequence | ID=VSP_053417;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8786119;Dbxref=PMID:8786119 |
Q13275 | 152 | 183 | 19 | 785 | Chain | ID=PRO_0000032320;Note=Semaphorin-3F |
Q13275 | 152 | 183 | 31 | 545 | Domain | Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00352 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SEMA3F |
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 SEMA3F |
- 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 SEMA3F |
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 SEMA3F |
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 SEMA3F |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SEMA3F |
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 SEMA3F |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |