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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 EFHD2 |
Gene summary |
Gene information | Gene symbol | EFHD2 | Gene ID | 79180 |
Gene name | EF-hand domain family member D2 | |
Synonyms | SWS1 | |
Cytomap | 1p36.21 | |
Type of gene | protein-coding | |
Description | EF-hand domain-containing protein D2EF hand domain containing 2swiprosin 1testicular tissue protein Li 62 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context | - 31456657(EFhd2 Affects Tau Liquid-Liquid Phase Separation) |
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 EFHD2 |
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 |
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 EFHD2 |
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_108700 | chr1 | 15425871:15426018:15427150:15427284:15428593:15428764 | 15427150:15427284 |
exon_skip_138363 | chr1 | 15425871:15426018:15427150:15427284:15428593:15428720 | 15427150:15427284 |
exon_skip_141443 | chr1 | 15425871:15426018:15427150:15427284:15428593:15428637 | 15427150:15427284 |
exon_skip_197432 | chr1 | 15427150:15427284:15427898:15428009:15428593:15428637 | 15427898:15428009 |
exon_skip_233531 | chr1 | 15427150:15427284:15427898:15428009:15428593:15429081 | 15427898:15428009 |
exon_skip_235108 | chr1 | 15427171:15427284:15427898:15428009:15428593:15429081 | 15427898:15428009 |
exon_skip_257554 | chr1 | 15425871:15426018:15427150:15427284:15428593:15429081 | 15427150:15427284 |
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 |
exon_skip_108700 | Mayo_CB | 7.475610e-01 | 8.649351e-01 | -1.173741e-01 | 1.718473e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for EFHD2 |
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 |
ENST00000375980 | 15427150 | 15427284 | 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 |
ENST00000375980 | 15427150 | 15427284 | 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 |
ENST00000375980 | 15427150 | 15427284 | In-frame |
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Infer the effects of exon skipping event on protein functional features for EFHD2 |
p-ENSG00000142634_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 |
ENST00000375980 | 2436 | 240 | 15427150 | 15427284 | 535 | 668 | 152 | 197 |
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 |
ENST00000375980 | 2436 | 240 | 15427150 | 15427284 | 535 | 668 | 152 | 197 |
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 |
ENST00000375980 | 2436 | 240 | 15427150 | 15427284 | 535 | 668 | 152 | 197 |
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 |
Q96C19 | 152 | 197 | 141 | 152 | Calcium binding | Note=2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
Q96C19 | 152 | 197 | 2 | 240 | Chain | ID=PRO_0000073645;Note=EF-hand domain-containing protein D2 |
Q96C19 | 152 | 197 | 128 | 163 | Domain | Note=EF-hand 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
Q96C19 | 152 | 197 | 150 | 161 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I2L |
Q96C19 | 152 | 197 | 170 | 177 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I2L |
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 |
Q96C19 | 152 | 197 | 141 | 152 | Calcium binding | Note=2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
Q96C19 | 152 | 197 | 2 | 240 | Chain | ID=PRO_0000073645;Note=EF-hand domain-containing protein D2 |
Q96C19 | 152 | 197 | 128 | 163 | Domain | Note=EF-hand 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
Q96C19 | 152 | 197 | 150 | 161 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I2L |
Q96C19 | 152 | 197 | 170 | 177 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I2L |
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 |
Q96C19 | 152 | 197 | 141 | 152 | Calcium binding | Note=2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
Q96C19 | 152 | 197 | 2 | 240 | Chain | ID=PRO_0000073645;Note=EF-hand domain-containing protein D2 |
Q96C19 | 152 | 197 | 128 | 163 | Domain | Note=EF-hand 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
Q96C19 | 152 | 197 | 150 | 161 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I2L |
Q96C19 | 152 | 197 | 170 | 177 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I2L |
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3'-UTR located exon skipping events that lost miRNA binding sites in EFHD2 |
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 EFHD2 |
- 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 EFHD2 |
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 EFHD2 |
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 EFHD2 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | TARDBP | exon_skip_108700 | -4.399896e-01 | 6.512320e-09 |
CB | ZNF638 | exon_skip_108700 | -5.344592e-01 | 3.990039e-13 |
CB | SAMD4A | exon_skip_108700 | -5.206556e-01 | 1.995033e-12 |
CB | RBM4 | exon_skip_108700 | -7.761730e-01 | 2.912574e-33 |
CB | RBM4B | exon_skip_108700 | -5.419057e-01 | 1.623801e-13 |
PCC | SAMD4A | exon_skip_108700 | -5.728866e-01 | 3.769279e-20 |
PCC | HNRNPF | exon_skip_108700 | -4.462044e-01 | 6.473037e-12 |
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RelatedDrugs for EFHD2 |
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 EFHD2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |