|
||||||
|
 | |
| |
| |
| 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 EFCAB6 |
 Gene summary |
| Gene information | Gene symbol | EFCAB6 | Gene ID | 64800 |
| Gene name | EF-hand calcium binding domain 6 | |
| Synonyms | DJBP|HSCBCIP1|dJ185D5.1 | |
| Cytomap | 22q13.2-q13.31 | |
| Type of gene | protein-coding | |
| Description | EF-hand calcium-binding domain-containing protein 6CAP-binding protein complex-interacting protein 1DJ-1-binding proteinepididymis secretory sperm binding protein | |
| Modification date | 20200313 | |
| UniProtAcc | B0QYI5, Q5THR3, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for EFCAB6 |
| 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. |
 |
ENSG00000186976
| 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 |
| CB | DOWN | ENST00000461800.5 | EFCAB6-205:lncRNA:EFCAB6 | 6.809305e+00 | -1.268531e+00 | 1.079076e-06 | 1.599974e-05 |
| TC | DOWN | ENST00000477145.1 | EFCAB6-208:lncRNA:EFCAB6 | 1.187429e+00 | -1.653240e+00 | 3.103077e-03 | 2.341453e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for EFCAB6 |
| 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_1017 | chr22 | 43765305:43765393:43808995:43809131:43812168:43812190 | 43808995:43809131 |
| exon_skip_104643 | chr22 | 43632105:43632238:43635102:43635216:43667104:43667272 | 43635102:43635216 |
| exon_skip_106444 | chr22 | 43782210:43782325:43808995:43809131:43812168:43812190 | 43808995:43809131 |
| exon_skip_114273 | chr22 | 43683747:43683855:43687471:43687581:43711475:43711623 | 43687471:43687581 |
| exon_skip_138163 | chr22 | 43765305:43765393:43797245:43797351:43808995:43809131 | 43797245:43797351 |
| exon_skip_206112 | chr22 | 43765305:43765393:43782180:43782325:43808995:43809131 | 43782180:43782325 |
| exon_skip_218347 | chr22 | 43667104:43667272:43668872:43669045:43671973:43672133 | 43668872:43669045 |
| exon_skip_22419 | chr22 | 43677996:43678163:43683747:43683855:43687471:43687581 | 43683747:43683855 |
| exon_skip_231626 | chr22 | 43528780:43528975:43530815:43530964:43534688:43534872 | 43530815:43530964 |
| exon_skip_233757 | chr22 | 43782210:43782325:43797245:43797351:43808995:43809131 | 43797245:43797351 |
| exon_skip_241121 | chr22 | 43668872:43669045:43671973:43672133:43672246:43672270 | 43671973:43672133 |
| exon_skip_279171 | chr22 | 43765305:43765393:43772892:43773103:43782180:43782325 | 43772892:43773103 |
| exon_skip_34822 | chr22 | 43731699:43731811:43735857:43735993:43755766:43755832 | 43735857:43735993 |
| exon_skip_43300 | chr22 | 43608482:43608600:43615826:43615922:43626447:43626679 | 43615826:43615922 |
| exon_skip_46149 | chr22 | 43600069:43600263:43608482:43608600:43626447:43626679 | 43608482:43608600 |
| exon_skip_52587 | chr22 | 43608482:43608600:43615826:43615922:43626447:43626651 | 43615826:43615922 |
| exon_skip_61056 | chr22 | 43772892:43773103:43782180:43782325:43808995:43809131 | 43782180:43782325 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for EFCAB6 |
| 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 |
| ENST00000262726 | 43808995 | 43809131 | 3UTR-3UTR |
| ENST00000262726 | 43615826 | 43615922 | Frame-shift |
| ENST00000262726 | 43635102 | 43635216 | Frame-shift |
| ENST00000262726 | 43671973 | 43672133 | Frame-shift |
| ENST00000262726 | 43683747 | 43683855 | Frame-shift |
| ENST00000262726 | 43735857 | 43735993 | Frame-shift |
| ENST00000262726 | 43772892 | 43773103 | Frame-shift |
| ENST00000262726 | 43530815 | 43530964 | In-frame |
| ENST00000262726 | 43668872 | 43669045 | In-frame |
| ENST00000262726 | 43687471 | 43687581 | 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 |
| ENST00000262726 | 43808995 | 43809131 | 3UTR-3UTR |
| ENST00000262726 | 43615826 | 43615922 | Frame-shift |
| ENST00000262726 | 43635102 | 43635216 | Frame-shift |
| ENST00000262726 | 43683747 | 43683855 | Frame-shift |
| ENST00000262726 | 43735857 | 43735993 | Frame-shift |
| ENST00000262726 | 43772892 | 43773103 | Frame-shift |
| ENST00000262726 | 43668872 | 43669045 | In-frame |
| ENST00000262726 | 43687471 | 43687581 | 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 |
| ENST00000262726 | 43782180 | 43782325 | 3UTR-3CDS |
| ENST00000262726 | 43808995 | 43809131 | 3UTR-3UTR |
| ENST00000262726 | 43615826 | 43615922 | Frame-shift |
| ENST00000262726 | 43635102 | 43635216 | Frame-shift |
| ENST00000262726 | 43683747 | 43683855 | Frame-shift |
| ENST00000262726 | 43772892 | 43773103 | Frame-shift |
| ENST00000262726 | 43530815 | 43530964 | In-frame |
| ENST00000262726 | 43668872 | 43669045 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for EFCAB6 |
p-ENSG00000186976_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 |
| ENST00000262726 | 4886 | 1501 | 43687471 | 43687581 | 1286 | 1395 | 344 | 380 |
| ENST00000262726 | 4886 | 1501 | 43668872 | 43669045 | 1895 | 2067 | 547 | 604 |
| ENST00000262726 | 4886 | 1501 | 43530815 | 43530964 | 4488 | 4636 | 1411 | 1460 |
| 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 |
| ENST00000262726 | 4886 | 1501 | 43687471 | 43687581 | 1286 | 1395 | 344 | 380 |
| ENST00000262726 | 4886 | 1501 | 43668872 | 43669045 | 1895 | 2067 | 547 | 604 |
| 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 |
| ENST00000262726 | 4886 | 1501 | 43668872 | 43669045 | 1895 | 2067 | 547 | 604 |
| ENST00000262726 | 4886 | 1501 | 43530815 | 43530964 | 4488 | 4636 | 1411 | 1460 |
| 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 |
| Q5THR3 | 344 | 380 | 1 | 1139 | Alternative sequence | ID=VSP_019808;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12529303;Dbxref=PMID:12529303 |
| Q5THR3 | 344 | 380 | 1 | 931 | Alternative sequence | ID=VSP_019809;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12612053,ECO:0000303|PubMed:14702039;Dbxref=PMID:12612053,PMID:14702039 |
| Q5THR3 | 344 | 380 | 1 | 1501 | Chain | ID=PRO_0000246024;Note=EF-hand calcium-binding domain-containing protein 6 |
| Q5THR3 | 344 | 380 | 351 | 351 | Natural variant | ID=VAR_048650;Note=T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14702039;Dbxref=dbSNP:rs5764214,PMID:14702039 |
| Q5THR3 | 547 | 604 | 1 | 1139 | Alternative sequence | ID=VSP_019808;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12529303;Dbxref=PMID:12529303 |
| Q5THR3 | 547 | 604 | 1 | 931 | Alternative sequence | ID=VSP_019809;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12612053,ECO:0000303|PubMed:14702039;Dbxref=PMID:12612053,PMID:14702039 |
| Q5THR3 | 547 | 604 | 421 | 1501 | Alternative sequence | ID=VSP_034832;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5THR3 | 547 | 604 | 1 | 1501 | Chain | ID=PRO_0000246024;Note=EF-hand calcium-binding domain-containing protein 6 |
| Q5THR3 | 1411 | 1460 | 421 | 1501 | Alternative sequence | ID=VSP_034832;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5THR3 | 1411 | 1460 | 1250 | 1501 | Alternative sequence | ID=VSP_019813;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11258795;Dbxref=PMID:11258795 |
| Q5THR3 | 1411 | 1460 | 1 | 1501 | Chain | ID=PRO_0000246024;Note=EF-hand calcium-binding domain-containing protein 6 |
| Q5THR3 | 1411 | 1460 | 1434 | 1469 | Domain | Note=EF-hand 16;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
| Q5THR3 | 1411 | 1460 | 1303 | 1501 | Region | Note=Interaction with PARK7;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12612053;Dbxref=PMID:12612053 |
| Q5THR3 | 1411 | 1460 | 1407 | 1501 | Region | Note=Interaction with AR;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12612053;Dbxref=PMID:12612053 |
| 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 |
| Q5THR3 | 344 | 380 | 1 | 1139 | Alternative sequence | ID=VSP_019808;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12529303;Dbxref=PMID:12529303 |
| Q5THR3 | 344 | 380 | 1 | 931 | Alternative sequence | ID=VSP_019809;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12612053,ECO:0000303|PubMed:14702039;Dbxref=PMID:12612053,PMID:14702039 |
| Q5THR3 | 344 | 380 | 1 | 1501 | Chain | ID=PRO_0000246024;Note=EF-hand calcium-binding domain-containing protein 6 |
| Q5THR3 | 344 | 380 | 351 | 351 | Natural variant | ID=VAR_048650;Note=T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14702039;Dbxref=dbSNP:rs5764214,PMID:14702039 |
| Q5THR3 | 547 | 604 | 1 | 1139 | Alternative sequence | ID=VSP_019808;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12529303;Dbxref=PMID:12529303 |
| Q5THR3 | 547 | 604 | 1 | 931 | Alternative sequence | ID=VSP_019809;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12612053,ECO:0000303|PubMed:14702039;Dbxref=PMID:12612053,PMID:14702039 |
| Q5THR3 | 547 | 604 | 421 | 1501 | Alternative sequence | ID=VSP_034832;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5THR3 | 547 | 604 | 1 | 1501 | Chain | ID=PRO_0000246024;Note=EF-hand calcium-binding domain-containing protein 6 |
| 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 |
| Q5THR3 | 547 | 604 | 1 | 1139 | Alternative sequence | ID=VSP_019808;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12529303;Dbxref=PMID:12529303 |
| Q5THR3 | 547 | 604 | 1 | 931 | Alternative sequence | ID=VSP_019809;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12612053,ECO:0000303|PubMed:14702039;Dbxref=PMID:12612053,PMID:14702039 |
| Q5THR3 | 547 | 604 | 421 | 1501 | Alternative sequence | ID=VSP_034832;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5THR3 | 547 | 604 | 1 | 1501 | Chain | ID=PRO_0000246024;Note=EF-hand calcium-binding domain-containing protein 6 |
| Q5THR3 | 1411 | 1460 | 421 | 1501 | Alternative sequence | ID=VSP_034832;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5THR3 | 1411 | 1460 | 1250 | 1501 | Alternative sequence | ID=VSP_019813;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11258795;Dbxref=PMID:11258795 |
| Q5THR3 | 1411 | 1460 | 1 | 1501 | Chain | ID=PRO_0000246024;Note=EF-hand calcium-binding domain-containing protein 6 |
| Q5THR3 | 1411 | 1460 | 1434 | 1469 | Domain | Note=EF-hand 16;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00448 |
| Q5THR3 | 1411 | 1460 | 1303 | 1501 | Region | Note=Interaction with PARK7;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12612053;Dbxref=PMID:12612053 |
| Q5THR3 | 1411 | 1460 | 1407 | 1501 | Region | Note=Interaction with AR;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12612053;Dbxref=PMID:12612053 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in EFCAB6 |
| 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 |
| Mayo | ENST00000262726 | 43808995 | 43809131 | hsa-miR-6754-5p | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| Mayo | ENST00000262726 | 43808995 | 43809131 | hsa-miR-203b-3p | chr22:43809023-43809030 | 8mer-1a | chr22:43809023-43809044 | 158.00 | -15.82 |
| Mayo | ENST00000262726 | 43808995 | 43809131 | hsa-miR-12128 | chr22:43809051-43809058 | 8mer-1a | chr22:43809035-43809058 | 150.00 | -18.34 |
| Mayo | ENST00000262726 | 43808995 | 43809131 | hsa-miR-27a-5p | chr22:43809071-43809078 | 8mer-1a | chr22:43809063-43809084 | 152.00 | -16.72 |
| Mayo | ENST00000262726 | 43808995 | 43809131 | hsa-miR-4441 | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| Mayo | ENST00000262726 | 43808995 | 43809131 | hsa-miR-4270 | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| Mayo | ENST00000262726 | 43808995 | 43809131 | hsa-miR-3202 | chr22:43809107-43809114 | 8mer-1a | chr22:43809101-43809124 | 147.00 | -23.75 |
| MSBB | ENST00000262726 | 43808995 | 43809131 | hsa-miR-6754-5p | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| MSBB | ENST00000262726 | 43808995 | 43809131 | hsa-miR-203b-3p | chr22:43809023-43809030 | 8mer-1a | chr22:43809023-43809044 | 158.00 | -15.82 |
| MSBB | ENST00000262726 | 43808995 | 43809131 | hsa-miR-12128 | chr22:43809051-43809058 | 8mer-1a | chr22:43809035-43809058 | 150.00 | -18.34 |
| MSBB | ENST00000262726 | 43808995 | 43809131 | hsa-miR-27a-5p | chr22:43809071-43809078 | 8mer-1a | chr22:43809063-43809084 | 152.00 | -16.72 |
| MSBB | ENST00000262726 | 43808995 | 43809131 | hsa-miR-4441 | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| MSBB | ENST00000262726 | 43808995 | 43809131 | hsa-miR-4270 | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| MSBB | ENST00000262726 | 43808995 | 43809131 | hsa-miR-3202 | chr22:43809107-43809114 | 8mer-1a | chr22:43809101-43809124 | 147.00 | -23.75 |
| ROSMAP | ENST00000262726 | 43808995 | 43809131 | hsa-miR-6754-5p | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| ROSMAP | ENST00000262726 | 43808995 | 43809131 | hsa-miR-203b-3p | chr22:43809023-43809030 | 8mer-1a | chr22:43809023-43809044 | 158.00 | -15.82 |
| ROSMAP | ENST00000262726 | 43808995 | 43809131 | hsa-miR-12128 | chr22:43809051-43809058 | 8mer-1a | chr22:43809035-43809058 | 150.00 | -18.34 |
| ROSMAP | ENST00000262726 | 43808995 | 43809131 | hsa-miR-27a-5p | chr22:43809071-43809078 | 8mer-1a | chr22:43809063-43809084 | 152.00 | -16.72 |
| ROSMAP | ENST00000262726 | 43808995 | 43809131 | hsa-miR-4441 | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| ROSMAP | ENST00000262726 | 43808995 | 43809131 | hsa-miR-4270 | chr22:43809050-43809057 | 8mer-1a | chr22:43809037-43809057 | 153.00 | -20.12 |
| ROSMAP | ENST00000262726 | 43808995 | 43809131 | hsa-miR-3202 | chr22:43809107-43809114 | 8mer-1a | chr22:43809101-43809124 | 147.00 | -23.75 |
Top |
SNVs in the skipped exons for EFCAB6 |
| - 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 |
Top |
AD stage-associated exon skippint events for EFCAB6 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for EFCAB6 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| PCC | exon_skip_279171 | rs2285162 | chr22:43853583 | 3.074565e-04 | 4.180722e-02 |
| PCC | exon_skip_279171 | rs2285166 | chr22:43854750 | 3.074565e-04 | 4.180722e-02 |
Top |
Correlation with RNA binding proteins (RBPs) for EFCAB6 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for EFCAB6 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for EFCAB6 |
| 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)
|