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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 FANCA |
Gene summary |
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 FANCA |
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 |
CB | UP | ENST00000563510.5 | FANCA-211:nonsense_mediated_decay:FANCA | 7.827247e-01 | 1.949097e+00 | 4.808566e-04 | 2.786871e-03 |
CB | DOWN | ENST00000567879.5 | FANCA-226:protein_coding:FANCA | 6.818938e-01 | -1.994273e+00 | 2.349563e-03 | 1.052898e-02 |
CB | UP | ENST00000563318.1 | FANCA-210:nonsense_mediated_decay:FANCA | 3.665246e+00 | 9.958524e-01 | 6.581354e-03 | 2.466228e-02 |
CB | DOWN | ENST00000562424.1 | FANCA-209:retained_intron:FANCA | 8.309883e+00 | -8.824702e-01 | 1.192187e-02 | 4.011946e-02 |
CB | DOWN | ENST00000564870.1 | FANCA-216:protein_coding:FANCA | 3.156650e+00 | -1.008425e+00 | 1.463544e-02 | 4.729383e-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 FANCA |
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_102912 | chr16 | 89749730:89749902:89758577:89758705:89761949:89762022 | 89758577:89758705 |
exon_skip_106825 | chr16 | 89792471:89792547:89795906:89796018:89799166:89799232 | 89795906:89796018 |
exon_skip_175993 | chr16 | 89761949:89762022:89762638:89762793:89764890:89765066 | 89762638:89762793 |
exon_skip_179504 | chr16 | 89761949:89762022:89764890:89765066:89767141:89767147 | 89764890:89765066 |
exon_skip_182435 | chr16 | 89739994:89740099:89740804:89740866:89742800:89742828 | 89740804:89740866 |
exon_skip_192223 | chr16 | 89739282:89739289:89739478:89739553:89739994:89740078 | 89739478:89739553 |
exon_skip_196285 | chr16 | 89749730:89749902:89752138:89752222:89761949:89762022 | 89752138:89752222 |
exon_skip_197885 | chr16 | 89752138:89752222:89758577:89758705:89761949:89762022 | 89758577:89758705 |
exon_skip_21765 | chr16 | 89805280:89805392:89808294:89808367:89810707:89810802 | 89808294:89808367 |
exon_skip_220197 | chr16 | 89749730:89749902:89752138:89752222:89758577:89758701 | 89752138:89752222 |
exon_skip_229850 | chr16 | 89799172:89799232:89799605:89799638:89803259:89803341 | 89799605:89799638 |
exon_skip_238166 | chr16 | 89740804:89740866:89742800:89742938:89744959:89745008 | 89742800:89742938 |
exon_skip_279804 | chr16 | 89810985:89811071:89814520:89814613:89815877:89815978 | 89814520:89814613 |
exon_skip_50927 | chr16 | 89775742:89775815:89778341:89778462:89778801:89778850 | 89778341:89778462 |
exon_skip_52824 | chr16 | 89803259:89803341:89805280:89805392:89808294:89808366 | 89805280:89805392 |
exon_skip_72391 | chr16 | 89784854:89784964:89791403:89791536:89791927:89792011 | 89791403:89791536 |
exon_skip_79060 | chr16 | 89752161:89752222:89758577:89758705:89761949:89762022 | 89758577:89758705 |
exon_skip_81085 | chr16 | 89748764:89748767:89749730:89749902:89752138:89752222 | 89749730:89749902 |
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 FANCA |
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 |
ENST00000389301 | 89742800 | 89742938 | Frame-shift |
ENST00000389301 | 89740804 | 89740866 | In-frame |
ENST00000389301 | 89758577 | 89758705 | 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 |
ENST00000389301 | 89758577 | 89758705 | 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 |
ENST00000389301 | 89739478 | 89739553 | Frame-shift |
ENST00000389301 | 89742800 | 89742938 | Frame-shift |
ENST00000389301 | 89749730 | 89749902 | Frame-shift |
ENST00000389301 | 89752138 | 89752222 | Frame-shift |
ENST00000389301 | 89791403 | 89791536 | Frame-shift |
ENST00000389301 | 89795906 | 89796018 | Frame-shift |
ENST00000389301 | 89799605 | 89799638 | Frame-shift |
ENST00000389301 | 89805280 | 89805392 | Frame-shift |
ENST00000389301 | 89808294 | 89808367 | Frame-shift |
ENST00000389301 | 89814520 | 89814613 | Frame-shift |
ENST00000389301 | 89740804 | 89740866 | In-frame |
ENST00000389301 | 89758577 | 89758705 | In-frame |
ENST00000389301 | 89764890 | 89765066 | In-frame |
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Infer the effects of exon skipping event on protein functional features for FANCA |
p-ENSG00000187741_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 |
ENST00000389301 | 5468 | 1455 | 89758577 | 89758705 | 2884 | 3011 | 951 | 993 |
ENST00000389301 | 5468 | 1455 | 89740804 | 89740866 | 3797 | 3858 | 1255 | 1275 |
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 |
ENST00000389301 | 5468 | 1455 | 89758577 | 89758705 | 2884 | 3011 | 951 | 993 |
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 |
ENST00000389301 | 5468 | 1455 | 89764890 | 89765066 | 2633 | 2808 | 867 | 925 |
ENST00000389301 | 5468 | 1455 | 89758577 | 89758705 | 2884 | 3011 | 951 | 993 |
ENST00000389301 | 5468 | 1455 | 89740804 | 89740866 | 3797 | 3858 | 1255 | 1275 |
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 |
O15360 | 951 | 993 | 298 | 1455 | Alternative sequence | ID=VSP_007039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
O15360 | 951 | 993 | 1 | 1455 | Chain | ID=PRO_0000087179;Note=Fanconi anemia group A protein |
O15360 | 951 | 993 | 951 | 951 | Natural variant | ID=VAR_038017;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17924555;Dbxref=dbSNP:rs755922289,PMID:17924555 |
O15360 | 951 | 993 | 951 | 951 | Natural variant | ID=VAR_038018;Note=R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17924555;Dbxref=dbSNP:rs755546887,PMID:17924555 |
O15360 | 1255 | 1275 | 298 | 1455 | Alternative sequence | ID=VSP_007039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
O15360 | 1255 | 1275 | 1 | 1455 | Chain | ID=PRO_0000087179;Note=Fanconi anemia group A protein |
O15360 | 1255 | 1275 | 1262 | 1262 | Natural variant | ID=VAR_017502;Note=In FANCA. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10521298;Dbxref=PMID:10521298 |
O15360 | 1255 | 1275 | 1263 | 1263 | Natural variant | ID=VAR_009654;Note=In FANCA. Missing;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10521298,ECO:0000269|PubMed:9371798;Dbxref=PMID:10521298,PMID:9371798 |
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 |
O15360 | 951 | 993 | 298 | 1455 | Alternative sequence | ID=VSP_007039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
O15360 | 951 | 993 | 1 | 1455 | Chain | ID=PRO_0000087179;Note=Fanconi anemia group A protein |
O15360 | 951 | 993 | 951 | 951 | Natural variant | ID=VAR_038017;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17924555;Dbxref=dbSNP:rs755922289,PMID:17924555 |
O15360 | 951 | 993 | 951 | 951 | Natural variant | ID=VAR_038018;Note=R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17924555;Dbxref=dbSNP:rs755546887,PMID:17924555 |
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 |
O15360 | 867 | 925 | 298 | 1455 | Alternative sequence | ID=VSP_007039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
O15360 | 867 | 925 | 1 | 1455 | Chain | ID=PRO_0000087179;Note=Fanconi anemia group A protein |
O15360 | 867 | 925 | 869 | 869 | Natural variant | ID=VAR_038016;Note=In FANCA. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17924555;Dbxref=dbSNP:rs780825099,PMID:17924555 |
O15360 | 951 | 993 | 298 | 1455 | Alternative sequence | ID=VSP_007039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
O15360 | 951 | 993 | 1 | 1455 | Chain | ID=PRO_0000087179;Note=Fanconi anemia group A protein |
O15360 | 951 | 993 | 951 | 951 | Natural variant | ID=VAR_038017;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17924555;Dbxref=dbSNP:rs755922289,PMID:17924555 |
O15360 | 951 | 993 | 951 | 951 | Natural variant | ID=VAR_038018;Note=R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17924555;Dbxref=dbSNP:rs755546887,PMID:17924555 |
O15360 | 1255 | 1275 | 298 | 1455 | Alternative sequence | ID=VSP_007039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
O15360 | 1255 | 1275 | 1 | 1455 | Chain | ID=PRO_0000087179;Note=Fanconi anemia group A protein |
O15360 | 1255 | 1275 | 1262 | 1262 | Natural variant | ID=VAR_017502;Note=In FANCA. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10521298;Dbxref=PMID:10521298 |
O15360 | 1255 | 1275 | 1263 | 1263 | Natural variant | ID=VAR_009654;Note=In FANCA. Missing;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10521298,ECO:0000269|PubMed:9371798;Dbxref=PMID:10521298,PMID:9371798 |
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3'-UTR located exon skipping events that lost miRNA binding sites in FANCA |
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 FANCA |
- 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 FANCA |
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 FANCA |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
CB | exon_skip_175993 | rs1800330 | chr16:89791556 | 3.504866e-14 | 7.284274e-11 |
CB | exon_skip_175993 | rs8049660 | chr16:89791292 | 1.024600e-13 | 1.939117e-10 |
CB | exon_skip_175993 | rs1061646 | chr16:89739569 | 1.678552e-13 | 3.008675e-10 |
CB | exon_skip_175993 | rs7190823 | chr16:89799635 | 2.310437e-08 | 1.328866e-05 |
CB | exon_skip_175993 | rs4420527 | chr16:89747780 | 3.441152e-08 | 1.877218e-05 |
CB | exon_skip_175993 | rs4785595 | chr16:89769113 | 3.441152e-08 | 1.877218e-05 |
CB | exon_skip_175993 | rs12599180 | chr16:89772898 | 3.441152e-08 | 1.877218e-05 |
CB | exon_skip_175993 | rs6500450 | chr16:89791616 | 3.441152e-08 | 1.877218e-05 |
CB | exon_skip_175993 | rs1230 | chr16:89738447 | 7.025440e-08 | 3.515501e-05 |
CB | exon_skip_175993 | rs3890534 | chr16:89768881 | 9.445154e-05 | 1.651040e-02 |
CB | exon_skip_175993 | rs1110331 | chr16:89707988 | 1.764695e-04 | 2.702631e-02 |
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Correlation with RNA binding proteins (RBPs) for FANCA |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for FANCA |
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 FANCA |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |