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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for NCKAP1 |
 Gene summary |
| Gene information | Gene symbol | NCKAP1 | Gene ID | 10787 |
| Gene name | NCK associated protein 1 | |
| Synonyms | HEM2|NAP1|NAP125|p125Nap1 | |
| Cytomap | 2q32.1 | |
| Type of gene | protein-coding | |
| Description | nck-associated protein 1membrane-associated protein HEM-2 | |
| Modification date | 20200327 | |
| UniProtAcc | Q9Y2A7, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| NCKAP1 | GO:0016601 | Rac protein signal transduction | 21107423 |
| NCKAP1 | GO:2000601 | positive regulation of Arp2/3 complex-mediated actin nucleation | 21107423 |
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Gene structures and expression levels for NCKAP1 |
| 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. |
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ENSG00000061676
| 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 NCKAP1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_106314 | chr2 | 183023806:183023916:183024978:183024995:183037992:183038086 | 183024978:183024995 |
| exon_skip_112608 | chr2 | 182983286:182983382:182986171:182986227:182989030:182989141 | 182986171:182986227 |
| exon_skip_120472 | chr2 | 183001953:183002043:183002127:183002269:183002974:183003030 | 183002127:183002269 |
| exon_skip_123813 | chr2 | 182983286:182983382:182986171:182986227:182989030:182989186 | 182986171:182986227 |
| exon_skip_124948 | chr2 | 182994839:182994887:182995701:182995838:183001953:183002043 | 182995701:182995838 |
| exon_skip_143216 | chr2 | 183023806:183023916:183024978:183024995:183037992:183038116 | 183024978:183024995 |
| exon_skip_148186 | chr2 | 182928119:182928226:182928783:182928899:182930695:182930788 | 182928783:182928899 |
| exon_skip_175001 | chr2 | 183023806:183023916:183024978:183024995:183037992:183038158 | 183024978:183024995 |
| exon_skip_17840 | chr2 | 182926816:182926905:182928117:182928226:182928783:182928889 | 182928117:182928226 |
| exon_skip_201335 | chr2 | 182952405:182952502:182952793:182952923:182953113:182953331 | 182952793:182952923 |
| exon_skip_22845 | chr2 | 183023806:183023916:183024978:183024995:183037992:183038043 | 183024978:183024995 |
| exon_skip_229504 | chr2 | 183023806:183023916:183024978:183024995:183037992:183038457 | 183024978:183024995 |
| exon_skip_250111 | chr2 | 182930725:182930788:182934752:182934832:182935293:182935375 | 182934752:182934832 |
| exon_skip_270665 | chr2 | 182935293:182935375:182942070:182942163:182952405:182952502 | 182942070:182942163 |
| exon_skip_292553 | chr2 | 182962159:182962278:182964676:182964808:182967216:182967321 | 182964676:182964808 |
| exon_skip_32999 | chr2 | 182964676:182964808:182967216:182967361:182976893:182976951 | 182967216:182967361 |
| exon_skip_62255 | chr2 | 182953300:182953331:182956462:182956593:182957457:182957596 | 182956462:182956593 |
| exon_skip_73874 | chr2 | 183023806:183023916:183024978:183024995:183037992:183038181 | 183024978:183024995 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_229504 | MSBB_STG | 6.355224e-01 | 7.500000e-01 | -1.144776e-01 | 3.809247e-02 |
| exon_skip_229504 | MSBB_PG | 5.477778e-01 | 7.194643e-01 | -1.716865e-01 | 1.485224e-06 |
| exon_skip_175001 | Mayo_TC | 4.192683e-01 | 5.482051e-01 | -1.289368e-01 | 2.586308e-04 |
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Open reading frame (ORF) annotation in the exon skipping event for NCKAP1 |
| 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 |
| ENST00000361354 | 182942070 | 182942163 | Frame-shift |
| ENST00000361354 | 182952793 | 182952923 | Frame-shift |
| ENST00000361354 | 183002127 | 183002269 | Frame-shift |
| ENST00000361354 | 182934752 | 182934832 | In-frame |
| ENST00000361354 | 182986171 | 182986227 | In-frame |
| ENST00000361354 | 182995701 | 182995838 | 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 |
| ENST00000361354 | 183002127 | 183002269 | 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 |
| ENST00000361354 | 182928117 | 182928226 | Frame-shift |
| ENST00000361354 | 182942070 | 182942163 | Frame-shift |
| ENST00000361354 | 182952793 | 182952923 | Frame-shift |
| ENST00000361354 | 182964676 | 182964808 | Frame-shift |
| ENST00000361354 | 182967216 | 182967361 | Frame-shift |
| ENST00000361354 | 183002127 | 183002269 | Frame-shift |
| ENST00000361354 | 182928783 | 182928899 | In-frame |
| ENST00000361354 | 182956462 | 182956593 | In-frame |
| ENST00000361354 | 182986171 | 182986227 | In-frame |
| ENST00000361354 | 182995701 | 182995838 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NCKAP1 |
p-ENSG00000061676_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 |
| ENST00000361354 | 20364 | 1128 | 182995701 | 182995838 | 977 | 1113 | 201 | 246 |
| ENST00000361354 | 20364 | 1128 | 182986171 | 182986227 | 1321 | 1376 | 316 | 334 |
| ENST00000361354 | 20364 | 1128 | 182934752 | 182934832 | 3152 | 3231 | 926 | 952 |
| 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 |
| ENST00000361354 | 20364 | 1128 | 182995701 | 182995838 | 977 | 1113 | 201 | 246 |
| ENST00000361354 | 20364 | 1128 | 182986171 | 182986227 | 1321 | 1376 | 316 | 334 |
| ENST00000361354 | 20364 | 1128 | 182956462 | 182956593 | 2395 | 2525 | 674 | 717 |
| ENST00000361354 | 20364 | 1128 | 182928783 | 182928899 | 3327 | 3442 | 984 | 1023 |
| 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 |
| Q9Y2A7 | 201 | 246 | 232 | 235 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 239 | 241 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N78 |
| Q9Y2A7 | 201 | 246 | 2 | 1128 | Chain | ID=PRO_0000216172;Note=Nck-associated protein 1 |
| Q9Y2A7 | 201 | 246 | 200 | 208 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 209 | 212 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 214 | 217 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 221 | 226 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 236 | 238 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 227 | 230 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 316 | 334 | 2 | 1128 | Chain | ID=PRO_0000216172;Note=Nck-associated protein 1 |
| Q9Y2A7 | 316 | 334 | 315 | 317 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 316 | 334 | 320 | 359 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 926 | 952 | 2 | 1128 | Chain | ID=PRO_0000216172;Note=Nck-associated protein 1 |
| Q9Y2A7 | 926 | 952 | 900 | 931 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 926 | 952 | 933 | 944 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| 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 |
| Q9Y2A7 | 201 | 246 | 232 | 235 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 239 | 241 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N78 |
| Q9Y2A7 | 201 | 246 | 2 | 1128 | Chain | ID=PRO_0000216172;Note=Nck-associated protein 1 |
| Q9Y2A7 | 201 | 246 | 200 | 208 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 209 | 212 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 214 | 217 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 221 | 226 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 236 | 238 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 201 | 246 | 227 | 230 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 316 | 334 | 2 | 1128 | Chain | ID=PRO_0000216172;Note=Nck-associated protein 1 |
| Q9Y2A7 | 316 | 334 | 315 | 317 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 316 | 334 | 320 | 359 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 674 | 717 | 695 | 697 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 674 | 717 | 700 | 702 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 674 | 717 | 2 | 1128 | Chain | ID=PRO_0000216172;Note=Nck-associated protein 1 |
| Q9Y2A7 | 674 | 717 | 674 | 689 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 674 | 717 | 704 | 723 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 984 | 1023 | 2 | 1128 | Chain | ID=PRO_0000216172;Note=Nck-associated protein 1 |
| Q9Y2A7 | 984 | 1023 | 989 | 1006 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 984 | 1023 | 1007 | 1012 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 984 | 1023 | 1014 | 1016 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
| Q9Y2A7 | 984 | 1023 | 995 | 1015 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y2A7 | 984 | 1023 | 1020 | 1023 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3P8C |
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3'-UTR located exon skipping events that lost miRNA binding sites in NCKAP1 |
| 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 NCKAP1 |
| - 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 NCKAP1 |
| 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 |
| CDR | MSBB | IFG | exon_skip_229504 | -3.755683e-01 | 4.889687e-02 | chr2 | - | 183023806 | 183023916 | 183024978 | 183024995 | 183037992 | 183038457 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NCKAP1 |
| 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 NCKAP1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | FXR2 | exon_skip_73874 | 4.174963e-01 | 4.829054e-08 |
| CB | SRSF9 | exon_skip_73874 | 5.240936e-01 | 1.584447e-12 |
| CB | EIF4B | exon_skip_73874 | 5.435606e-01 | 1.584301e-13 |
| FL | FXR2 | exon_skip_229504 | 5.641246e-01 | 4.959107e-18 |
| FL | SRSF9 | exon_skip_229504 | 4.307387e-01 | 2.384243e-10 |
| FL | EIF4B | exon_skip_229504 | 5.053802e-01 | 3.114580e-14 |
| HCC | RBM5 | exon_skip_106314 | -6.749713e-01 | 2.177409e-37 |
| HCC | TRA2A | exon_skip_106314 | -4.555813e-01 | 2.713784e-15 |
| IFG | RBM5 | exon_skip_229504 | -4.601683e-01 | 1.374078e-02 |
| IFG | FXR2 | exon_skip_229504 | 4.637968e-01 | 1.292065e-02 |
| IFG | TRA2A | exon_skip_229504 | -4.250660e-01 | 2.414318e-02 |
| PG | FXR2 | exon_skip_229504 | 6.533566e-01 | 1.004002e-25 |
| STG | FXR2 | exon_skip_229504 | 4.942891e-01 | 6.372907e-07 |
| TC | FXR2 | exon_skip_175001 | 4.402874e-01 | 5.678982e-09 |
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RelatedDrugs for NCKAP1 |
| 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 NCKAP1 |
| 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)
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