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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 NAB2 |
Gene summary |
Gene information | Gene symbol | NAB2 | Gene ID | 4665 |
Gene name | NGFI-A binding protein 2 | |
Synonyms | MADER | |
Cytomap | 12q13.3 | |
Type of gene | protein-coding | |
Description | NGFI-A-binding protein 2EGR1 binding protein 2melanoma-associated delayed early response protein | |
Modification date | 20200329 | |
UniProtAcc | Q15742, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
NAB2 | GO:0016480 | negative regulation of transcription by RNA polymerase III | 8668170 |
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Gene structures and expression levels for NAB2 |
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 |
PCC | UP | ENST00000342556.6 | NAB2-202:protein_coding:NAB2 | 8.591674e+01 | 8.004193e-01 | 8.161416e-08 | 4.564966e-05 |
STG | UP | ENST00000665338.1 | KCNAB2-241:retained_intron:KCNAB2 | 3.450838e+01 | 8.781841e-01 | 1.476085e-05 | 3.507735e-03 |
PG | DOWN | ENST00000654144.1 | KCNAB2-224:retained_intron:KCNAB2 | 1.329931e+00 | -3.245117e+00 | 3.663085e-03 | 3.679263e-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 NAB2 |
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_227985 | chr12 | 57093063:57093195:57093407:57093598:57094612:57094636 | 57093407:57093598 |
exon_skip_23176 | chr12 | 57091912:57091998:57092448:57092581:57092917:57092968 | 57092448:57092581 |
exon_skip_277578 | chr12 | 57093063:57093195:57093407:57093598:57094612:57094920 | 57093407:57093598 |
exon_skip_69768 | chr12 | 57091125:57091998:57092448:57092581:57092917:57092968 | 57092448:57092581 |
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_277578 | Mayo_CB | 7.124390e-01 | 8.551948e-01 | -1.427558e-01 | 1.033022e-05 |
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Open reading frame (ORF) annotation in the exon skipping event for NAB2 |
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 |
ENST00000300131 | 57092448 | 57092581 | Frame-shift |
ENST00000300131 | 57093407 | 57093598 | 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 |
ENST00000300131 | 57093407 | 57093598 | 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 |
ENST00000300131 | 57092448 | 57092581 | Frame-shift |
ENST00000300131 | 57093407 | 57093598 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NAB2 |
p-ENSG00000166886_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 |
ENST00000300131 | 2728 | 525 | 57093407 | 57093598 | 1656 | 1846 | 426 | 489 |
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 |
ENST00000300131 | 2728 | 525 | 57093407 | 57093598 | 1656 | 1846 | 426 | 489 |
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 |
ENST00000300131 | 2728 | 525 | 57093407 | 57093598 | 1656 | 1846 | 426 | 489 |
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 |
Q15742 | 426 | 489 | 323 | 525 | Alternative sequence | ID=VSP_003386;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8668170;Dbxref=PMID:8668170 |
Q15742 | 426 | 489 | 426 | 489 | Alternative sequence | ID=VSP_003387;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q15742 | 426 | 489 | 1 | 525 | Chain | ID=PRO_0000077042;Note=NGFI-A-binding protein 2 |
Q15742 | 426 | 489 | 479 | 479 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q61127 |
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 |
Q15742 | 426 | 489 | 323 | 525 | Alternative sequence | ID=VSP_003386;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8668170;Dbxref=PMID:8668170 |
Q15742 | 426 | 489 | 426 | 489 | Alternative sequence | ID=VSP_003387;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q15742 | 426 | 489 | 1 | 525 | Chain | ID=PRO_0000077042;Note=NGFI-A-binding protein 2 |
Q15742 | 426 | 489 | 479 | 479 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q61127 |
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 |
Q15742 | 426 | 489 | 323 | 525 | Alternative sequence | ID=VSP_003386;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8668170;Dbxref=PMID:8668170 |
Q15742 | 426 | 489 | 426 | 489 | Alternative sequence | ID=VSP_003387;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q15742 | 426 | 489 | 1 | 525 | Chain | ID=PRO_0000077042;Note=NGFI-A-binding protein 2 |
Q15742 | 426 | 489 | 479 | 479 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q61127 |
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3'-UTR located exon skipping events that lost miRNA binding sites in NAB2 |
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 NAB2 |
- 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 NAB2 |
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 NAB2 |
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 NAB2 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | TARDBP | exon_skip_277578 | -4.474350e-01 | 3.360357e-09 |
CB | RBM6 | exon_skip_277578 | -4.837673e-01 | 1.048874e-10 |
CB | CNOT4 | exon_skip_277578 | -5.168077e-01 | 3.084880e-12 |
CB | PCBP1 | exon_skip_277578 | -4.474320e-01 | 3.361260e-09 |
CB | NUP42 | exon_skip_277578 | 4.643827e-01 | 7.013972e-10 |
CB | RBM4B | exon_skip_277578 | -5.850107e-01 | 5.616392e-16 |
DLPFC | SRSF5 | exon_skip_227985 | 4.118290e-01 | 2.297957e-11 |
DLPFC | NOVA1 | exon_skip_227985 | 4.392862e-01 | 6.928024e-13 |
HCC | HNRNPF | exon_skip_277578 | -4.531100e-01 | 3.551973e-15 |
HCC | RBM4B | exon_skip_277578 | -4.233380e-01 | 2.972367e-13 |
IFG | HNRNPF | exon_skip_277578 | -4.052334e-01 | 3.599941e-02 |
TC | NOVA1 | exon_skip_277578 | 4.972634e-01 | 3.005480e-11 |
TC | RBM4B | exon_skip_277578 | -4.436069e-01 | 5.295378e-09 |
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RelatedDrugs for NAB2 |
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 NAB2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |