|
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 NFKB2 |
Gene summary |
Gene information | Gene symbol | NFKB2 | Gene ID | 4791 |
Gene name | nuclear factor kappa B subunit 2 | |
Synonyms | CVID10|H2TF1|LYT-10|LYT10|NF-kB2|p100|p49/p100|p52 | |
Cytomap | 10q24.32 | |
Type of gene | protein-coding | |
Description | nuclear factor NF-kappa-B p100 subunitDNA-binding factor KBF2NFKB, p52/p100 subunitlymphocyte translocation chromosome 10 proteinnuclear factor Kappa-B, subunit 2nuclear factor NF-kappa-B p52 subunitnuclear factor of Kappa light chain gene enhancer | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
NFKB2 | GO:0006355 | regulation of transcription, DNA-templated | 8360178 |
NFKB2 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 12835724 |
Top |
Gene structures and expression levels for NFKB2 |
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 | DOWN | ENST00000651907.1 | NFKB2-209:lncRNA:NFKB2 | 1.220430e+00 | -1.875359e+00 | 2.972337e-03 | 1.280595e-02 |
TC | DOWN | ENST00000651907.1 | NFKB2-209:lncRNA:NFKB2 | 2.169337e+00 | -3.133346e+00 | 4.123361e-07 | 1.970105e-05 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NFKB2 |
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_190371 | chr10 | 102401449:102401518:102401745:102401917:102402048:102402159 | 102401745:102401917 |
exon_skip_216199 | chr10 | 102396449:102396489:102396725:102396823:102396904:102396973 | 102396725:102396823 |
exon_skip_274330 | chr10 | 102398385:102398523:102398739:102398864:102399288:102399497 | 102398739:102398864 |
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 NFKB2 |
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 |
ENST00000369966 | 102396725 | 102396823 | In-frame |
ENST00000369966 | 102398739 | 102398864 | 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 |
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 |
ENST00000369966 | 102401745 | 102401917 | Frame-shift |
ENST00000369966 | 102398739 | 102398864 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for NFKB2 |
p-ENSG00000077150_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 |
ENST00000369966 | 3118 | 900 | 102396725 | 102396823 | 396 | 493 | 48 | 81 |
ENST00000369966 | 3118 | 900 | 102398739 | 102398864 | 1243 | 1367 | 331 | 372 |
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 |
ENST00000369966 | 3118 | 900 | 102398739 | 102398864 | 1243 | 1367 | 331 | 372 |
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 |
Q00653 | 48 | 81 | 48 | 51 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A3Q |
Q00653 | 48 | 81 | 79 | 83 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A3Q |
Q00653 | 48 | 81 | 1 | 900 | Chain | ID=PRO_0000030321;Note=Nuclear factor NF-kappa-B p100 subunit |
Q00653 | 48 | 81 | 1 | 454 | Chain | ID=PRO_0000030322;Note=Nuclear factor NF-kappa-B p52 subunit |
Q00653 | 48 | 81 | 38 | 343 | Domain | Note=RHD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00265 |
Q00653 | 48 | 81 | 56 | 58 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1A3Q |
Q00653 | 331 | 372 | 1 | 900 | Chain | ID=PRO_0000030321;Note=Nuclear factor NF-kappa-B p100 subunit |
Q00653 | 331 | 372 | 1 | 454 | Chain | ID=PRO_0000030322;Note=Nuclear factor NF-kappa-B p52 subunit |
Q00653 | 331 | 372 | 350 | 400 | Compositional bias | Note=Gly-rich |
Q00653 | 331 | 372 | 38 | 343 | Domain | Note=RHD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00265 |
Q00653 | 331 | 372 | 337 | 341 | Motif | Note=Nuclear localization signal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q00653 | 331 | 372 | 351 | 351 | Natural variant | ID=VAR_022224;Note=G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.7;Dbxref=dbSNP:rs45580031 |
Q00653 | 331 | 372 | 346 | 377 | Region | Note=GRR |
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 |
Q00653 | 331 | 372 | 1 | 900 | Chain | ID=PRO_0000030321;Note=Nuclear factor NF-kappa-B p100 subunit |
Q00653 | 331 | 372 | 1 | 454 | Chain | ID=PRO_0000030322;Note=Nuclear factor NF-kappa-B p52 subunit |
Q00653 | 331 | 372 | 350 | 400 | Compositional bias | Note=Gly-rich |
Q00653 | 331 | 372 | 38 | 343 | Domain | Note=RHD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00265 |
Q00653 | 331 | 372 | 337 | 341 | Motif | Note=Nuclear localization signal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q00653 | 331 | 372 | 351 | 351 | Natural variant | ID=VAR_022224;Note=G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.7;Dbxref=dbSNP:rs45580031 |
Q00653 | 331 | 372 | 346 | 377 | Region | Note=GRR |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in NFKB2 |
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 |
Top |
SNVs in the skipped exons for NFKB2 |
- 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 NFKB2 |
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 NFKB2 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for NFKB2 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for NFKB2 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Q00653 | approved|vet_approved | DB00945 | Acetylsalicylic acid | small molecule | Q00653 |
Q00653 | approved|investigational | DB01296 | Glucosamine | small molecule | Q00653 |
Q00653 | approved|experimental | DB13751 | Glycyrrhizic acid | small molecule | Q00653 |
Top |
RelatedDiseases for NFKB2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |