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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 PALB2 |
 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 |
| PALB2 | GO:0000724 | double-strand break repair via homologous recombination | 19369211|19423707 |
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Gene structures and expression levels for PALB2 |
| 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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ENSG00000083093
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | DOWN | ENST00000566069.5 | PALB2-204:protein_coding:PALB2 | 5.675022e+01 | -1.248762e+00 | 2.988813e-11 | 2.357406e-09 |
| 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 PALB2 |
| 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_116865 | chr16 | 23607864:23608012:23614004:23614091:23621362:23621389 | 23614004:23614091 |
| exon_skip_149932 | chr16 | 23621362:23621478:23622969:23623130:23624009:23624094 | 23622969:23623130 |
| exon_skip_153045 | chr16 | 23603397:23603669:23607864:23608012:23614004:23614091 | 23607864:23608012 |
| exon_skip_286869 | chr16 | 23603160:23603669:23607864:23608012:23614004:23614091 | 23607864:23608012 |
| exon_skip_37572 | chr16 | 23638070:23638129:23638459:23638592:23641110:23641301 | 23638459:23638592 |
| exon_skip_4811 | chr16 | 23603170:23603669:23607864:23608012:23614004:23614091 | 23607864:23608012 |
| exon_skip_60887 | chr16 | 23614004:23614091:23621362:23621478:23622969:23623130 | 23621362:23621478 |
| exon_skip_74372 | chr16 | 23624071:23624094:23626236:23626397:23629204:23629275 | 23626236:23626397 |
| 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 PALB2 |
| 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 |
| ENST00000261584 | 23607864 | 23608012 | Frame-shift |
| ENST00000261584 | 23614004 | 23614091 | Frame-shift |
| ENST00000261584 | 23626236 | 23626397 | 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 |
| ENST00000261584 | 23607864 | 23608012 | Frame-shift |
| ENST00000261584 | 23614004 | 23614091 | 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 |
| ENST00000261584 | 23607864 | 23608012 | Frame-shift |
| ENST00000261584 | 23614004 | 23614091 | Frame-shift |
| ENST00000261584 | 23621362 | 23621478 | In-frame |
| ENST00000261584 | 23622969 | 23623130 | In-frame |
| ENST00000261584 | 23626236 | 23626397 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PALB2 |
p-ENSG00000083093_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 |
| ENST00000261584 | 4020 | 1186 | 23626236 | 23626397 | 2740 | 2900 | 862 | 915 |
| 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 |
| ENST00000261584 | 4020 | 1186 | 23626236 | 23626397 | 2740 | 2900 | 862 | 915 |
| ENST00000261584 | 4020 | 1186 | 23622969 | 23623130 | 2988 | 3148 | 945 | 998 |
| ENST00000261584 | 4020 | 1186 | 23621362 | 23621478 | 3150 | 3265 | 999 | 1037 |
| 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 |
| Q86YC2 | 862 | 915 | 869 | 877 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 862 | 915 | 884 | 913 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 862 | 915 | 1 | 1186 | Chain | ID=PRO_0000252391;Note=Partner and localizer of BRCA2 |
| Q86YC2 | 862 | 915 | 864 | 864 | Natural variant | ID=VAR_054150;Note=P->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18987736,ECO:0000269|PubMed:21618343;Dbxref=dbSNP:rs45568339,PMID:18987736,PMID:21618343 |
| Q86YC2 | 862 | 915 | 775 | 1186 | Region | Note=Required for interaction with POLH and POLH DNA synthesis stimulation;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 862 | 915 | 853 | 1186 | Region | Note=Interaction with RAD51%2C BRCA2 and POLH;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 862 | 915 | 854 | 915 | Repeat | Note=WD 1 |
| 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 |
| Q86YC2 | 862 | 915 | 869 | 877 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 862 | 915 | 884 | 913 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 862 | 915 | 1 | 1186 | Chain | ID=PRO_0000252391;Note=Partner and localizer of BRCA2 |
| Q86YC2 | 862 | 915 | 864 | 864 | Natural variant | ID=VAR_054150;Note=P->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18987736,ECO:0000269|PubMed:21618343;Dbxref=dbSNP:rs45568339,PMID:18987736,PMID:21618343 |
| Q86YC2 | 862 | 915 | 775 | 1186 | Region | Note=Required for interaction with POLH and POLH DNA synthesis stimulation;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 862 | 915 | 853 | 1186 | Region | Note=Interaction with RAD51%2C BRCA2 and POLH;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 862 | 915 | 854 | 915 | Repeat | Note=WD 1 |
| Q86YC2 | 945 | 998 | 938 | 947 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 945 | 998 | 958 | 972 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 945 | 998 | 976 | 984 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 945 | 998 | 988 | 994 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 945 | 998 | 1 | 1186 | Chain | ID=PRO_0000252391;Note=Partner and localizer of BRCA2 |
| Q86YC2 | 945 | 998 | 966 | 966 | Natural variant | ID=VAR_066376;Note=I->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21618343;Dbxref=dbSNP:rs786204248,PMID:21618343 |
| Q86YC2 | 945 | 998 | 998 | 998 | Natural variant | ID=VAR_066377;Note=May be associated with breast cancer susceptibility. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21618343;Dbxref=dbSNP:rs45551636,PMID:21618343 |
| Q86YC2 | 945 | 998 | 775 | 1186 | Region | Note=Required for interaction with POLH and POLH DNA synthesis stimulation;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 945 | 998 | 853 | 1186 | Region | Note=Interaction with RAD51%2C BRCA2 and POLH;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 945 | 998 | 917 | 961 | Repeat | Note=WD 2 |
| Q86YC2 | 945 | 998 | 962 | 1009 | Repeat | Note=WD 3 |
| Q86YC2 | 945 | 998 | 973 | 975 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 999 | 1037 | 1000 | 1006 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 999 | 1037 | 1013 | 1020 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 999 | 1037 | 1025 | 1030 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 999 | 1037 | 1033 | 1039 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W18 |
| Q86YC2 | 999 | 1037 | 1 | 1186 | Chain | ID=PRO_0000252391;Note=Partner and localizer of BRCA2 |
| Q86YC2 | 999 | 1037 | 1030 | 1030 | Mutagenesis | Note=Unstable and promotes protein degradation%3B reduces interaction with RAD51C and RAD51. T->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24141787;Dbxref=PMID:24141787 |
| Q86YC2 | 999 | 1037 | 1025 | 1025 | Natural variant | ID=VAR_066378;Note=A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21618343;Dbxref=dbSNP:rs746872839,PMID:21618343 |
| Q86YC2 | 999 | 1037 | 775 | 1186 | Region | Note=Required for interaction with POLH and POLH DNA synthesis stimulation;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 999 | 1037 | 853 | 1186 | Region | Note=Interaction with RAD51%2C BRCA2 and POLH;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24485656;Dbxref=PMID:24485656 |
| Q86YC2 | 999 | 1037 | 962 | 1009 | Repeat | Note=WD 3 |
| Q86YC2 | 999 | 1037 | 1010 | 1052 | Repeat | Note=WD 4 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PALB2 |
| 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 PALB2 |
| - 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 PALB2 |
| 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 PALB2 |
| 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 PALB2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PALB2 |
| 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 PALB2 |
| 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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