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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 CUX2 |
 Gene summary |
| Gene information | Gene symbol | CUX2 | Gene ID | 23316 |
| Gene name | cut like homeobox 2 | |
| Synonyms | CDP2|CUTL2|EIEE67 | |
| Cytomap | 12q24.11-q24.12 | |
| Type of gene | protein-coding | |
| Description | homeobox protein cut-like 2homeobox protein cux-2 | |
| 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 |
| CUX2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 15656993 |
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Gene structures and expression levels for CUX2 |
| 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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ENSG00000111249
| 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 CUX2 |
| 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_121890 | chr12 | 111099446:111099636:111099930:111100117:111214200:111214310 | 111099930:111100117 |
| exon_skip_197860 | chr12 | 111320012:111320775:111322421:111322580:111334441:111334710 | 111322421:111322580 |
| exon_skip_208451 | chr12 | 111322421:111322580:111334441:111334710:111338286:111338474 | 111334441:111334710 |
| exon_skip_25654 | chr12 | 111307199:111307257:111308285:111308333:111308427:111308526 | 111308285:111308333 |
| exon_skip_278945 | chr12 | 111217890:111217937:111263761:111263839:111291418:111291552 | 111263761:111263839 |
| exon_skip_28624 | chr12 | 111214301:111214310:111217890:111217937:111263761:111263839 | 111217890:111217937 |
| exon_skip_66091 | chr12 | 111263761:111263839:111291418:111291552:111293446:111293569 | 111291418:111291552 |
| exon_skip_88719 | chr12 | 111291418:111291552:111293446:111293569:111295333:111295346 | 111293446:111293569 |
| 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 CUX2 |
| 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 |
| ENST00000261726 | 111263761 | 111263839 | Frame-shift |
| ENST00000261726 | 111293446 | 111293569 | Frame-shift |
| ENST00000261726 | 111308285 | 111308333 | Frame-shift |
| ENST00000261726 | 111322421 | 111322580 | Frame-shift |
| ENST00000261726 | 111217890 | 111217937 | In-frame |
| ENST00000261726 | 111291418 | 111291552 | In-frame |
| ENST00000261726 | 111334441 | 111334710 | 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 |
| ENST00000261726 | 111263761 | 111263839 | Frame-shift |
| ENST00000261726 | 111293446 | 111293569 | Frame-shift |
| ENST00000261726 | 111217890 | 111217937 | In-frame |
| ENST00000261726 | 111291418 | 111291552 | In-frame |
| ENST00000261726 | 111334441 | 111334710 | 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 |
| ENST00000261726 | 111293446 | 111293569 | Frame-shift |
| ENST00000261726 | 111308285 | 111308333 | Frame-shift |
| ENST00000261726 | 111217890 | 111217937 | In-frame |
| ENST00000261726 | 111291418 | 111291552 | In-frame |
| ENST00000261726 | 111334441 | 111334710 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CUX2 |
p-ENSG00000111249_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 |
| ENST00000261726 | 6861 | 1486 | 111217890 | 111217937 | 330 | 376 | 58 | 74 |
| ENST00000261726 | 6861 | 1486 | 111291418 | 111291552 | 457 | 590 | 101 | 145 |
| ENST00000261726 | 6861 | 1486 | 111334441 | 111334710 | 3082 | 3350 | 976 | 1065 |
| 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 |
| ENST00000261726 | 6861 | 1486 | 111217890 | 111217937 | 330 | 376 | 58 | 74 |
| ENST00000261726 | 6861 | 1486 | 111291418 | 111291552 | 457 | 590 | 101 | 145 |
| ENST00000261726 | 6861 | 1486 | 111334441 | 111334710 | 3082 | 3350 | 976 | 1065 |
| 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 |
| ENST00000261726 | 6861 | 1486 | 111217890 | 111217937 | 330 | 376 | 58 | 74 |
| ENST00000261726 | 6861 | 1486 | 111291418 | 111291552 | 457 | 590 | 101 | 145 |
| ENST00000261726 | 6861 | 1486 | 111334441 | 111334710 | 3082 | 3350 | 976 | 1065 |
| 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 |
| O14529 | 58 | 74 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 101 | 145 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 101 | 145 | 143 | 143 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| O14529 | 976 | 1065 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 976 | 1065 | 1038 | 1125 | DNA binding | Note=CUT 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00374 |
| O14529 | 976 | 1065 | 1037 | 1043 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WH8 |
| O14529 | 976 | 1065 | 1049 | 1062 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WH8 |
| 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 |
| O14529 | 58 | 74 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 101 | 145 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 101 | 145 | 143 | 143 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| O14529 | 976 | 1065 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 976 | 1065 | 1038 | 1125 | DNA binding | Note=CUT 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00374 |
| O14529 | 976 | 1065 | 1037 | 1043 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WH8 |
| O14529 | 976 | 1065 | 1049 | 1062 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WH8 |
| 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 |
| O14529 | 58 | 74 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 101 | 145 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 101 | 145 | 143 | 143 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| O14529 | 976 | 1065 | 1 | 1486 | Chain | ID=PRO_0000202396;Note=Homeobox protein cut-like 2 |
| O14529 | 976 | 1065 | 1038 | 1125 | DNA binding | Note=CUT 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00374 |
| O14529 | 976 | 1065 | 1037 | 1043 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WH8 |
| O14529 | 976 | 1065 | 1049 | 1062 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WH8 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CUX2 |
| 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 CUX2 |
| - 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 CUX2 |
| 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 CUX2 |
| 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 CUX2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for CUX2 |
| 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 CUX2 |
| 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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