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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 CLDND1 |
 Gene summary |
| Gene information | Gene symbol | CLDND1 | Gene ID | 56650 |
| Gene name | claudin domain containing 1 | |
| Synonyms | C3orf4|GENX-3745|Z38 | |
| Cytomap | 3q11.2 | |
| Type of gene | protein-coding | |
| Description | claudin domain-containing protein 1claudin domain containing 1 proteinmembrane protein GENX-3745 | |
| Modification date | 20200313 | |
| UniProtAcc | A0A0R4J2F2, D6R9K1, D6R9S8, D6RA76, D6RAZ7, D6RB31, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for CLDND1 |
| 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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ENSG00000080822
| 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 |
| PG | UP | ENST00000503621.5 | CLDND1-209:protein_coding:CLDND1 | 1.223825e+01 | 9.564234e-01 | 7.852255e-04 | 1.223720e-02 |
| PG | UP | ENST00000513287.5 | CLDND1-226:protein_coding:CLDND1 | 2.172086e+01 | 8.417452e-01 | 1.628019e-03 | 2.064672e-02 |
| PG | UP | ENST00000506575.1 | CLDND1-211:protein_coding:CLDND1 | 3.460800e+00 | 1.513521e+00 | 4.087677e-03 | 3.967904e-02 |
| PG | UP | ENST00000515620.5 | CLDND1-231:protein_coding:CLDND1 | 3.797913e+00 | 1.846344e+00 | 4.215835e-03 | 4.055348e-02 |
| CB | DOWN | ENST00000513873.1 | CLDND1-228:protein_coding:CLDND1 | 1.682874e+01 | -4.047426e+00 | 2.992046e-13 | 5.513474e-11 |
| CB | UP | ENST00000513452.5 | CLDND1-227:protein_coding:CLDND1 | 2.677288e+00 | 2.509726e+00 | 6.749752e-03 | 2.516830e-02 |
| TC | DOWN | ENST00000513873.1 | CLDND1-228:protein_coding:CLDND1 | 1.756533e+01 | -2.669061e+00 | 1.339640e-15 | 1.225812e-12 |
| TC | UP | ENST00000513287.5 | CLDND1-226:protein_coding:CLDND1 | 1.019921e+02 | 9.651561e-01 | 1.954768e-08 | 1.568889e-06 |
| TC | UP | ENST00000513452.5 | CLDND1-227:protein_coding:CLDND1 | 2.530794e+01 | 1.825523e+00 | 1.283840e-04 | 1.972576e-03 |
| 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 CLDND1 |
| 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_118050 | chr3 | 98516800:98516879:98517158:98517189:98518885:98518995 | 98517158:98517189 |
| exon_skip_170218 | chr3 | 98515484:98515832:98516800:98516879:98517052:98517147 | 98516800:98516879 |
| exon_skip_194109 | chr3 | 98516800:98516879:98517052:98517189:98518885:98518995 | 98517052:98517189 |
| exon_skip_197354 | chr3 | 98515483:98515832:98516800:98516879:98517052:98517189 | 98516800:98516879 |
| exon_skip_198745 | chr3 | 98515483:98515832:98516800:98516879:98517052:98517064 | 98516800:98516879 |
| exon_skip_249662 | chr3 | 98515484:98515832:98516800:98516879:98517052:98517160 | 98516800:98516879 |
| exon_skip_274051 | chr3 | 98521133:98521442:98521653:98521703:98522849:98522875 | 98521653:98521703 |
| exon_skip_274984 | chr3 | 98516815:98516879:98517052:98517189:98518885:98518995 | 98517052:98517189 |
| exon_skip_32476 | chr3 | 98516777:98516879:98517158:98517189:98518885:98518995 | 98517158:98517189 |
| exon_skip_48889 | chr3 | 98516815:98516879:98517158:98517189:98518885:98518995 | 98517158:98517189 |
| 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_274051 | MSBB_STG | 2.357353e-01 | 3.656522e-01 | -1.299169e-01 | 1.282682e-03 |
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Open reading frame (ORF) annotation in the exon skipping event for CLDND1 |
| 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 |
| ENST00000394180 | 98521653 | 98521703 | 3UTR-3UTR |
| ENST00000341181 | 98517052 | 98517189 | In-frame |
| ENST00000394180 | 98517052 | 98517189 | In-frame |
| ENST00000394185 | 98517052 | 98517189 | In-frame |
| ENST00000503004 | 98517052 | 98517189 | In-frame |
| ENST00000510545 | 98517052 | 98517189 | In-frame |
| ENST00000513287 | 98517052 | 98517189 | 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 |
| ENST00000394180 | 98521653 | 98521703 | 3UTR-3UTR |
| ENST00000341181 | 98517052 | 98517189 | In-frame |
| ENST00000394180 | 98517052 | 98517189 | In-frame |
| ENST00000394185 | 98517052 | 98517189 | In-frame |
| ENST00000503004 | 98517052 | 98517189 | In-frame |
| ENST00000510545 | 98517052 | 98517189 | In-frame |
| ENST00000513287 | 98517052 | 98517189 | 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 |
| ENST00000394180 | 98521653 | 98521703 | 3UTR-3UTR |
| ENST00000341181 | 98517052 | 98517189 | In-frame |
| ENST00000394180 | 98517052 | 98517189 | In-frame |
| ENST00000394185 | 98517052 | 98517189 | In-frame |
| ENST00000503004 | 98517052 | 98517189 | In-frame |
| ENST00000510545 | 98517052 | 98517189 | In-frame |
| ENST00000513287 | 98517052 | 98517189 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLDND1 |
p-ENSG00000080822_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 |
| ENST00000341181 | 2178 | 253 | 98517052 | 98517189 | 617 | 753 | 134 | 180 |
| ENST00000394180 | 2245 | 253 | 98517052 | 98517189 | 691 | 827 | 134 | 180 |
| ENST00000394185 | 2176 | 253 | 98517052 | 98517189 | 625 | 761 | 134 | 180 |
| ENST00000503004 | 2835 | 253 | 98517052 | 98517189 | 1284 | 1420 | 134 | 180 |
| ENST00000510545 | 2141 | 253 | 98517052 | 98517189 | 594 | 730 | 134 | 180 |
| ENST00000513287 | 1016 | 253 | 98517052 | 98517189 | 635 | 771 | 134 | 180 |
| 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 |
| ENST00000341181 | 2178 | 253 | 98517052 | 98517189 | 617 | 753 | 134 | 180 |
| ENST00000394180 | 2245 | 253 | 98517052 | 98517189 | 691 | 827 | 134 | 180 |
| ENST00000394185 | 2176 | 253 | 98517052 | 98517189 | 625 | 761 | 134 | 180 |
| ENST00000503004 | 2835 | 253 | 98517052 | 98517189 | 1284 | 1420 | 134 | 180 |
| ENST00000510545 | 2141 | 253 | 98517052 | 98517189 | 594 | 730 | 134 | 180 |
| ENST00000513287 | 1016 | 253 | 98517052 | 98517189 | 635 | 771 | 134 | 180 |
| 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 |
| ENST00000341181 | 2178 | 253 | 98517052 | 98517189 | 617 | 753 | 134 | 180 |
| ENST00000394180 | 2245 | 253 | 98517052 | 98517189 | 691 | 827 | 134 | 180 |
| ENST00000394185 | 2176 | 253 | 98517052 | 98517189 | 625 | 761 | 134 | 180 |
| ENST00000503004 | 2835 | 253 | 98517052 | 98517189 | 1284 | 1420 | 134 | 180 |
| ENST00000510545 | 2141 | 253 | 98517052 | 98517189 | 594 | 730 | 134 | 180 |
| ENST00000513287 | 1016 | 253 | 98517052 | 98517189 | 635 | 771 | 134 | 180 |
| 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 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 1 | 253 | Chain | ID=PRO_0000164694;Note=Claudin domain-containing protein 1 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 141 | 161 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NY35 | 134 | 180 | 175 | 195 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CLDND1 |
| 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 |
| Mayo | ENST00000394180 | 98521653 | 98521703 | hsa-miR-3665 | chr3:98521694-98521701 | 8mer-1a | chr3:98521684-98521701 | 146.00 | -16.96 |
| Mayo | ENST00000394180 | 98521653 | 98521703 | hsa-miR-3925-5p | chr3:98521680-98521687 | 8mer-1a | chr3:98521679-98521700 | 156.00 | -21.96 |
| MSBB | ENST00000394180 | 98521653 | 98521703 | hsa-miR-3665 | chr3:98521694-98521701 | 8mer-1a | chr3:98521684-98521701 | 146.00 | -16.96 |
| MSBB | ENST00000394180 | 98521653 | 98521703 | hsa-miR-3925-5p | chr3:98521680-98521687 | 8mer-1a | chr3:98521679-98521700 | 156.00 | -21.96 |
| ROSMAP | ENST00000394180 | 98521653 | 98521703 | hsa-miR-3665 | chr3:98521694-98521701 | 8mer-1a | chr3:98521684-98521701 | 146.00 | -16.96 |
| ROSMAP | ENST00000394180 | 98521653 | 98521703 | hsa-miR-3925-5p | chr3:98521680-98521687 | 8mer-1a | chr3:98521679-98521700 | 156.00 | -21.96 |
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SNVs in the skipped exons for CLDND1 |
| - 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 CLDND1 |
| 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 CLDND1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| DLPFC | exon_skip_274051 | rs3762655 | chr3:98507717 | 2.470077e-04 | 1.836267e-02 |
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Correlation with RNA binding proteins (RBPs) for CLDND1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | DAZAP1 | exon_skip_274051 | -4.625455e-01 | 8.347073e-10 |
| CB | TARDBP | exon_skip_274051 | -5.215377e-01 | 1.803937e-12 |
| CB | RBM4B | exon_skip_274051 | -5.414026e-01 | 1.726685e-13 |
| FL | SRSF9 | exon_skip_274051 | 4.589951e-01 | 1.172248e-11 |
| STG | SRSF9 | exon_skip_274051 | 4.987431e-01 | 4.867387e-07 |
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RelatedDrugs for CLDND1 |
| 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 CLDND1 |
| 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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