|
||||||
|
 | |
| |
| |
| 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 CLIP1 |
 Gene summary |
| Gene information | Gene symbol | CLIP1 | Gene ID | 6249 |
| Gene name | CAP-Gly domain containing linker protein 1 | |
| Synonyms | CLIP|CLIP-170|CLIP170|CYLN1|RSN | |
| Cytomap | 12q24.31 | |
| Type of gene | protein-coding | |
| Description | CAP-Gly domain-containing linker protein 1cytoplasmic linker protein 1cytoplasmic linker protein 170 alpha-2cytoplasmic linker protein CLIP-170restin (Reed-Steinberg cell-expressed intermediate filament-associated protein) | |
| 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 |
Top |
Gene structures and expression levels for CLIP1 |
| 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. |
 |
ENSG00000130779
| 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 | UP | ENST00000537178.5 | CLIP1-210:protein_coding:CLIP1 | 1.386386e+02 | 9.464651e-01 | 5.118777e-05 | 4.195346e-04 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CLIP1 |
| 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_106778 | chr12 | 122354910:122355312:122360816:122361181:122363983:122364017 | 122360816:122361181 |
| exon_skip_118242 | chr12 | 122319232:122319348:122322114:122324381:122327947:122328162 | 122322114:122324381 |
| exon_skip_132809 | chr12 | 122288489:122288541:122309762:122309882:122316749:122316855 | 122309762:122309882 |
| exon_skip_13428 | chr12 | 122360959:122361181:122363983:122364107:122377389:122377960 | 122363983:122364107 |
| exon_skip_138102 | chr12 | 122354453:122354556:122355115:122355312:122360959:122361181 | 122355115:122355312 |
| exon_skip_159291 | chr12 | 122334648:122334705:122336632:122336748:122340753:122340908 | 122336632:122336748 |
| exon_skip_162401 | chr12 | 122279028:122279145:122288489:122288541:122309762:122309882 | 122288489:122288541 |
| exon_skip_166123 | chr12 | 122274038:122274162:122278154:122278203:122278792:122278935 | 122278154:122278203 |
| exon_skip_167703 | chr12 | 122272834:122273100:122274038:122274162:122276439:122276444 | 122274038:122274162 |
| exon_skip_179485 | chr12 | 122347375:122347479:122351111:122351143:122352726:122352782 | 122351111:122351143 |
| exon_skip_181374 | chr12 | 122336632:122336748:122340753:122341697:122352726:122352786 | 122340753:122341697 |
| exon_skip_197543 | chr12 | 122336632:122336748:122340753:122341697:122347375:122347479 | 122340753:122341697 |
| exon_skip_205038 | chr12 | 122380368:122380558:122400132:122400243:122422521:122422612 | 122400132:122400243 |
| exon_skip_20849 | chr12 | 122274038:122274162:122278154:122278203:122278792:122278942 | 122278154:122278203 |
| exon_skip_216665 | chr12 | 122336632:122336748:122340981:122341697:122352726:122352786 | 122340981:122341697 |
| exon_skip_227211 | chr12 | 122380368:122380558:122400132:122400243:122422521:122422569 | 122400132:122400243 |
| exon_skip_230912 | chr12 | 122341088:122341697:122347375:122347479:122352726:122352786 | 122347375:122347479 |
| exon_skip_231630 | chr12 | 122354488:122354556:122355115:122355312:122360959:122361181 | 122355115:122355312 |
| exon_skip_233432 | chr12 | 122334648:122334705:122336632:122336748:122340753:122341256 | 122336632:122336748 |
| exon_skip_234789 | chr12 | 122334676:122334705:122336632:122336748:122340981:122341697 | 122336632:122336748 |
| exon_skip_236846 | chr12 | 122347375:122347479:122351111:122351143:122352726:122352786 | 122351111:122351143 |
| exon_skip_244537 | chr12 | 122352726:122352786:122354453:122354556:122355115:122355312 | 122354453:122354556 |
| exon_skip_245147 | chr12 | 122354453:122354556:122355115:122355312:122360959:122361013 | 122355115:122355312 |
| exon_skip_246928 | chr12 | 122355115:122355312:122360959:122361181:122363983:122364017 | 122360959:122361181 |
| exon_skip_262217 | chr12 | 122341088:122341697:122347375:122347479:122352726:122352782 | 122347375:122347479 |
| exon_skip_26746 | chr12 | 122341088:122341697:122352726:122352786:122354453:122354556 | 122352726:122352786 |
| exon_skip_276494 | chr12 | 122309762:122309882:122316749:122316855:122319232:122319348 | 122316749:122316855 |
| exon_skip_278290 | chr12 | 122334648:122334705:122336632:122336748:122340981:122341697 | 122336632:122336748 |
| exon_skip_35308 | chr12 | 122334648:122334705:122336632:122336748:122340753:122340847 | 122336632:122336748 |
| exon_skip_53798 | chr12 | 122274090:122274162:122276439:122276444:122278154:122278203 | 122276439:122276444 |
| exon_skip_62046 | chr12 | 122274038:122274162:122276439:122276444:122278154:122278203 | 122276439:122276444 |
| exon_skip_64364 | chr12 | 122272834:122273100:122274038:122274162:122278154:122278203 | 122274038:122274162 |
| exon_skip_65849 | chr12 | 122341088:122341697:122347375:122347479:122351111:122351143 | 122347375:122347479 |
| exon_skip_77793 | chr12 | 122316749:122316855:122319232:122319348:122327947:122328162 | 122319232:122319348 |
| exon_skip_83918 | chr12 | 122272834:122273100:122274038:122274143:122278154:122278203 | 122274038:122274143 |
| exon_skip_94419 | chr12 | 122319232:122319348:122322114:122324381:122327947:122328073 | 122322114:122324381 |
| exon_skip_97799 | chr12 | 122319233:122319348:122322114:122324381:122327947:122328162 | 122322114:122324381 |
| exon_skip_98468 | chr12 | 122336632:122336748:122340981:122341697:122347375:122347479 | 122340981:122341697 |
| 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_62046 | MSBB_PG | 4.285926e-01 | 6.516981e-01 | -2.231055e-01 | 3.520076e-05 |
| exon_skip_262217 | MSBB_PG | 4.460630e-01 | 6.084906e-01 | -1.624276e-01 | 1.893349e-04 |
| exon_skip_179485 | MSBB_PG | 3.771186e-01 | 2.331373e-01 | 1.439814e-01 | 4.057861e-06 |
| exon_skip_62046 | MSBB_IFG | 6.335294e-01 | 7.863636e-01 | -1.528342e-01 | 3.228745e-02 |
| exon_skip_295212 | Mayo_CB | 5.391463e-01 | 7.267692e-01 | -1.876229e-01 | 5.181549e-10 |
| exon_skip_262217 | Mayo_TC | 3.230488e-01 | 4.729851e-01 | -1.499363e-01 | 7.906715e-07 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CLIP1 |
| 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 |
| ENST00000302528 | 122274038 | 122274162 | Frame-shift |
| ENST00000358808 | 122274038 | 122274162 | Frame-shift |
| ENST00000302528 | 122278154 | 122278203 | Frame-shift |
| ENST00000358808 | 122278154 | 122278203 | Frame-shift |
| ENST00000302528 | 122354453 | 122354556 | Frame-shift |
| ENST00000358808 | 122354453 | 122354556 | Frame-shift |
| ENST00000302528 | 122319232 | 122319348 | In-frame |
| ENST00000358808 | 122319232 | 122319348 | In-frame |
| ENST00000302528 | 122336632 | 122336748 | In-frame |
| ENST00000358808 | 122336632 | 122336748 | In-frame |
| ENST00000302528 | 122347375 | 122347479 | In-frame |
| ENST00000358808 | 122347375 | 122347479 | In-frame |
| ENST00000302528 | 122355115 | 122355312 | In-frame |
| ENST00000358808 | 122355115 | 122355312 | 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 |
| ENST00000302528 | 122336632 | 122336748 | In-frame |
| ENST00000358808 | 122336632 | 122336748 | In-frame |
| ENST00000302528 | 122347375 | 122347479 | In-frame |
| ENST00000358808 | 122347375 | 122347479 | In-frame |
| ENST00000302528 | 122355115 | 122355312 | In-frame |
| ENST00000358808 | 122355115 | 122355312 | 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 |
| ENST00000302528 | 122274038 | 122274162 | Frame-shift |
| ENST00000358808 | 122274038 | 122274162 | Frame-shift |
| ENST00000302528 | 122278154 | 122278203 | Frame-shift |
| ENST00000358808 | 122278154 | 122278203 | Frame-shift |
| ENST00000302528 | 122288489 | 122288541 | Frame-shift |
| ENST00000358808 | 122288489 | 122288541 | Frame-shift |
| ENST00000302528 | 122309762 | 122309882 | Frame-shift |
| ENST00000358808 | 122309762 | 122309882 | Frame-shift |
| ENST00000302528 | 122316749 | 122316855 | Frame-shift |
| ENST00000358808 | 122316749 | 122316855 | Frame-shift |
| ENST00000302528 | 122354453 | 122354556 | Frame-shift |
| ENST00000358808 | 122354453 | 122354556 | Frame-shift |
| ENST00000302528 | 122360959 | 122361181 | Frame-shift |
| ENST00000358808 | 122360959 | 122361181 | Frame-shift |
| ENST00000302528 | 122363983 | 122364107 | Frame-shift |
| ENST00000358808 | 122363983 | 122364107 | Frame-shift |
| ENST00000302528 | 122319232 | 122319348 | In-frame |
| ENST00000358808 | 122319232 | 122319348 | In-frame |
| ENST00000302528 | 122336632 | 122336748 | In-frame |
| ENST00000358808 | 122336632 | 122336748 | In-frame |
| ENST00000302528 | 122340753 | 122341697 | In-frame |
| ENST00000358808 | 122340753 | 122341697 | In-frame |
| ENST00000302528 | 122347375 | 122347479 | In-frame |
| ENST00000358808 | 122347375 | 122347479 | In-frame |
| ENST00000302528 | 122355115 | 122355312 | In-frame |
| ENST00000358808 | 122355115 | 122355312 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for CLIP1 |
p-ENSG00000130779_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 |
| 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 |
| 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 |
| 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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in CLIP1 |
| 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 CLIP1 |
| - 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 CLIP1 |
| 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 |
| ADstage | MSBB | IFG | exon_skip_62046 | -5.246431e-01 | 4.154376e-03 | chr12 | - | 122274038 | 122274162 | 122276439 | 122276444 | 122278154 | 122278203 |
| CDR | MSBB | IFG | exon_skip_62046 | -5.198441e-01 | 4.577814e-03 | chr12 | - | 122274038 | 122274162 | 122276439 | 122276444 | 122278154 | 122278203 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CLIP1 |
| 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 CLIP1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_295212 | -6.231692e-01 | 3.494257e-17 |
| CB | MBNL1 | exon_skip_295212 | -5.656144e-01 | 8.366242e-14 |
| CB | HNRNPL | exon_skip_295212 | -4.730739e-01 | 1.442113e-09 |
| CB | HNRNPF | exon_skip_295212 | -6.764041e-01 | 5.364616e-21 |
| CB | RBM3 | exon_skip_262217 | 4.116739e-01 | 9.339952e-08 |
| CB | TRA2A | exon_skip_262217 | -4.910649e-01 | 7.589501e-11 |
| CB | RBM4 | exon_skip_262217 | -5.137306e-01 | 6.959145e-12 |
| FL | RBFOX2 | exon_skip_230912 | 4.619918e-01 | 1.057845e-11 |
| HCC | RBM47 | exon_skip_62046 | -5.074745e-01 | 2.832238e-19 |
| HCC | RBFOX2 | exon_skip_230912 | 4.997058e-01 | 1.591850e-18 |
| HCC | MSI1 | exon_skip_230912 | -5.389580e-01 | 8.060672e-22 |
| HCC | SFPQ | exon_skip_230912 | -4.581422e-01 | 1.813358e-15 |
| HCC | RBM5 | exon_skip_230912 | -4.732627e-01 | 1.564090e-16 |
| HCC | HNRNPF | exon_skip_230912 | -5.856937e-01 | 2.372575e-26 |
| HCC | RBM4 | exon_skip_230912 | -4.347669e-01 | 6.360305e-14 |
| IFG | PABPN1L | exon_skip_233432 | 4.629334e-01 | 3.457480e-02 |
| IFG | PTBP3 | exon_skip_233432 | 4.687555e-01 | 3.207648e-02 |
| IFG | PABPC4 | exon_skip_233432 | 4.995257e-01 | 2.113303e-02 |
| IFG | RBFOX2 | exon_skip_230912 | 4.334612e-01 | 2.120550e-02 |
| PCC | RBFOX2 | exon_skip_262217 | 6.698624e-01 | 2.558676e-28 |
| PCC | MSI1 | exon_skip_262217 | -4.212114e-01 | 2.615796e-10 |
| PCC | RALYL | exon_skip_262217 | 4.479258e-01 | 1.310897e-11 |
| PCC | HNRNPF | exon_skip_262217 | -5.180272e-01 | 1.307971e-15 |
| PG | RBFOX2 | exon_skip_262217 | 5.888770e-01 | 3.484848e-18 |
| PG | RBM3 | exon_skip_262217 | 4.342974e-01 | 1.121347e-09 |
| PG | HNRNPK | exon_skip_262217 | 4.154579e-01 | 6.654851e-09 |
| PG | HNRNPA0 | exon_skip_262217 | 4.174477e-01 | 5.542186e-09 |
| PG | RALYL | exon_skip_262217 | 5.499094e-01 | 1.292374e-15 |
| PG | HNRNPH2 | exon_skip_262217 | 4.322413e-01 | 1.369223e-09 |
| STG | RBM47 | exon_skip_62046 | -4.487317e-01 | 1.469273e-05 |
| STG | HNRNPL | exon_skip_233432 | -4.184187e-01 | 3.840659e-04 |
| TC | HNRNPA0 | exon_skip_159291 | -4.024986e-01 | 5.701498e-07 |
| TC | HNRNPH2 | exon_skip_159291 | -4.024337e-01 | 5.727638e-07 |
| TC | RBFOX2 | exon_skip_262217 | 7.455190e-01 | 1.096241e-27 |
| TC | MSI1 | exon_skip_262217 | -5.802190e-01 | 8.836458e-15 |
| TC | ILF2 | exon_skip_262217 | 4.728428e-01 | 1.135857e-09 |
| TC | HNRNPA0 | exon_skip_262217 | 6.259177e-01 | 1.397791e-17 |
| TC | RALYL | exon_skip_262217 | 7.482920e-01 | 5.486198e-28 |
| TC | HNRNPH2 | exon_skip_262217 | 6.345929e-01 | 3.635324e-18 |
| TC | ESRP1 | exon_skip_262217 | 6.000980e-01 | 6.062434e-16 |
Top |
RelatedDrugs for CLIP1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for CLIP1 |
| 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)
|