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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for PDLIM4 |
 Gene summary |
| Gene information | Gene symbol | PDLIM4 | Gene ID | 8572 |
| Gene name | PDZ and LIM domain 4 | |
| Synonyms | RIL | |
| Cytomap | 5q31.1 | |
| Type of gene | protein-coding | |
| Description | PDZ and LIM domain protein 4LIM domain proteinLIM protein RILenigma homologreversion-induced LIM protein | |
| Modification date | 20180519 | |
| UniProtAcc | P50479 | |
| Context | PubMed: PDLIM4 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PDLIM4 | GO:0031532 | actin cytoskeleton reorganization | 21636573 |
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Exon skipping events across known transcript of Ensembl for PDLIM4 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for PDLIM4 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PDLIM4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_437172 | 5 | 131593399:131593520:131598301:131598453:131602156:131602238 | 131598301:131598453 | ENSG00000131435.8 | ENST00000463615.1,ENST00000379018.3 |
| exon_skip_437189 | 5 | 131598301:131598453:131602156:131602238:131606607:131606786 | 131602156:131602238 | ENSG00000131435.8 | ENST00000253754.3,ENST00000379018.3,ENST00000418373.1 |
| exon_skip_437198 | 5 | 131602156:131602238:131606607:131606786:131606995:131607029 | 131606607:131606786 | ENSG00000131435.8 | ENST00000253754.3,ENST00000379018.3,ENST00000418373.1 |
| exon_skip_437203 | 5 | 131606664:131606786:131606995:131607159:131607483:131607526 | 131606995:131607159 | ENSG00000131435.8 | ENST00000253754.3,ENST00000484620.1 |
| exon_skip_437204 | 5 | 131606664:131606786:131606995:131607159:131607717:131607756 | 131606995:131607159 | ENSG00000131435.8 | ENST00000379018.3 |
| exon_skip_437206 | 5 | 131606664:131606786:131606995:131607601:131607717:131607756 | 131606995:131607601 | ENSG00000131435.8 | ENST00000462597.1 |
| exon_skip_437208 | 5 | 131606995:131607159:131607483:131607601:131607717:131607756 | 131607483:131607601 | ENSG00000131435.8 | ENST00000253754.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PDLIM4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_437172 | 5 | 131593399:131593520:131598301:131598453:131602156:131602238 | 131598301:131598453 | ENSG00000131435.8 | ENST00000463615.1,ENST00000379018.3 |
| exon_skip_437189 | 5 | 131598301:131598453:131602156:131602238:131606607:131606786 | 131602156:131602238 | ENSG00000131435.8 | ENST00000253754.3,ENST00000379018.3,ENST00000418373.1 |
| exon_skip_437198 | 5 | 131602156:131602238:131606607:131606786:131606995:131607029 | 131606607:131606786 | ENSG00000131435.8 | ENST00000253754.3,ENST00000379018.3,ENST00000418373.1 |
| exon_skip_437203 | 5 | 131606664:131606786:131606995:131607159:131607483:131607526 | 131606995:131607159 | ENSG00000131435.8 | ENST00000253754.3,ENST00000484620.1 |
| exon_skip_437204 | 5 | 131606664:131606786:131606995:131607159:131607717:131607756 | 131606995:131607159 | ENSG00000131435.8 | ENST00000379018.3 |
| exon_skip_437206 | 5 | 131606664:131606786:131606995:131607601:131607717:131607756 | 131606995:131607601 | ENSG00000131435.8 | ENST00000462597.1 |
| exon_skip_437208 | 5 | 131606995:131607159:131607483:131607601:131607717:131607756 | 131607483:131607601 | ENSG00000131435.8 | ENST00000253754.3 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PDLIM4 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000253754 | 131602156 | 131602238 | Frame-shift |
| ENST00000253754 | 131606607 | 131606786 | Frame-shift |
| ENST00000253754 | 131606995 | 131607159 | Frame-shift |
| ENST00000253754 | 131607483 | 131607601 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000253754 | 131602156 | 131602238 | Frame-shift |
| ENST00000253754 | 131606607 | 131606786 | Frame-shift |
| ENST00000253754 | 131606995 | 131607159 | Frame-shift |
| ENST00000253754 | 131607483 | 131607601 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for PDLIM4 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 GTEx 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 TCGA. |
| 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 GTEx. |
| 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 |
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SNVs in the skipped exons for PDLIM4 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| KIRP | TCGA-2Z-A9JS-01 | exon_skip_437198 | 131606608 | 131606786 | 131606622 | 131606622 | Frame_Shift_Del | A | - | p.T114fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_437198 | 131606608 | 131606786 | 131606750 | 131606750 | Frame_Shift_Del | C | - | p.A157fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_437198 | 131606608 | 131606786 | 131606779 | 131606779 | Frame_Shift_Del | C | - | p.P168fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_437198 | 131606608 | 131606786 | 131606779 | 131606779 | Frame_Shift_Del | C | - | p.P168fs |
| STAD | TCGA-CG-5721-01 | exon_skip_437198 | 131606608 | 131606786 | 131606779 | 131606779 | Frame_Shift_Del | C | - | p.P166fs |
| UCEC | TCGA-D1-A0ZS-01 | exon_skip_437198 | 131606608 | 131606786 | 131606779 | 131606779 | Frame_Shift_Del | C | - | p.P167fs |
| UCEC | TCGA-B5-A0JZ-01 | exon_skip_437198 | 131606608 | 131606786 | 131606680 | 131606680 | Nonsense_Mutation | G | T | p.G134* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| SNU1040_LARGE_INTESTINE | 131598302 | 131598453 | 131598326 | 131598326 | Missense_Mutation | T | A | p.L40M |
| LS1034_LARGE_INTESTINE | 131598302 | 131598453 | 131598411 | 131598411 | Missense_Mutation | G | A | p.R68H |
| LS411N_LARGE_INTESTINE | 131602157 | 131602238 | 131602195 | 131602195 | Missense_Mutation | G | A | p.S95N |
| NCIH2023_LUNG | 131602157 | 131602238 | 131602196 | 131602196 | Missense_Mutation | C | A | p.S95R |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 131606608 | 131606786 | 131606627 | 131606627 | Missense_Mutation | G | A | p.S116N |
| SW756_CERVIX | 131606608 | 131606786 | 131606719 | 131606719 | Missense_Mutation | C | G | p.H147D |
| LS411N_LARGE_INTESTINE | 131606996 | 131607159 | 131607155 | 131607155 | Missense_Mutation | G | T | p.E222D |
| LS411N_LARGE_INTESTINE | 131606996 | 131607601 | 131607155 | 131607155 | Missense_Mutation | G | T | p.E222D |
| 639V_URINARY_TRACT | 131607484 | 131607601 | 131607543 | 131607543 | Missense_Mutation | G | A | p.A244T |
| 639V_URINARY_TRACT | 131606996 | 131607601 | 131607543 | 131607543 | Missense_Mutation | G | A | p.A244T |
| HSC4_UPPER_AERODIGESTIVE_TRACT | 131607484 | 131607601 | 131607546 | 131607546 | Missense_Mutation | C | T | p.P245S |
| HSC4_UPPER_AERODIGESTIVE_TRACT | 131606996 | 131607601 | 131607546 | 131607546 | Missense_Mutation | C | T | p.P245S |
| SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 131607484 | 131607601 | 131607580 | 131607580 | Missense_Mutation | C | T | p.T256M |
| SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 131606996 | 131607601 | 131607580 | 131607580 | Missense_Mutation | C | T | p.T256M |
| SNUC4_LARGE_INTESTINE | 131607484 | 131607601 | 131607491 | 131607491 | Nonsense_Mutation | G | A | p.W226* |
| SNUC4_LARGE_INTESTINE | 131606996 | 131607601 | 131607491 | 131607491 | Nonsense_Mutation | G | A | p.W226* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDLIM4 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
| exon_skip_437189 | 5 | 131598301:131598453:131602156:131602238:131606607:131606786 | 131602156:131602238 | ENST00000253754.3,ENST00000379018.3,ENST00000418373.1 | PRAD | rs1007602 | chr5:131602166 | T/C | 1.77e-03 |
| exon_skip_437203 | 5 | 131606664:131606786:131606995:131607159:131607483:131607526 | 131606995:131607159 | ENST00000253754.3,ENST00000484620.1 | THCA | rs270619 | chr5:131607080 | A/G | 3.18e-04 |
| exon_skip_437204 | 5 | 131606664:131606786:131606995:131607159:131607717:131607756 | 131606995:131607159 | ENST00000379018.3 | THCA | rs270619 | chr5:131607080 | A/G | 3.18e-04 |
| exon_skip_437206 | 5 | 131606664:131606786:131606995:131607601:131607717:131607756 | 131606995:131607601 | ENST00000462597.1 | THCA | rs270619 | chr5:131607080 | A/G | 3.18e-04 |
| exon_skip_437206 | 5 | 131606664:131606786:131606995:131607601:131607717:131607756 | 131606995:131607601 | ENST00000462597.1 | THCA | rs162886 | chr5:131607297 | A/G | 5.15e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDLIM4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDLIM4 |
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RelatedDrugs for PDLIM4 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PDLIM4 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PDLIM4 | C0032460 | Polycystic Ovary Syndrome | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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