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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 HLTF |
 Gene summary |
| Gene information | Gene symbol | HLTF | Gene ID | 6596 |
| Gene name | helicase like transcription factor | |
| Synonyms | HIP116|HIP116A|HLTF1|RNF80|SMARCA3|SNF2L3|ZBU1 | |
| Cytomap | 3q24 | |
| Type of gene | protein-coding | |
| Description | helicase-like transcription factorDNA-binding protein/plasminogen activator inhibitor-1 regulatorRING finger protein 80RING-type E3 ubiquitin transferase HLTFSNF2-like 3SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfa | |
| Modification date | 20180519 | |
| UniProtAcc | Q14527 | |
| Context | PubMed: HLTF [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 |
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Exon skipping events across known transcript of Ensembl for HLTF 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 HLTF |
| 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 HLTF |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_389288 | 3 | 148749987:148750159:148752704:148752785:148756835:148757016 | 148752704:148752785 | ENSG00000071794.11 | ENST00000392912.2,ENST00000494055.1,ENST00000310053.5,ENST00000465259.1 |
| exon_skip_389289 | 3 | 148757928:148757943:148759276:148759455:148759952:148760077 | 148759276:148759455 | ENSG00000071794.11 | ENST00000392912.2,ENST00000494055.1,ENST00000310053.5,ENST00000465259.1 |
| exon_skip_389290 | 3 | 148757928:148757943:148759276:148759467:148759952:148760077 | 148759276:148759467 | ENSG00000071794.11 | ENST00000467858.1 |
| exon_skip_389293 | 3 | 148759952:148760077:148763866:148764046:148765814:148765950 | 148763866:148764046 | ENSG00000071794.11 | ENST00000392912.2,ENST00000467858.1,ENST00000494055.1,ENST00000310053.5,ENST00000465259.1 |
| exon_skip_389294 | 3 | 148768056:148768162:148769831:148769931:148773089:148773187 | 148769831:148769931 | ENSG00000071794.11 | ENST00000493881.1 |
| exon_skip_389296 | 3 | 148773089:148773187:148777504:148777591:148778429:148778474 | 148777504:148777591 | ENSG00000071794.11 | ENST00000465259.1 |
| exon_skip_389297 | 3 | 148773089:148773187:148777504:148777594:148778429:148778474 | 148777504:148777594 | ENSG00000071794.11 | ENST00000392912.2,ENST00000494055.1,ENST00000310053.5,ENST00000493881.1 |
| exon_skip_389298 | 3 | 148781217:148781311:148782577:148782653:148786026:148786122 | 148782577:148782653 | ENSG00000071794.11 | ENST00000392912.2,ENST00000494055.1,ENST00000310053.5,ENST00000465259.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for HLTF |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_389288 | 3 | 148749987:148750159:148752704:148752785:148756835:148757016 | 148752704:148752785 | ENSG00000071794.11 | ENST00000465259.1,ENST00000310053.5,ENST00000392912.2,ENST00000494055.1 |
| exon_skip_389289 | 3 | 148757928:148757943:148759276:148759455:148759952:148760077 | 148759276:148759455 | ENSG00000071794.11 | ENST00000465259.1,ENST00000310053.5,ENST00000392912.2,ENST00000494055.1 |
| exon_skip_389290 | 3 | 148757928:148757943:148759276:148759467:148759952:148760077 | 148759276:148759467 | ENSG00000071794.11 | ENST00000467858.1 |
| exon_skip_389293 | 3 | 148759952:148760077:148763866:148764046:148765814:148765950 | 148763866:148764046 | ENSG00000071794.11 | ENST00000465259.1,ENST00000310053.5,ENST00000392912.2,ENST00000494055.1,ENST00000467858.1 |
| exon_skip_389294 | 3 | 148768056:148768162:148769831:148769931:148773089:148773187 | 148769831:148769931 | ENSG00000071794.11 | ENST00000493881.1 |
| exon_skip_389296 | 3 | 148773089:148773187:148777504:148777591:148778429:148778474 | 148777504:148777591 | ENSG00000071794.11 | ENST00000465259.1 |
| exon_skip_389297 | 3 | 148773089:148773187:148777504:148777594:148778429:148778474 | 148777504:148777594 | ENSG00000071794.11 | ENST00000310053.5,ENST00000392912.2,ENST00000494055.1,ENST00000493881.1 |
| exon_skip_389298 | 3 | 148781217:148781311:148782577:148782653:148786026:148786122 | 148782577:148782653 | ENSG00000071794.11 | ENST00000465259.1,ENST00000310053.5,ENST00000392912.2,ENST00000494055.1 |
| 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 HLTF |
| 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 |
| ENST00000310053 | 148759276 | 148759455 | Frame-shift |
| ENST00000392912 | 148759276 | 148759455 | Frame-shift |
| ENST00000494055 | 148759276 | 148759455 | Frame-shift |
| ENST00000310053 | 148782577 | 148782653 | Frame-shift |
| ENST00000392912 | 148782577 | 148782653 | Frame-shift |
| ENST00000494055 | 148782577 | 148782653 | Frame-shift |
| ENST00000310053 | 148752704 | 148752785 | In-frame |
| ENST00000392912 | 148752704 | 148752785 | In-frame |
| ENST00000494055 | 148752704 | 148752785 | In-frame |
| ENST00000310053 | 148763866 | 148764046 | In-frame |
| ENST00000392912 | 148763866 | 148764046 | In-frame |
| ENST00000494055 | 148763866 | 148764046 | In-frame |
| ENST00000310053 | 148777504 | 148777594 | In-frame |
| ENST00000392912 | 148777504 | 148777594 | In-frame |
| ENST00000494055 | 148777504 | 148777594 | In-frame |
| 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 |
| ENST00000310053 | 148759276 | 148759455 | Frame-shift |
| ENST00000392912 | 148759276 | 148759455 | Frame-shift |
| ENST00000494055 | 148759276 | 148759455 | Frame-shift |
| ENST00000310053 | 148782577 | 148782653 | Frame-shift |
| ENST00000392912 | 148782577 | 148782653 | Frame-shift |
| ENST00000494055 | 148782577 | 148782653 | Frame-shift |
| ENST00000310053 | 148752704 | 148752785 | In-frame |
| ENST00000392912 | 148752704 | 148752785 | In-frame |
| ENST00000494055 | 148752704 | 148752785 | In-frame |
| ENST00000310053 | 148763866 | 148764046 | In-frame |
| ENST00000392912 | 148763866 | 148764046 | In-frame |
| ENST00000494055 | 148763866 | 148764046 | In-frame |
| ENST00000310053 | 148777504 | 148777594 | In-frame |
| ENST00000392912 | 148777504 | 148777594 | In-frame |
| ENST00000494055 | 148777504 | 148777594 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HLTF |
| 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 |
| ENST00000310053 | 5334 | 1009 | 148777504 | 148777594 | 1480 | 1569 | 428 | 458 |
| ENST00000392912 | 3913 | 1009 | 148777504 | 148777594 | 1454 | 1543 | 428 | 458 |
| ENST00000494055 | 3650 | 1009 | 148777504 | 148777594 | 1504 | 1593 | 428 | 458 |
| ENST00000310053 | 5334 | 1009 | 148763866 | 148764046 | 2087 | 2266 | 631 | 690 |
| ENST00000392912 | 3913 | 1009 | 148763866 | 148764046 | 2061 | 2240 | 631 | 690 |
| ENST00000494055 | 3650 | 1009 | 148763866 | 148764046 | 2111 | 2290 | 631 | 690 |
| ENST00000310053 | 5334 | 1009 | 148752704 | 148752785 | 2991 | 3071 | 932 | 959 |
| ENST00000392912 | 3913 | 1009 | 148752704 | 148752785 | 2965 | 3045 | 932 | 959 |
| ENST00000494055 | 3650 | 1009 | 148752704 | 148752785 | 3015 | 3095 | 932 | 959 |
| 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 |
| ENST00000310053 | 5334 | 1009 | 148777504 | 148777594 | 1480 | 1569 | 428 | 458 |
| ENST00000392912 | 3913 | 1009 | 148777504 | 148777594 | 1454 | 1543 | 428 | 458 |
| ENST00000494055 | 3650 | 1009 | 148777504 | 148777594 | 1504 | 1593 | 428 | 458 |
| ENST00000310053 | 5334 | 1009 | 148763866 | 148764046 | 2087 | 2266 | 631 | 690 |
| ENST00000392912 | 3913 | 1009 | 148763866 | 148764046 | 2061 | 2240 | 631 | 690 |
| ENST00000494055 | 3650 | 1009 | 148763866 | 148764046 | 2111 | 2290 | 631 | 690 |
| ENST00000310053 | 5334 | 1009 | 148752704 | 148752785 | 2991 | 3071 | 932 | 959 |
| ENST00000392912 | 3913 | 1009 | 148752704 | 148752785 | 2965 | 3045 | 932 | 959 |
| ENST00000494055 | 3650 | 1009 | 148752704 | 148752785 | 3015 | 3095 | 932 | 959 |
| 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 |
| Q14527 | 428 | 458 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 428 | 458 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 428 | 458 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 428 | 458 | 435 | 606 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| Q14527 | 428 | 458 | 435 | 606 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| Q14527 | 428 | 458 | 435 | 606 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| Q14527 | 428 | 458 | 429 | 429 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q14527 | 428 | 458 | 429 | 429 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q14527 | 428 | 458 | 429 | 429 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q14527 | 631 | 690 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 631 | 690 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 631 | 690 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 837 | 996 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q14527 | 932 | 959 | 837 | 996 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q14527 | 932 | 959 | 837 | 996 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q14527 | 932 | 959 | 925 | 1009 | Region | Note=Interaction with SP1 and SP3;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10391891;Dbxref=PMID:10391891 |
| Q14527 | 932 | 959 | 925 | 1009 | Region | Note=Interaction with SP1 and SP3;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10391891;Dbxref=PMID:10391891 |
| Q14527 | 932 | 959 | 925 | 1009 | Region | Note=Interaction with SP1 and SP3;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10391891;Dbxref=PMID:10391891 |
| 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 |
| Q14527 | 428 | 458 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 428 | 458 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 428 | 458 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 428 | 458 | 435 | 606 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| Q14527 | 428 | 458 | 435 | 606 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| Q14527 | 428 | 458 | 435 | 606 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| Q14527 | 428 | 458 | 429 | 429 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q14527 | 428 | 458 | 429 | 429 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q14527 | 428 | 458 | 429 | 429 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q14527 | 631 | 690 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 631 | 690 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 631 | 690 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 1 | 1009 | Chain | ID=PRO_0000030722;Note=Helicase-like transcription factor |
| Q14527 | 932 | 959 | 837 | 996 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q14527 | 932 | 959 | 837 | 996 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q14527 | 932 | 959 | 837 | 996 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q14527 | 932 | 959 | 925 | 1009 | Region | Note=Interaction with SP1 and SP3;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10391891;Dbxref=PMID:10391891 |
| Q14527 | 932 | 959 | 925 | 1009 | Region | Note=Interaction with SP1 and SP3;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10391891;Dbxref=PMID:10391891 |
| Q14527 | 932 | 959 | 925 | 1009 | Region | Note=Interaction with SP1 and SP3;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10391891;Dbxref=PMID:10391891 |
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SNVs in the skipped exons for HLTF |
| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_389289 | 148759277 | 148759455 | 148759411 | 148759411 | Frame_Shift_Del | T | - | p.M748fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_389290 | 148759277 | 148759467 | 148759411 | 148759411 | Frame_Shift_Del | T | - | p.M748fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_389293 | 148763867 | 148764046 | 148763891 | 148763891 | Frame_Shift_Del | T | - | p.N683fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_389293 | 148763867 | 148764046 | 148763980 | 148763980 | Frame_Shift_Del | T | - | p.K653fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_389296 | 148777505 | 148777591 | 148777507 | 148777507 | Frame_Shift_Del | T | - | p.K458fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_389297 | 148777505 | 148777594 | 148777507 | 148777507 | Frame_Shift_Del | T | - | p.K458fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_389296 | 148777505 | 148777591 | 148777522 | 148777522 | Frame_Shift_Del | T | - | p.K454fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_389297 | 148777505 | 148777594 | 148777522 | 148777522 | Frame_Shift_Del | T | - | p.K454fs |
| - 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 |
| BHT101_THYROID | 148759277 | 148759455 | 148759282 | 148759282 | Missense_Mutation | C | T | p.E791K |
| BHT101_THYROID | 148759277 | 148759467 | 148759282 | 148759282 | Missense_Mutation | C | T | p.E791K |
| SNU182_LIVER | 148759277 | 148759455 | 148759321 | 148759321 | Missense_Mutation | C | T | p.V778I |
| SNU182_LIVER | 148759277 | 148759467 | 148759321 | 148759321 | Missense_Mutation | C | T | p.V778I |
| NCIH1299_LUNG | 148759277 | 148759455 | 148759407 | 148759407 | Missense_Mutation | T | G | p.K749T |
| NCIH1299_LUNG | 148759277 | 148759467 | 148759407 | 148759407 | Missense_Mutation | T | G | p.K749T |
| SNU81_LARGE_INTESTINE | 148759277 | 148759455 | 148759431 | 148759431 | Missense_Mutation | C | A | p.R741I |
| SNU81_LARGE_INTESTINE | 148759277 | 148759467 | 148759431 | 148759431 | Missense_Mutation | C | A | p.R741I |
| CW2_LARGE_INTESTINE | 148763867 | 148764046 | 148763930 | 148763930 | Missense_Mutation | A | G | p.L670P |
| BALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 148763867 | 148764046 | 148763954 | 148763954 | Missense_Mutation | T | A | p.K662I |
| EVSAT_BREAST | 148777505 | 148777591 | 148777569 | 148777569 | Missense_Mutation | A | C | p.D437E |
| EVSAT_BREAST | 148777505 | 148777594 | 148777569 | 148777569 | Missense_Mutation | A | C | p.D437E |
| SNUC4_LARGE_INTESTINE | 148782578 | 148782653 | 148782631 | 148782631 | Missense_Mutation | G | T | p.S338Y |
| HCC2998_LARGE_INTESTINE | 148759277 | 148759455 | 148759455 | 148759455 | Splice_Site | C | T | p.G733E |
| HCC2998_LARGE_INTESTINE | 148759277 | 148759467 | 148759455 | 148759455 | Splice_Site | C | T | p.G733E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HLTF |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HLTF |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HLTF |
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RelatedDrugs for HLTF |
| 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 HLTF |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| HLTF | C0022665 | Kidney Neoplasm | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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