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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 HACL1 |
 Gene summary |
| Gene information | Gene symbol | HACL1 | Gene ID | 26061 |
| Gene name | 2-hydroxyacyl-CoA lyase 1 | |
| Synonyms | 2-HPCL|HPCL|HPCL2|PHYH2 | |
| Cytomap | 3p25.1 | |
| Type of gene | protein-coding | |
| Description | 2-hydroxyacyl-CoA lyase 11600020H07Rik2-hydroxyphytanol-CoA lyase2-hydroxyphytanoyl-CoA lyasephytanoyl-CoA 2-hydroxylase 2phytanoyl-CoA hydroxylase 2 | |
| Modification date | 20200327 | |
| 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 |
| HACL1 | GO:0001561 | fatty acid alpha-oxidation | 10468558 |
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Gene structures and expression levels for HACL1 |
| 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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ENSG00000131373
| 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 |
| CB | UP | ENST00000472857.1 | HACL1-212:retained_intron:HACL1 | 2.381982e+00 | 8.513672e-01 | 1.110343e-04 | 8.083948e-04 |
| TC | DOWN | ENST00000435217.6 | HACL1-206:protein_coding:HACL1 | 5.830521e+01 | -9.231439e-01 | 8.263996e-05 | 1.388327e-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 HACL1 |
| 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_115673 | chr3 | 15571668:15571769:15573159:15573242:15574977:15575082 | 15573159:15573242 |
| exon_skip_150847 | chr3 | 15586525:15586602:15589540:15589612:15596384:15596424 | 15589540:15589612 |
| exon_skip_16311 | chr3 | 15589540:15589612:15596384:15596424:15601090:15601185 | 15596384:15596424 |
| exon_skip_16332 | chr3 | 15589540:15589612:15591600:15591680:15596384:15596424 | 15591600:15591680 |
| exon_skip_172066 | chr3 | 15586525:15586602:15589540:15589612:15591600:15591680 | 15589540:15589612 |
| exon_skip_180931 | chr3 | 15568432:15568586:15571668:15571769:15573159:15573242 | 15571668:15571769 |
| exon_skip_188992 | chr3 | 15582878:15582989:15591600:15591680:15596384:15596424 | 15591600:15591680 |
| exon_skip_203601 | chr3 | 15574977:15575082:15579910:15580045:15582877:15582989 | 15579910:15580045 |
| exon_skip_204950 | chr3 | 15585248:15585342:15586525:15586602:15589540:15589612 | 15586525:15586602 |
| exon_skip_210961 | chr3 | 15573159:15573242:15579910:15580045:15582877:15582989 | 15579910:15580045 |
| exon_skip_218452 | chr3 | 15586525:15586602:15591600:15591680:15596384:15596424 | 15591600:15591680 |
| exon_skip_228278 | chr3 | 15579910:15580045:15582877:15582989:15589540:15589612 | 15582877:15582989 |
| exon_skip_246191 | chr3 | 15582877:15582989:15591600:15591680:15596384:15596424 | 15591600:15591680 |
| exon_skip_26433 | chr3 | 15582878:15582989:15589540:15589612:15591600:15591680 | 15589540:15589612 |
| exon_skip_280690 | chr3 | 15582878:15582989:15585248:15585342:15589540:15589612 | 15585248:15585342 |
| exon_skip_288311 | chr3 | 15582878:15582989:15585248:15585342:15586525:15586602 | 15585248:15585342 |
| exon_skip_288884 | chr3 | 15582877:15582989:15589540:15589612:15591600:15591680 | 15589540:15589612 |
| exon_skip_56672 | chr3 | 15573159:15573242:15574977:15575082:15579910:15580045 | 15574977:15575082 |
| 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 HACL1 |
| 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 |
| ENST00000321169 | 15574977 | 15575082 | Frame-shift |
| ENST00000321169 | 15579910 | 15580045 | Frame-shift |
| ENST00000321169 | 15585248 | 15585342 | Frame-shift |
| ENST00000321169 | 15589540 | 15589612 | Frame-shift |
| ENST00000321169 | 15571668 | 15571769 | In-frame |
| ENST00000321169 | 15586525 | 15586602 | In-frame |
| ENST00000321169 | 15591600 | 15591680 | 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 |
| ENST00000321169 | 15574977 | 15575082 | Frame-shift |
| ENST00000321169 | 15579910 | 15580045 | Frame-shift |
| ENST00000321169 | 15585248 | 15585342 | Frame-shift |
| ENST00000321169 | 15589540 | 15589612 | Frame-shift |
| ENST00000321169 | 15571668 | 15571769 | In-frame |
| ENST00000321169 | 15586525 | 15586602 | In-frame |
| ENST00000321169 | 15591600 | 15591680 | 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 |
| ENST00000321169 | 15574977 | 15575082 | Frame-shift |
| ENST00000321169 | 15579910 | 15580045 | Frame-shift |
| ENST00000321169 | 15585248 | 15585342 | Frame-shift |
| ENST00000321169 | 15589540 | 15589612 | Frame-shift |
| ENST00000321169 | 15571668 | 15571769 | In-frame |
| ENST00000321169 | 15573159 | 15573242 | In-frame |
| ENST00000321169 | 15586525 | 15586602 | In-frame |
| ENST00000321169 | 15591600 | 15591680 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HACL1 |
p-ENSG00000131373_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 |
| ENST00000321169 | 2283 | 578 | 15591600 | 15591680 | 596 | 675 | 76 | 102 |
| ENST00000321169 | 2283 | 578 | 15586525 | 15586602 | 750 | 826 | 127 | 152 |
| ENST00000321169 | 2283 | 578 | 15571668 | 15571769 | 1362 | 1462 | 331 | 364 |
| 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 |
| ENST00000321169 | 2283 | 578 | 15591600 | 15591680 | 596 | 675 | 76 | 102 |
| ENST00000321169 | 2283 | 578 | 15586525 | 15586602 | 750 | 826 | 127 | 152 |
| ENST00000321169 | 2283 | 578 | 15571668 | 15571769 | 1362 | 1462 | 331 | 364 |
| 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 |
| ENST00000321169 | 2283 | 578 | 15591600 | 15591680 | 596 | 675 | 76 | 102 |
| ENST00000321169 | 2283 | 578 | 15586525 | 15586602 | 750 | 826 | 127 | 152 |
| ENST00000321169 | 2283 | 578 | 15573159 | 15573242 | 1278 | 1360 | 303 | 330 |
| ENST00000321169 | 2283 | 578 | 15571668 | 15571769 | 1362 | 1462 | 331 | 364 |
| 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 |
| Q9UJ83 | 76 | 102 | 77 | 103 | Alternative sequence | ID=VSP_054191;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UJ83 | 76 | 102 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 127 | 152 | 104 | 185 | Alternative sequence | ID=VSP_054192;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UJ83 | 127 | 152 | 128 | 153 | Alternative sequence | ID=VSP_054749;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UJ83 | 127 | 152 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 331 | 364 | 332 | 365 | Alternative sequence | ID=VSP_054750;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UJ83 | 331 | 364 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 331 | 364 | 351 | 351 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QXE0 |
| Q9UJ83 | 331 | 364 | 358 | 358 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QXE0 |
| 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 |
| Q9UJ83 | 76 | 102 | 77 | 103 | Alternative sequence | ID=VSP_054191;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UJ83 | 76 | 102 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 127 | 152 | 104 | 185 | Alternative sequence | ID=VSP_054192;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UJ83 | 127 | 152 | 128 | 153 | Alternative sequence | ID=VSP_054749;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UJ83 | 127 | 152 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 331 | 364 | 332 | 365 | Alternative sequence | ID=VSP_054750;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UJ83 | 331 | 364 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 331 | 364 | 351 | 351 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QXE0 |
| Q9UJ83 | 331 | 364 | 358 | 358 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QXE0 |
| 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 |
| Q9UJ83 | 76 | 102 | 77 | 103 | Alternative sequence | ID=VSP_054191;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UJ83 | 76 | 102 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 127 | 152 | 104 | 185 | Alternative sequence | ID=VSP_054192;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UJ83 | 127 | 152 | 128 | 153 | Alternative sequence | ID=VSP_054749;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UJ83 | 127 | 152 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 303 | 330 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 331 | 364 | 332 | 365 | Alternative sequence | ID=VSP_054750;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UJ83 | 331 | 364 | 1 | 578 | Chain | ID=PRO_0000090816;Note=2-hydroxyacyl-CoA lyase 1 |
| Q9UJ83 | 331 | 364 | 351 | 351 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QXE0 |
| Q9UJ83 | 331 | 364 | 358 | 358 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QXE0 |
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3'-UTR located exon skipping events that lost miRNA binding sites in HACL1 |
| 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 HACL1 |
| - 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 HACL1 |
| 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 HACL1 |
| 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 HACL1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_56672 | -5.258479e-01 | 1.801518e-12 |
| CB | FUBP1 | exon_skip_56672 | -4.905729e-01 | 7.978165e-11 |
| CB | PCBP1 | exon_skip_210961 | -4.487761e-01 | 6.038158e-08 |
| CB | TRA2A | exon_skip_210961 | -5.786855e-01 | 2.977502e-13 |
| CB | HNRNPC | exon_skip_210961 | -5.407759e-01 | 1.825729e-11 |
| CB | SRSF4 | exon_skip_210961 | -4.264855e-01 | 3.076901e-07 |
| CB | RBM6 | exon_skip_203601 | -4.153945e-01 | 1.522349e-07 |
| CB | TRA2A | exon_skip_203601 | -5.400700e-01 | 1.401723e-12 |
| CB | TARDBP | exon_skip_288311 | -4.187133e-01 | 2.624935e-06 |
| CB | SRSF4 | exon_skip_288311 | -4.619174e-01 | 1.585624e-07 |
| CB | ZNF638 | exon_skip_16332 | -5.050303e-01 | 9.304622e-11 |
| CB | SAMD4A | exon_skip_16332 | -4.780185e-01 | 1.199300e-09 |
| CB | FUBP1 | exon_skip_16332 | -5.003743e-01 | 1.469066e-10 |
| CB | RBM4B | exon_skip_16332 | -4.918317e-01 | 3.336364e-10 |
| IFG | ELAVL4 | exon_skip_56672 | -4.770212e-01 | 1.842492e-02 |
| IFG | KHDRBS2 | exon_skip_56672 | -5.441091e-01 | 5.984935e-03 |
| IFG | RALYL | exon_skip_56672 | -4.791994e-01 | 1.782350e-02 |
| IFG | NOVA1 | exon_skip_56672 | -5.336538e-01 | 7.238322e-03 |
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RelatedDrugs for HACL1 |
| 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 HACL1 |
| 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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