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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 HMBOX1 |
 Gene summary |
| Gene information | Gene symbol | HMBOX1 | Gene ID | 79618 |
| Gene name | homeobox containing 1 | |
| Synonyms | HNF1LA|HOT1|PBHNF|TAH1 | |
| Cytomap | 8p21.1-p12 | |
| Type of gene | protein-coding | |
| Description | homeobox-containing protein 1homeobox telomere-binding protein 1homeobox-containing protein PBHNFtelomere-associated homeobox-containing protein 1 | |
| 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 |
| HMBOX1 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 21839858 |
| HMBOX1 | GO:0032212 | positive regulation of telomere maintenance via telomerase | 23685356 |
| HMBOX1 | GO:0045892 | negative regulation of transcription, DNA-templated | 19757162 |
| HMBOX1 | GO:0051972 | regulation of telomerase activity | 23685356 |
| HMBOX1 | GO:0051973 | positive regulation of telomerase activity | 23685356 |
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Gene structures and expression levels for HMBOX1 |
| 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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ENSG00000147421
| 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 | ENST00000517386.1 | HMBOX1-204:lncRNA:HMBOX1 | 9.704534e+00 | 8.649744e-01 | 4.760100e-08 | 1.130587e-06 |
| CB | UP | ENST00000560269.1 | HMBOX1-213:lncRNA:HMBOX1 | 2.815499e+00 | 9.065641e-01 | 1.854182e-03 | 8.658453e-03 |
| TC | UP | ENST00000517386.1 | HMBOX1-204:lncRNA:HMBOX1 | 8.291198e+00 | 9.762881e-01 | 6.355510e-09 | 6.147951e-07 |
| TC | UP | ENST00000355231.9 | HMBOX1-202:protein_coding:HMBOX1 | 5.391895e+00 | 1.380248e+00 | 3.060519e-04 | 3.908213e-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 HMBOX1 |
| 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_114820 | chr8 | 29048960:29049048:29049290:29049361:29051018:29051163 | 29049290:29049361 |
| exon_skip_117557 | chr8 | 28890924:28891019:28891760:28891790:28963811:28963890 | 28891760:28891790 |
| exon_skip_159391 | chr8 | 29045361:29045443:29047358:29047453:29048954:29049048 | 29047358:29047453 |
| exon_skip_159415 | chr8 | 28980071:28980156:29009072:29009182:29018760:29018899 | 29009072:29009182 |
| exon_skip_22993 | chr8 | 29009072:29009182:29009684:29009821:29018760:29018899 | 29009684:29009821 |
| exon_skip_24905 | chr8 | 29018760:29018913:29042639:29042718:29045361:29045443 | 29042639:29042718 |
| exon_skip_289919 | chr8 | 28970436:28970519:28980071:28980156:29009072:29009182 | 28980071:28980156 |
| 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_114820 | MSBB_IFG | 1.852941e-01 | 3.120000e-01 | -1.267059e-01 | 3.874185e-02 |
| exon_skip_163796 | MSBB_IFG | 1.723529e-01 | 2.740000e-01 | -1.016471e-01 | 4.818922e-02 |
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Open reading frame (ORF) annotation in the exon skipping event for HMBOX1 |
| 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 |
| ENST00000287701 | 28980071 | 28980156 | Frame-shift |
| ENST00000397358 | 28980071 | 28980156 | Frame-shift |
| ENST00000287701 | 29009072 | 29009182 | In-frame |
| ENST00000397358 | 29009072 | 29009182 | In-frame |
| ENST00000287701 | 29047358 | 29047453 | In-frame |
| ENST00000397358 | 29047358 | 29047453 | 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 |
| ENST00000287701 | 28980071 | 28980156 | Frame-shift |
| ENST00000397358 | 28980071 | 28980156 | Frame-shift |
| 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 |
| ENST00000397358 | 28891760 | 28891790 | 5UTR-5UTR |
| ENST00000287701 | 28980071 | 28980156 | Frame-shift |
| ENST00000397358 | 28980071 | 28980156 | Frame-shift |
| ENST00000287701 | 29047358 | 29047453 | In-frame |
| ENST00000397358 | 29047358 | 29047453 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HMBOX1 |
p-ENSG00000147421_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 |
| ENST00000287701 | 3201 | 420 | 29009072 | 29009182 | 930 | 1039 | 196 | 232 |
| ENST00000397358 | 4099 | 420 | 29009072 | 29009182 | 1292 | 1401 | 196 | 232 |
| ENST00000287701 | 3201 | 420 | 29047358 | 29047453 | 1278 | 1372 | 312 | 343 |
| ENST00000397358 | 4099 | 420 | 29047358 | 29047453 | 1640 | 1734 | 312 | 343 |
| 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 |
| ENST00000287701 | 3201 | 420 | 29047358 | 29047453 | 1278 | 1372 | 312 | 343 |
| ENST00000397358 | 4099 | 420 | 29047358 | 29047453 | 1640 | 1734 | 312 | 343 |
| 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 |
| Q6NT76 | 196 | 232 | 1 | 420 | Chain | ID=PRO_0000233287;Note=Homeobox-containing protein 1 |
| Q6NT76 | 196 | 232 | 1 | 420 | Chain | ID=PRO_0000233287;Note=Homeobox-containing protein 1 |
| Q6NT76 | 196 | 232 | 217 | 217 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25755297,ECO:0000244|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733 |
| Q6NT76 | 196 | 232 | 217 | 217 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25755297,ECO:0000244|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733 |
| Q6NT76 | 312 | 343 | 305 | 420 | Alternative sequence | ID=VSP_038984;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:19757162;Dbxref=PMID:19757162 |
| Q6NT76 | 312 | 343 | 305 | 420 | Alternative sequence | ID=VSP_038984;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:19757162;Dbxref=PMID:19757162 |
| Q6NT76 | 312 | 343 | 1 | 420 | Chain | ID=PRO_0000233287;Note=Homeobox-containing protein 1 |
| Q6NT76 | 312 | 343 | 1 | 420 | Chain | ID=PRO_0000233287;Note=Homeobox-containing protein 1 |
| Q6NT76 | 312 | 343 | 267 | 341 | DNA binding | Note=Homeobox;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00108,ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 267 | 341 | DNA binding | Note=Homeobox;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00108,ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 323 | 343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
| Q6NT76 | 312 | 343 | 323 | 343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
| Q6NT76 | 312 | 343 | 325 | 325 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 325 | 325 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 327 | 327 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 327 | 327 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 334 | 334 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 334 | 334 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. Confers binding to the non-telomeric 5'-GTGAGT-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. Confers binding to the non-telomeric 5'-GTGAGT-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 338 | 338 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 338 | 338 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 339 | 339 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 339 | 339 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Site | Note=Critical for recognition and binding of 5'-TTAGGG-3' motifs in telomeric DNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Site | Note=Critical for recognition and binding of 5'-TTAGGG-3' motifs in telomeric DNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 317 | 319 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
| Q6NT76 | 312 | 343 | 317 | 319 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
| 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 |
| Q6NT76 | 312 | 343 | 305 | 420 | Alternative sequence | ID=VSP_038984;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:19757162;Dbxref=PMID:19757162 |
| Q6NT76 | 312 | 343 | 305 | 420 | Alternative sequence | ID=VSP_038984;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:19757162;Dbxref=PMID:19757162 |
| Q6NT76 | 312 | 343 | 1 | 420 | Chain | ID=PRO_0000233287;Note=Homeobox-containing protein 1 |
| Q6NT76 | 312 | 343 | 1 | 420 | Chain | ID=PRO_0000233287;Note=Homeobox-containing protein 1 |
| Q6NT76 | 312 | 343 | 267 | 341 | DNA binding | Note=Homeobox;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00108,ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 267 | 341 | DNA binding | Note=Homeobox;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00108,ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 323 | 343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
| Q6NT76 | 312 | 343 | 323 | 343 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
| Q6NT76 | 312 | 343 | 325 | 325 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 325 | 325 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 327 | 327 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 327 | 327 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 334 | 334 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 334 | 334 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. Confers binding to the non-telomeric 5'-GTGAGT-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. Confers binding to the non-telomeric 5'-GTGAGT-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 338 | 338 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 338 | 338 | Mutagenesis | Note=Impairs binding to telomeric 5'-TTAGGG-3' motif. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 339 | 339 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 339 | 339 | Mutagenesis | Note=Abolishes binding to telomeric 5'-TTAGGG-3' motif. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Site | Note=Critical for recognition and binding of 5'-TTAGGG-3' motifs in telomeric DNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 335 | 335 | Site | Note=Critical for recognition and binding of 5'-TTAGGG-3' motifs in telomeric DNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23685356;Dbxref=PMID:23685356 |
| Q6NT76 | 312 | 343 | 317 | 319 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
| Q6NT76 | 312 | 343 | 317 | 319 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4J19 |
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3'-UTR located exon skipping events that lost miRNA binding sites in HMBOX1 |
| 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 HMBOX1 |
| - 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 HMBOX1 |
| 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 HMBOX1 |
| 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 HMBOX1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | RBM25 | exon_skip_163796 | -4.206026e-01 | 2.892009e-02 |
| IFG | RBM5 | exon_skip_163796 | -4.533093e-01 | 1.756442e-02 |
| IFG | TRA2A | exon_skip_163796 | -4.740949e-01 | 1.247938e-02 |
| IFG | G3BP2 | exon_skip_163796 | 4.643134e-01 | 1.469418e-02 |
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RelatedDrugs for HMBOX1 |
| 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 HMBOX1 |
| 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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