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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 HMGA1 |
 Gene summary |
| Gene information | Gene symbol | HMGA1 | Gene ID | 3159 |
| Gene name | high mobility group AT-hook 1 | |
| Synonyms | HMG-R|HMGA1A|HMGIY | |
| Cytomap | 6p21.31 | |
| Type of gene | protein-coding | |
| Description | high mobility group protein HMG-I/HMG-Yhigh mobility group protein A1high mobility group protein Rhigh-mobility group (nonhistone chromosomal) protein isoforms I and Ynonhistone chromosomal high-mobility group protein HMG-I/HMG-Y | |
| Modification date | 20200315 | |
| 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 |
| HMGA1 | GO:0035986 | senescence-associated heterochromatin focus assembly | 16901784 |
| HMGA1 | GO:0090402 | oncogene-induced cell senescence | 16901784 |
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Gene structures and expression levels for HMGA1 |
| 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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ENSG00000137309
| 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 |
| 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 HMGA1 |
| 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_137815 | chr6 | 34242712:34242795:34243468:34243518:34244831:34245151 | 34243468:34243518 |
| exon_skip_279054 | chr6 | 34236873:34236963:34237204:34237317:34240737:34240882 | 34237204:34237317 |
| 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 HMGA1 |
| 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 |
| ENST00000311487 | 34237204 | 34237317 | 5UTR-5UTR |
| ENST00000311487 | 34243468 | 34243518 | In-frame |
| ENST00000447654 | 34243468 | 34243518 | 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 |
| ENST00000311487 | 34237204 | 34237317 | 5UTR-5UTR |
| 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 |
| ENST00000311487 | 34237204 | 34237317 | 5UTR-5UTR |
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Infer the effects of exon skipping event on protein functional features for HMGA1 |
p-ENSG00000137309_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 |
| ENST00000311487 | 1937 | 107 | 34243468 | 34243518 | 470 | 519 | 73 | 90 |
| ENST00000447654 | 2176 | 107 | 34243468 | 34243518 | 710 | 759 | 73 | 90 |
| 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 |
| P17096 | 73 | 90 | 66 | 107 | Alternative sequence | ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10428 |
| P17096 | 73 | 90 | 66 | 107 | Alternative sequence | ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10428 |
| P17096 | 73 | 90 | 2 | 107 | Chain | ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y |
| P17096 | 73 | 90 | 2 | 107 | Chain | ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y |
| P17096 | 73 | 90 | 78 | 89 | DNA binding | Note=A.T hook 3 |
| P17096 | 73 | 90 | 78 | 89 | DNA binding | Note=A.T hook 3 |
| P17096 | 73 | 90 | 78 | 78 | Modified residue | Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12653562;Dbxref=PMID:12653562 |
| P17096 | 73 | 90 | 78 | 78 | Modified residue | Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12653562;Dbxref=PMID:12653562 |
| P17096 | 73 | 90 | 53 | 77 | Region | Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P17096 | 73 | 90 | 53 | 77 | Region | Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| 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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in HMGA1 |
| 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 HMGA1 |
| - 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 HMGA1 |
| 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 HMGA1 |
| 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 HMGA1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM4 | exon_skip_279054 | -5.607012e-01 | 1.838107e-14 |
| CB | RBM4B | exon_skip_279054 | -4.277204e-01 | 2.077848e-08 |
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RelatedDrugs for HMGA1 |
| 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 HMGA1 |
| 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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