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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 HMGA2 |
 Gene summary |
| Gene information | Gene symbol | HMGA2 | Gene ID | 8091 |
| Gene name | high mobility group AT-hook 2 | |
| Synonyms | BABL|HMGI-C|HMGIC|LIPO|STQTL9 | |
| Cytomap | 12q14.3 | |
| Type of gene | protein-coding | |
| Description | high mobility group protein HMGI-CHMGA2/KRT121P fusionhigh-mobility group (nonhistone chromosomal) protein isoform I-C | |
| Modification date | 20180523 | |
| UniProtAcc | P52926 | |
| Context | PubMed: HMGA2 [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 |
| HMGA2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 14627817 |
| HMGA2 | GO:0002062 | chondrocyte differentiation | 21484705 |
| HMGA2 | GO:0006284 | base-excision repair | 19465398 |
| HMGA2 | GO:0007095 | mitotic G2 DNA damage checkpoint | 16061642 |
| HMGA2 | GO:0010564 | regulation of cell cycle process | 14645522 |
| HMGA2 | GO:0010628 | positive regulation of gene expression | 18832382 |
| HMGA2 | GO:0031052 | chromosome breakage | 19549901 |
| HMGA2 | GO:0031507 | heterochromatin assembly | 16901784 |
| HMGA2 | GO:0035978 | histone H2A-S139 phosphorylation | 16061642 |
| HMGA2 | GO:0035986 | senescence-associated heterochromatin focus assembly | 16901784 |
| HMGA2 | GO:0035988 | chondrocyte proliferation | 21484705 |
| HMGA2 | GO:0042769 | DNA damage response, detection of DNA damage | 19465398 |
| HMGA2 | GO:0043065 | positive regulation of apoptotic process | 16061642 |
| HMGA2 | GO:0043066 | negative regulation of apoptotic process | 19465398 |
| HMGA2 | GO:0043392 | negative regulation of DNA binding | 14645522 |
| HMGA2 | GO:0043922 | negative regulation by host of viral transcription | 17005673 |
| HMGA2 | GO:0045869 | negative regulation of single stranded viral RNA replication via double stranded DNA intermediate | 17005673 |
| HMGA2 | GO:0045892 | negative regulation of transcription, DNA-templated | 18832382 |
| HMGA2 | GO:0045893 | positive regulation of transcription, DNA-templated | 15225648|15755872|17005673|17324944|17426251 |
| HMGA2 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 14645522|18832382 |
| HMGA2 | GO:0071158 | positive regulation of cell cycle arrest | 16061642 |
| HMGA2 | GO:0090402 | oncogene-induced cell senescence | 16901784 |
| HMGA2 | GO:2000648 | positive regulation of stem cell proliferation | 21484705 |
| HMGA2 | GO:2000679 | positive regulation of transcription regulatory region DNA binding | 18832382 |
| HMGA2 | GO:2000685 | positive regulation of cellular response to X-ray | 16061642 |
| HMGA2 | GO:2001022 | positive regulation of response to DNA damage stimulus | 16061642|19465398 |
| HMGA2 | GO:2001033 | negative regulation of double-strand break repair via nonhomologous end joining | 19549901 |
| HMGA2 | GO:2001038 | regulation of cellular response to drug | 16061642 |
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Exon skipping events across known transcript of Ensembl for HMGA2 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 HMGA2 |
| 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 HMGA2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_85012 | 12 | 66218902:66219161:66221780:66221867:66232298:66232349 | 66221780:66221867 | ENSG00000149948.9 | ENST00000536545.1,ENST00000537275.1,ENST00000537429.1,ENST00000354636.3,ENST00000541363.1,ENST00000393578.3,ENST00000393577.3,ENST00000425208.2 |
| exon_skip_85014 | 12 | 66221780:66221867:66232298:66232349:66345162:66345195 | 66232298:66232349 | ENSG00000149948.9 | ENST00000541363.1,ENST00000393577.3,ENST00000403681.2 |
| exon_skip_85015 | 12 | 66232298:66232349:66235913:66236034:66236370:66236697 | 66235913:66236034 | ENSG00000149948.9 | ENST00000537275.1 |
| exon_skip_85016 | 12 | 66232298:66232349:66261268:66261587:66275522:66275670 | 66261268:66261587 | ENSG00000149948.9 | ENST00000537429.1 |
| exon_skip_85017 | 12 | 66232298:66232349:66275522:66275670:66345162:66345195 | 66275522:66275670 | ENSG00000149948.9 | ENST00000539662.1 |
| exon_skip_85019 | 12 | 66232298:66232349:66345162:66345195:66357024:66357190 | 66345162:66345195 | ENSG00000149948.9 | ENST00000403681.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for HMGA2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_85012 | 12 | 66218902:66219161:66221780:66221867:66232298:66232349 | 66221780:66221867 | ENSG00000149948.9 | ENST00000537275.1,ENST00000393578.3,ENST00000537429.1,ENST00000425208.2,ENST00000536545.1,ENST00000354636.3,ENST00000541363.1,ENST00000393577.3 |
| exon_skip_85017 | 12 | 66232298:66232349:66275522:66275670:66345162:66345195 | 66275522:66275670 | ENSG00000149948.9 | ENST00000539662.1 |
| exon_skip_85019 | 12 | 66232298:66232349:66345162:66345195:66357024:66357190 | 66345162:66345195 | ENSG00000149948.9 | ENST00000403681.2 |
| 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 HMGA2 |
| 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 |
| ENST00000403681 | 66232298 | 66232349 | In-frame |
| ENST00000403681 | 66345162 | 66345195 | 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 |
| ENST00000403681 | 66345162 | 66345195 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HMGA2 |
| 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 |
| ENST00000403681 | 4490 | 109 | 66232298 | 66232349 | 1339 | 1389 | 66 | 83 |
| ENST00000403681 | 4490 | 109 | 66345162 | 66345195 | 1390 | 1422 | 83 | 94 |
| 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 |
| ENST00000403681 | 4490 | 109 | 66345162 | 66345195 | 1390 | 1422 | 83 | 94 |
| 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 |
| P52926 | 66 | 83 | 2 | 109 | Chain | ID=PRO_0000206711;Note=High mobility group protein HMGI-C |
| P52926 | 66 | 83 | 71 | 82 | DNA binding | Note=A.T hook 3 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_042564;Note=In isoform 2. PQQVVQKKPAQEETEETSSQESAEED->DNLLPRTSSKKKTSLGNSTKRSH;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047772;Note=In isoform 3. PQQVVQKKPAQEETEETSSQESAEED->LQN;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047773;Note=In isoform 4. PQQVVQKKPAQEETEETSSQESAEED->WLLMKSPCW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047774;Note=In isoform 5. PQQVVQKKPAQEETEETSSQESAEED->LRAQALDSDGLGSNSGPSLS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047775;Note=In isoform 6. PQQVVQKKPAQEETEETSSQESAEED->EEFYIAA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 2 | 109 | Chain | ID=PRO_0000206711;Note=High mobility group protein HMGI-C |
| 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 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_042564;Note=In isoform 2. PQQVVQKKPAQEETEETSSQESAEED->DNLLPRTSSKKKTSLGNSTKRSH;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047772;Note=In isoform 3. PQQVVQKKPAQEETEETSSQESAEED->LQN;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047773;Note=In isoform 4. PQQVVQKKPAQEETEETSSQESAEED->WLLMKSPCW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047774;Note=In isoform 5. PQQVVQKKPAQEETEETSSQESAEED->LRAQALDSDGLGSNSGPSLS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 84 | 109 | Alternative sequence | ID=VSP_047775;Note=In isoform 6. PQQVVQKKPAQEETEETSSQESAEED->EEFYIAA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15882911;Dbxref=PMID:15882911 |
| P52926 | 83 | 94 | 2 | 109 | Chain | ID=PRO_0000206711;Note=High mobility group protein HMGI-C |
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SNVs in the skipped exons for HMGA2 |
| - 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 |
| STAD | TCGA-CG-4442-01 | exon_skip_85012 | 66221781 | 66221867 | 66221835 | 66221835 | Frame_Shift_Del | A | - | p.K56fs |
| STAD | TCGA-CG-4442-01 | exon_skip_85012 | 66221781 | 66221867 | 66221835 | 66221835 | Frame_Shift_Del | A | - | p.S55fs |
| - 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 |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 66221781 | 66221867 | 66221790 | 66221790 | Missense_Mutation | G | T | p.G41C |
| MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 66221781 | 66221867 | 66221850 | 66221850 | Missense_Mutation | T | C | p.S61P |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 66232299 | 66232349 | 66232312 | 66232312 | Missense_Mutation | C | T | p.T71I |
| CL40_LARGE_INTESTINE | 66232299 | 66232349 | 66232324 | 66232324 | Missense_Mutation | G | A | p.R75Q |
| NCIH2291_LUNG | 66232299 | 66232349 | 66232327 | 66232327 | Missense_Mutation | C | A | p.P76Q |
| RL952_ENDOMETRIUM | 66345163 | 66345195 | 66345175 | 66345175 | Missense_Mutation | G | A | p.V88I |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HMGA2 |
| 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 HMGA2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HMGA2 |
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RelatedDrugs for HMGA2 |
| 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 HMGA2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| HMGA2 | C0005612 | Birth Weight | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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