|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for HMG20B |
 Gene summary |
| Gene information | Gene symbol | HMG20B | Gene ID | 10362 |
| Gene name | high mobility group 20B | |
| Synonyms | BRAF25|BRAF35|HMGX2|HMGXB2|PP7706|SMARCE1r|SOXL|pp8857 | |
| Cytomap | 19p13.3 | |
| Type of gene | protein-coding | |
| Description | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-relatedBRCA2-associated factor 35HMG box domain containing 2HMG box-containing protein 20BHMG domain-containing protein 2HMG domain-containing protein HMGX2 | |
| Modification date | 20180522 | |
| UniProtAcc | Q9P0W2 | |
| Context | PubMed: HMG20B [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 |
Top |
Exon skipping events across known transcript of Ensembl for HMG20B 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. |
 |
Top |
Gene isoform structures and expression levels for HMG20B |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for HMG20B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_300951 | 19 | 3572983:3572992:3573289:3573345:3573689:3573798 | 3573289:3573345 | ENSG00000064961.14 | ENST00000470356.1,ENST00000262949.7,ENST00000417382.1,ENST00000333651.6,ENST00000435022.1 |
| exon_skip_300956 | 19 | 3573694:3573798:3574338:3574584:3575537:3575612 | 3574338:3574584 | ENSG00000064961.14 | ENST00000417382.1 |
| exon_skip_300957 | 19 | 3573694:3573798:3574367:3574584:3575537:3575612 | 3574367:3574584 | ENSG00000064961.14 | ENST00000435022.1 |
| exon_skip_300958 | 19 | 3573694:3573798:3574380:3574584:3575537:3575612 | 3574380:3574584 | ENSG00000064961.14 | ENST00000333651.6,ENST00000416526.1,ENST00000453933.1 |
| exon_skip_300962 | 19 | 3574407:3574584:3575499:3575658:3576258:3576305 | 3575499:3575658 | ENSG00000064961.14 | ENST00000262949.7 |
| exon_skip_300965 | 19 | 3574530:3574584:3575537:3575658:3576258:3576305 | 3575537:3575658 | ENSG00000064961.14 | ENST00000488973.2,ENST00000333651.6,ENST00000435022.1,ENST00000416526.1 |
| exon_skip_300972 | 19 | 3575539:3575658:3576258:3576305:3576550:3576600 | 3576258:3576305 | ENSG00000064961.14 | ENST00000488973.2,ENST00000262949.7,ENST00000333651.6,ENST00000435022.1,ENST00000416526.1 |
| exon_skip_300974 | 19 | 3576613:3576623:3576889:3577105:3577978:3578111 | 3576889:3577105 | ENSG00000064961.14 | ENST00000488973.2,ENST00000487894.1,ENST00000585900.1,ENST00000333651.6,ENST00000493191.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for HMG20B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_300951 | 19 | 3572983:3572992:3573289:3573345:3573689:3573798 | 3573289:3573345 | ENSG00000064961.14 | ENST00000470356.1,ENST00000333651.6,ENST00000417382.1,ENST00000435022.1,ENST00000262949.7 |
| exon_skip_300962 | 19 | 3574407:3574584:3575499:3575658:3576258:3576305 | 3575499:3575658 | ENSG00000064961.14 | ENST00000262949.7 |
| exon_skip_300965 | 19 | 3574530:3574584:3575537:3575658:3576258:3576305 | 3575537:3575658 | ENSG00000064961.14 | ENST00000416526.1,ENST00000333651.6,ENST00000435022.1,ENST00000488973.2 |
| exon_skip_300972 | 19 | 3575539:3575658:3576258:3576305:3576550:3576600 | 3576258:3576305 | ENSG00000064961.14 | ENST00000416526.1,ENST00000333651.6,ENST00000435022.1,ENST00000488973.2,ENST00000262949.7 |
| exon_skip_300974 | 19 | 3576613:3576623:3576889:3577105:3577978:3578111 | 3576889:3577105 | ENSG00000064961.14 | ENST00000333651.6,ENST00000488973.2,ENST00000487894.1,ENST00000493191.1,ENST00000585900.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for HMG20B |
| 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 |
| ENST00000333651 | 3573289 | 3573345 | 5CDS-5UTR |
| ENST00000333651 | 3575537 | 3575658 | Frame-shift |
| ENST00000333651 | 3576258 | 3576305 | Frame-shift |
| ENST00000333651 | 3574380 | 3574584 | In-frame |
| ENST00000333651 | 3576889 | 3577105 | 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 |
| ENST00000333651 | 3573289 | 3573345 | 5CDS-5UTR |
| ENST00000333651 | 3575537 | 3575658 | Frame-shift |
| ENST00000333651 | 3576258 | 3576305 | Frame-shift |
| ENST00000333651 | 3576889 | 3577105 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for HMG20B |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
| ENST00000333651 | 1613 | 317 | 3574380 | 3574584 | 223 | 426 | 49 | 117 |
| ENST00000333651 | 1613 | 317 | 3576889 | 3577105 | 668 | 883 | 197 | 269 |
| 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 |
| ENST00000333651 | 1613 | 317 | 3576889 | 3577105 | 668 | 883 | 197 | 269 |
| 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 |
| Q9P0W2 | 49 | 117 | 1 | 102 | Alternative sequence | ID=VSP_037131;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12083779;Dbxref=PMID:12083779 |
| Q9P0W2 | 49 | 117 | 83 | 106 | Alternative sequence | ID=VSP_037132;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9P0W2 | 49 | 117 | 1 | 317 | Chain | ID=PRO_0000048575;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related |
| Q9P0W2 | 49 | 117 | 70 | 138 | DNA binding | Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00267 |
| Q9P0W2 | 49 | 117 | 116 | 116 | Mutagenesis | Note=Loss of DNA binding activity of the BHC histone deacetylase complex. K->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12032298;Dbxref=PMID:12032298 |
| Q9P0W2 | 197 | 269 | 1 | 317 | Chain | ID=PRO_0000048575;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related |
| Q9P0W2 | 197 | 269 | 190 | 257 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9P0W2 | 197 | 269 | 223 | 223 | Sequence conflict | Note=H->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q9P0W2 | 197 | 269 | 1 | 317 | Chain | ID=PRO_0000048575;Note=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related |
| Q9P0W2 | 197 | 269 | 190 | 257 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9P0W2 | 197 | 269 | 223 | 223 | Sequence conflict | Note=H->Q;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Top |
SNVs in the skipped exons for HMG20B |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - 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 |
| CESC | TCGA-DR-A0ZM-01 | exon_skip_300972 | 3576259 | 3576305 | 3576258 | 3576258 | Splice_Site | G | C | e5-1 |
| - 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 |
| FTC238_THYROID | 3575500 | 3575658 | 3575556 | 3575557 | Frame_Shift_Del | GA | - | p.E124fs |
| FTC238_THYROID | 3575538 | 3575658 | 3575556 | 3575557 | Frame_Shift_Del | GA | - | p.E124fs |
| RPMI7951_SKIN | 3575500 | 3575658 | 3575556 | 3575557 | Frame_Shift_Ins | - | AA | p.E124fs |
| RPMI7951_SKIN | 3575538 | 3575658 | 3575556 | 3575557 | Frame_Shift_Ins | - | AA | p.E124fs |
| 5637_URINARY_TRACT | 3573290 | 3573345 | 3573341 | 3573341 | Missense_Mutation | G | T | p.A12S |
| SNU520_STOMACH | 3574339 | 3574584 | 3574401 | 3574401 | Missense_Mutation | G | T | p.W56C |
| SNU520_STOMACH | 3574368 | 3574584 | 3574401 | 3574401 | Missense_Mutation | G | T | p.W56C |
| SNU520_STOMACH | 3574381 | 3574584 | 3574401 | 3574401 | Missense_Mutation | G | T | p.W56C |
| RVH421_SKIN | 3574339 | 3574584 | 3574418 | 3574418 | Missense_Mutation | G | A | p.R62Q |
| RVH421_SKIN | 3574368 | 3574584 | 3574418 | 3574418 | Missense_Mutation | G | A | p.R62Q |
| RVH421_SKIN | 3574381 | 3574584 | 3574418 | 3574418 | Missense_Mutation | G | A | p.R62Q |
| HEC6_ENDOMETRIUM | 3574339 | 3574584 | 3574508 | 3574508 | Missense_Mutation | A | G | p.H92R |
| HEC6_ENDOMETRIUM | 3574368 | 3574584 | 3574508 | 3574508 | Missense_Mutation | A | G | p.H92R |
| HEC6_ENDOMETRIUM | 3574381 | 3574584 | 3574508 | 3574508 | Missense_Mutation | A | G | p.H92R |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3574339 | 3574584 | 3574549 | 3574549 | Missense_Mutation | G | A | p.A106T |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3574368 | 3574584 | 3574549 | 3574549 | Missense_Mutation | G | A | p.A106T |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3574381 | 3574584 | 3574549 | 3574549 | Missense_Mutation | G | A | p.A106T |
| SNU620_STOMACH | 3575500 | 3575658 | 3575589 | 3575589 | Missense_Mutation | C | T | p.R135W |
| SNU620_STOMACH | 3575538 | 3575658 | 3575589 | 3575589 | Missense_Mutation | C | T | p.R135W |
| HCC2998_LARGE_INTESTINE | 3575500 | 3575658 | 3575602 | 3575602 | Missense_Mutation | A | C | p.Q139P |
| HCC2998_LARGE_INTESTINE | 3575538 | 3575658 | 3575602 | 3575602 | Missense_Mutation | A | C | p.Q139P |
| 639V_URINARY_TRACT | 3576890 | 3577105 | 3576892 | 3576892 | Missense_Mutation | C | T | p.R199C |
| MDAMB231_BREAST | 3576890 | 3577105 | 3576901 | 3576901 | Missense_Mutation | G | C | p.E202Q |
| AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3576890 | 3577105 | 3576905 | 3576905 | Missense_Mutation | T | G | p.L203R |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3576890 | 3577105 | 3576991 | 3576991 | Missense_Mutation | G | A | p.E232K |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3576890 | 3577105 | 3577018 | 3577018 | Missense_Mutation | G | A | p.E241K |
| NCIH2073_LUNG | 3576890 | 3577105 | 3577036 | 3577036 | Missense_Mutation | G | C | p.A247P |
| NCIH1339_LUNG | 3576890 | 3577105 | 3577043 | 3577043 | Missense_Mutation | A | T | p.Q249L |
| NB7_AUTONOMIC_GANGLIA | 3574339 | 3574584 | 3574382 | 3574382 | Splice_Site | C | T | p.P50L |
| NB7_AUTONOMIC_GANGLIA | 3574368 | 3574584 | 3574382 | 3574382 | Splice_Site | C | T | p.P50L |
| NB7_AUTONOMIC_GANGLIA | 3574381 | 3574584 | 3574382 | 3574382 | Splice_Site | C | T | p.P50L |
| MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3575500 | 3575658 | 3575539 | 3575539 | Splice_Site | G | A | p.R118Q |
| MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 3575538 | 3575658 | 3575539 | 3575539 | Splice_Site | G | A | p.R118Q |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HMG20B |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HMG20B |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HMG20B |
Top |
RelatedDrugs for HMG20B |
| 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 |
Top |
RelatedDiseases for HMG20B |
| 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)
|