|
||||||
|
 | |
| |
| |
| |
| 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 HDAC3 |
 Gene summary |
| Gene information | Gene symbol | HDAC3 | Gene ID | 8841 |
| Gene name | histone deacetylase 3 | |
| Synonyms | HD3|RPD3|RPD3-2 | |
| Cytomap | 5q31.3 | |
| Type of gene | protein-coding | |
| Description | histone deacetylase 3SMAP45 | |
| Modification date | 20180520 | |
| UniProtAcc | O15379 | |
| Context | PubMed: HDAC3 [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 |
| HDAC3 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 16569215|18417529|18854353 |
| HDAC3 | GO:0001934 | positive regulation of protein phosphorylation | 25190803 |
| HDAC3 | GO:0006476 | protein deacetylation | 17172643|21030595 |
| HDAC3 | GO:0031647 | regulation of protein stability | 25190803 |
| HDAC3 | GO:0042307 | positive regulation of protein import into nucleus | 25190803 |
| HDAC3 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 25190803 |
| HDAC3 | GO:0071498 | cellular response to fluid shear stress | 25190803 |
Top |
Exon skipping events across known transcript of Ensembl for HDAC3 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 HDAC3 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for HDAC3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_444899 | 5 | 141004774:141004932:141005251:141005331:141005579:141005637 | 141005251:141005331 | ENSG00000171720.5 | ENST00000491581.1,ENST00000486618.1,ENST00000305264.3,ENST00000469550.2 |
| exon_skip_444900 | 5 | 141004774:141004932:141005251:141005331:141005760:141005850 | 141005251:141005331 | ENSG00000171720.5 | ENST00000459727.1 |
| exon_skip_444902 | 5 | 141005316:141005331:141005579:141005638:141005760:141005850 | 141005579:141005638 | ENSG00000171720.5 | ENST00000491581.1,ENST00000305264.3,ENST00000469550.2 |
| exon_skip_444903 | 5 | 141005592:141005638:141005760:141005850:141007459:141007503 | 141005760:141005850 | ENSG00000171720.5 | ENST00000491581.1,ENST00000305264.3,ENST00000469550.2 |
| exon_skip_444907 | 5 | 141005799:141005850:141007459:141007524:141007680:141007754 | 141007459:141007524 | ENSG00000171720.5 | ENST00000523088.1,ENST00000459727.1,ENST00000467533.1,ENST00000492407.1,ENST00000305264.3,ENST00000469550.2 |
| exon_skip_444910 | 5 | 141007459:141007524:141007680:141007754:141008125:141008129 | 141007680:141007754 | ENSG00000171720.5 | ENST00000519474.1,ENST00000523088.1,ENST00000459727.1,ENST00000467533.1,ENST00000305264.3,ENST00000469550.2 |
| exon_skip_444911 | 5 | 141008171:141008206:141008739:141008873:141009250:141009306 | 141008739:141008873 | ENSG00000171720.5 | ENST00000519474.1,ENST00000523088.1,ENST00000305264.3,ENST00000469550.2 |
| exon_skip_444915 | 5 | 141008832:141008873:141009250:141009306:141009426:141009483 | 141009250:141009306 | ENSG00000171720.5 | ENST00000519474.1,ENST00000523088.1,ENST00000305264.3,ENST00000469550.2 |
| exon_skip_444920 | 5 | 141009426:141009483:141009610:141009692:141014377:141014423 | 141009610:141009692 | ENSG00000171720.5 | ENST00000305264.3 |
| exon_skip_444921 | 5 | 141009426:141009483:141009610:141009692:141016114:141016197 | 141009610:141009692 | ENSG00000171720.5 | ENST00000519474.1 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENSG00000171720.5 | ENST00000495485.1,ENST00000305264.3 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for HDAC3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_444899 | 5 | 141004774:141004932:141005251:141005331:141005579:141005637 | 141005251:141005331 | ENSG00000171720.5 | ENST00000469550.2,ENST00000305264.3,ENST00000491581.1,ENST00000486618.1 |
| exon_skip_444900 | 5 | 141004774:141004932:141005251:141005331:141005760:141005850 | 141005251:141005331 | ENSG00000171720.5 | ENST00000459727.1 |
| exon_skip_444902 | 5 | 141005316:141005331:141005579:141005638:141005760:141005850 | 141005579:141005638 | ENSG00000171720.5 | ENST00000469550.2,ENST00000305264.3,ENST00000491581.1 |
| exon_skip_444903 | 5 | 141005592:141005638:141005760:141005850:141007459:141007503 | 141005760:141005850 | ENSG00000171720.5 | ENST00000469550.2,ENST00000305264.3,ENST00000491581.1 |
| exon_skip_444907 | 5 | 141005799:141005850:141007459:141007524:141007680:141007754 | 141007459:141007524 | ENSG00000171720.5 | ENST00000469550.2,ENST00000305264.3,ENST00000459727.1,ENST00000467533.1,ENST00000492407.1,ENST00000523088.1 |
| exon_skip_444910 | 5 | 141007459:141007524:141007680:141007754:141008125:141008129 | 141007680:141007754 | ENSG00000171720.5 | ENST00000469550.2,ENST00000305264.3,ENST00000459727.1,ENST00000467533.1,ENST00000523088.1,ENST00000519474.1 |
| exon_skip_444911 | 5 | 141008171:141008206:141008739:141008873:141009250:141009306 | 141008739:141008873 | ENSG00000171720.5 | ENST00000469550.2,ENST00000305264.3,ENST00000523088.1,ENST00000519474.1 |
| exon_skip_444915 | 5 | 141008832:141008873:141009250:141009306:141009426:141009483 | 141009250:141009306 | ENSG00000171720.5 | ENST00000469550.2,ENST00000305264.3,ENST00000523088.1,ENST00000519474.1 |
| exon_skip_444920 | 5 | 141009426:141009483:141009610:141009692:141014377:141014423 | 141009610:141009692 | ENSG00000171720.5 | ENST00000305264.3 |
| exon_skip_444921 | 5 | 141009426:141009483:141009610:141009692:141016114:141016197 | 141009610:141009692 | ENSG00000171720.5 | ENST00000519474.1 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENSG00000171720.5 | ENST00000305264.3,ENST00000495485.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for HDAC3 |
| 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 |
| ENST00000305264 | 141005251 | 141005331 | Frame-shift |
| ENST00000305264 | 141005579 | 141005638 | Frame-shift |
| ENST00000305264 | 141007459 | 141007524 | Frame-shift |
| ENST00000305264 | 141007680 | 141007754 | Frame-shift |
| ENST00000305264 | 141008739 | 141008873 | Frame-shift |
| ENST00000305264 | 141009250 | 141009306 | Frame-shift |
| ENST00000305264 | 141009610 | 141009692 | Frame-shift |
| ENST00000305264 | 141014377 | 141014520 | Frame-shift |
| ENST00000305264 | 141005760 | 141005850 | 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 |
| ENST00000305264 | 141005251 | 141005331 | Frame-shift |
| ENST00000305264 | 141005579 | 141005638 | Frame-shift |
| ENST00000305264 | 141007459 | 141007524 | Frame-shift |
| ENST00000305264 | 141007680 | 141007754 | Frame-shift |
| ENST00000305264 | 141008739 | 141008873 | Frame-shift |
| ENST00000305264 | 141009250 | 141009306 | Frame-shift |
| ENST00000305264 | 141009610 | 141009692 | Frame-shift |
| ENST00000305264 | 141014377 | 141014520 | Frame-shift |
| ENST00000305264 | 141005760 | 141005850 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for HDAC3 |
| 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 |
| ENST00000305264 | 1976 | 428 | 141005760 | 141005850 | 911 | 1000 | 277 | 306 |
| 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 |
| ENST00000305264 | 1976 | 428 | 141005760 | 141005850 | 911 | 1000 | 277 | 306 |
| 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 |
| O15379 | 277 | 306 | 290 | 293 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4A69 |
| O15379 | 277 | 306 | 1 | 428 | Chain | ID=PRO_0000114696;Note=Histone deacetylase 3 |
| O15379 | 277 | 306 | 273 | 284 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4A69 |
| O15379 | 277 | 306 | 300 | 314 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4A69 |
| O15379 | 277 | 306 | 3 | 316 | Region | Note=Histone deacetylase |
| 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 |
| O15379 | 277 | 306 | 290 | 293 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4A69 |
| O15379 | 277 | 306 | 1 | 428 | Chain | ID=PRO_0000114696;Note=Histone deacetylase 3 |
| O15379 | 277 | 306 | 273 | 284 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4A69 |
| O15379 | 277 | 306 | 300 | 314 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4A69 |
| O15379 | 277 | 306 | 3 | 316 | Region | Note=Histone deacetylase |
Top |
SNVs in the skipped exons for HDAC3 |
| - 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 |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_444899 exon_skip_444900 | 141005252 | 141005331 | 141005310 | 141005310 | Frame_Shift_Del | G | - | p.P334fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_444911 | 141008740 | 141008873 | 141008808 | 141008808 | Frame_Shift_Del | A | - | p.F181fs |
| LUSC | TCGA-33-4586-01 | exon_skip_444902 | 141005580 | 141005638 | 141005610 | 141005610 | Nonsense_Mutation | C | A | p.E317* |
| SKCM | TCGA-BF-A5ES-01 | exon_skip_444910 | 141007681 | 141007754 | 141007683 | 141007683 | Nonsense_Mutation | G | A | p.Q255* |
| LIHC | TCGA-DD-A4NP-01 | exon_skip_444910 | 141007681 | 141007754 | 141007750 | 141007750 | Nonsense_Mutation | G | C | p.Y232* |
| SKCM | TCGA-EB-A44N-01 | exon_skip_444911 | 141008740 | 141008873 | 141008818 | 141008818 | Nonsense_Mutation | G | A | p.Q178* |
| THYM | TCGA-XM-A8RI-01 | exon_skip_444911 | 141008740 | 141008873 | 141008852 | 141008852 | Nonsense_Mutation | G | T | p.Y166X |
| LUAD | TCGA-86-A4JF-01 | exon_skip_444925 | 141014378 | 141014520 | 141014505 | 141014505 | Nonsense_Mutation | G | A | p.Q52* |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_444899 exon_skip_444900 | 141005252 | 141005331 | 141005332 | 141005332 | Splice_Site | C | A | e13-1 |
| READ | TCGA-EI-6514-01 | exon_skip_444911 | 141008740 | 141008873 | 141008874 | 141008874 | Splice_Site | C | A | . |
| SKCM | TCGA-GN-A263-01 | exon_skip_444911 | 141008740 | 141008873 | 141008874 | 141008874 | Splice_Site | C | T | . |
| - 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 |
| SKLU1_LUNG | 141005252 | 141005331 | 141005278 | 141005278 | Missense_Mutation | G | A | p.R345C |
| KYSE70_OESOPHAGUS | 141005761 | 141005850 | 141005843 | 141005843 | Missense_Mutation | C | T | p.V280I |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 141007460 | 141007524 | 141007485 | 141007485 | Missense_Mutation | A | G | p.F269L |
| NCIH2347_LUNG | 141007681 | 141007754 | 141007744 | 141007744 | Missense_Mutation | G | C | p.H234Q |
| SNU175_LARGE_INTESTINE | 141008740 | 141008873 | 141008779 | 141008779 | Missense_Mutation | A | G | p.S191P |
| HRT18_LARGE_INTESTINE | 141008740 | 141008873 | 141008779 | 141008779 | Missense_Mutation | A | G | p.S191P |
| OVMANA_OVARY | 141009611 | 141009692 | 141009646 | 141009646 | Missense_Mutation | C | T | p.A110T |
| VAESBJ_SOFT_TISSUE | 141009611 | 141009692 | 141009685 | 141009685 | Missense_Mutation | A | G | p.F97L |
| SMZ1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 141014378 | 141014520 | 141014481 | 141014481 | Missense_Mutation | G | A | p.R60C |
| HEC251_ENDOMETRIUM | 141005580 | 141005638 | 141005610 | 141005610 | Nonsense_Mutation | C | A | p.E317* |
| CW2_LARGE_INTESTINE | 141005761 | 141005850 | 141005780 | 141005780 | Nonsense_Mutation | G | A | p.R301* |
| DMS53_LUNG | 141009611 | 141009692 | 141009612 | 141009612 | Splice_Site | T | G | p.K121T |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HDAC3 |
| 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 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | GBM | rs2530223 | chr5:141014494 | T/C | 7.08e-07 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | BLCA | rs2530223 | chr5:141014494 | T/C | 1.29e-07 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | KIRP | rs2530223 | chr5:141014494 | T/C | 2.29e-08 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | KIRC | rs2530223 | chr5:141014494 | T/C | 4.21e-15 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | LIHC | rs2530223 | chr5:141014494 | T/C | 6.61e-04 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | PRAD | rs2530223 | chr5:141014494 | T/C | 4.07e-20 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | TGCT | rs2530223 | chr5:141014494 | T/C | 4.69e-04 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | STAD | rs2530223 | chr5:141014494 | T/C | 6.01e-09 |
| exon_skip_444925 | 5 | 141009610:141009692:141014377:141014520:141016114:141016197 | 141014377:141014520 | ENST00000495485.1,ENST00000305264.3 | THCA | rs2530223 | chr5:141014494 | T/C | 7.74e-17 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HDAC3 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HDAC3 |
Top |
RelatedDrugs for HDAC3 |
| 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 |
| O15379 | DB02546 | Vorinostat | Histone deacetylase 3 | small molecule | approved|investigational |
Top |
RelatedDiseases for HDAC3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| HDAC3 | C0036341 | Schizophrenia | 4 | PSYGENET |
| HDAC3 | C0018799 | Heart Diseases | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|