|
||||||
|
 | |
| |
| |
| |
| 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 CBX3 |
 Gene summary |
| Gene information | Gene symbol | CBX3 | Gene ID | 11335 |
| Gene name | chromobox 3 | |
| Synonyms | HECH|HP1-GAMMA|HP1Hs-gamma | |
| Cytomap | 7p15.2 | |
| Type of gene | protein-coding | |
| Description | chromobox protein homolog 3HP1 gamma homologchromobox homolog 3 (HP1 gamma homolog, Drosophila)heterochromatin protein 1 homolog gammaheterochromatin protein HP1 gammaheterochromatin-like protein 1modifier 2 protein | |
| Modification date | 20180519 | |
| UniProtAcc | Q13185 | |
| Context | PubMed: CBX3 [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 |
| CBX3 | GO:0045892 | negative regulation of transcription, DNA-templated | 9636147 |
Top |
Exon skipping events across known transcript of Ensembl for CBX3 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 CBX3 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CBX3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_464949 | 7 | 26241384:26241446:26242590:26242642:26245987:26246130 | 26242590:26242642 | ENSG00000122565.14 | ENST00000396386.2,ENST00000409747.1 |
| exon_skip_464954 | 7 | 26242596:26242642:26245987:26246130:26248012:26248032 | 26245987:26246130 | ENSG00000122565.14 | ENST00000497498.1,ENST00000396386.2,ENST00000456948.1,ENST00000337620.4 |
| exon_skip_464958 | 7 | 26245987:26246130:26248012:26248175:26251281:26251337 | 26248012:26248175 | ENSG00000122565.14 | ENST00000497498.1,ENST00000396386.2,ENST00000337620.4 |
| exon_skip_464960 | 7 | 26245987:26246130:26248085:26248175:26251281:26251337 | 26248085:26248175 | ENSG00000122565.14 | ENST00000409747.1 |
| exon_skip_464964 | 7 | 26248085:26248175:26251281:26251376:26251701:26252043 | 26251281:26251376 | ENSG00000122565.14 | ENST00000396386.2,ENST00000409747.1,ENST00000337620.4,ENST00000481057.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CBX3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_464949 | 7 | 26241384:26241446:26242590:26242642:26245987:26246130 | 26242590:26242642 | ENSG00000122565.14 | ENST00000396386.2,ENST00000409747.1 |
| exon_skip_464954 | 7 | 26242596:26242642:26245987:26246130:26248012:26248032 | 26245987:26246130 | ENSG00000122565.14 | ENST00000337620.4,ENST00000396386.2,ENST00000456948.1,ENST00000497498.1 |
| exon_skip_464958 | 7 | 26245987:26246130:26248012:26248175:26251281:26251337 | 26248012:26248175 | ENSG00000122565.14 | ENST00000337620.4,ENST00000396386.2,ENST00000497498.1 |
| exon_skip_464960 | 7 | 26245987:26246130:26248085:26248175:26251281:26251337 | 26248085:26248175 | ENSG00000122565.14 | ENST00000409747.1 |
| exon_skip_464964 | 7 | 26248085:26248175:26251281:26251376:26251701:26252043 | 26251281:26251376 | ENSG00000122565.14 | ENST00000337620.4,ENST00000396386.2,ENST00000409747.1,ENST00000481057.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CBX3 |
| 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 |
| ENST00000396386 | 26242590 | 26242642 | 5CDS-5UTR |
| ENST00000337620 | 26245987 | 26246130 | Frame-shift |
| ENST00000396386 | 26245987 | 26246130 | Frame-shift |
| ENST00000337620 | 26248012 | 26248175 | Frame-shift |
| ENST00000396386 | 26248012 | 26248175 | Frame-shift |
| ENST00000337620 | 26251281 | 26251376 | Frame-shift |
| ENST00000396386 | 26251281 | 26251376 | Frame-shift |
| 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 |
| ENST00000396386 | 26242590 | 26242642 | 5CDS-5UTR |
| ENST00000337620 | 26245987 | 26246130 | Frame-shift |
| ENST00000396386 | 26245987 | 26246130 | Frame-shift |
| ENST00000337620 | 26248012 | 26248175 | Frame-shift |
| ENST00000396386 | 26248012 | 26248175 | Frame-shift |
| ENST00000337620 | 26251281 | 26251376 | Frame-shift |
| ENST00000396386 | 26251281 | 26251376 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for CBX3 |
| 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 |
| 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 |
| 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 |
| 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 |
Top |
SNVs in the skipped exons for CBX3 |
| - 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. |
CBX3_BRCA_exon_skip_464958_psi_boxplot.png |
CBX3_BRCA_exon_skip_464960_psi_boxplot.png |
CBX3_COAD_exon_skip_464954_psi_boxplot.png |
CBX3_DLBC_exon_skip_464954_psi_boxplot.png |
CBX3_ESCA_exon_skip_464954_psi_boxplot.png |
CBX3_KIRC_exon_skip_464958_psi_boxplot.png |
CBX3_KIRC_exon_skip_464960_psi_boxplot.png |
CBX3_LGG_exon_skip_464954_psi_boxplot.png |
CBX3_LIHC_exon_skip_464954_psi_boxplot.png |
CBX3_PAAD_exon_skip_464958_psi_boxplot.png |
CBX3_STAD_exon_skip_464954_psi_boxplot.png |
CBX3_STAD_exon_skip_464958_psi_boxplot.png |
CBX3_TGCT_exon_skip_464958_psi_boxplot.png |
| - 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 |
| COAD | TCGA-A6-6780-01 | exon_skip_464954 | 26245988 | 26246130 | 26245989 | 26245989 | Frame_Shift_Del | A | - | p.Q9fs |
| COAD | TCGA-AD-6889-01 | exon_skip_464954 | 26245988 | 26246130 | 26245989 | 26245989 | Frame_Shift_Del | A | - | p.Q9fs |
| COAD | TCGA-G4-6586-01 | exon_skip_464954 | 26245988 | 26246130 | 26245989 | 26245989 | Frame_Shift_Del | A | - | p.Q9fs |
| COAD | TCGA-A6-5661-01 | exon_skip_464954 | 26245988 | 26246130 | 26245999 | 26245999 | Frame_Shift_Del | A | - | p.G12fs |
| STAD | TCGA-CG-5726-01 | exon_skip_464954 | 26245988 | 26246130 | 26245999 | 26245999 | Frame_Shift_Del | A | - | p.G12fs |
| STAD | TCGA-MX-A5UJ-01 | exon_skip_464954 | 26245988 | 26246130 | 26245999 | 26245999 | Frame_Shift_Del | A | - | p.G12fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_464954 | 26245988 | 26246130 | 26246104 | 26246104 | Frame_Shift_Del | T | - | p.Y47fs |
| BRCA | TCGA-E9-A229-01 | exon_skip_464958 exon_skip_464960 | 26248013 | 26248175 | 26248161 | 26248165 | Frame_Shift_Del | AAGAA | - | p.K107fs |
| BRCA | TCGA-E9-A229-01 | exon_skip_464958 exon_skip_464960 | 26248086 | 26248175 | 26248161 | 26248165 | Frame_Shift_Del | AAGAA | - | p.K107fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_464954 | 26245988 | 26246130 | 26246020 | 26246021 | Frame_Shift_Ins | - | A | p.RK19fs |
| ESCA | TCGA-L5-A8NH-01 | exon_skip_464954 | 26245988 | 26246130 | 26246030 | 26246030 | Nonsense_Mutation | G | T | p.E23* |
| LIHC | TCGA-EP-A2KA-01 | exon_skip_464958 exon_skip_464960 | 26248013 | 26248175 | 26248156 | 26248156 | Nonsense_Mutation | C | A | p.S104X |
| LIHC | TCGA-EP-A2KA-01 | exon_skip_464958 exon_skip_464960 | 26248086 | 26248175 | 26248156 | 26248156 | Nonsense_Mutation | C | A | p.S104X |
| LUAD | TCGA-55-7914-01 | exon_skip_464949 | 26242591 | 26242642 | 26242643 | 26242643 | Splice_Site | G | A | p.L8_splice |
| DLBC | TCGA-FF-8061-01 | exon_skip_464954 | 26245988 | 26246130 | 26245986 | 26245986 | Splice_Site | A | T | . |
| DLBC | TCGA-G8-6909-01 | exon_skip_464954 | 26245988 | 26246130 | 26245986 | 26245986 | Splice_Site | A | T | . |
| DLBC | TCGA-GR-A4D9-01 | exon_skip_464954 | 26245988 | 26246130 | 26245986 | 26245986 | Splice_Site | A | T | . |
| LGG | TCGA-FG-6689-01 | exon_skip_464954 | 26245988 | 26246130 | 26245986 | 26245986 | Splice_Site | A | T | . |
| PAAD | TCGA-HZ-7919-01 | exon_skip_464958 exon_skip_464960 | 26248013 | 26248175 | 26248012 | 26248012 | Splice_Site | G | A | . |
| STAD | TCGA-BR-4363-01 | exon_skip_464958 exon_skip_464960 | 26248013 | 26248175 | 26248012 | 26248012 | Splice_Site | G | A | . |
| TGCT | TCGA-S6-A8JY-01 | exon_skip_464958 exon_skip_464960 | 26248013 | 26248175 | 26248012 | 26248012 | Splice_Site | G | A | . |
| KIRC | TCGA-BP-5009-01 | exon_skip_464958 exon_skip_464960 | 26248013 | 26248175 | 26248177 | 26248177 | Splice_Site | T | C | . |
| KIRC | TCGA-BP-5009-01 | exon_skip_464958 exon_skip_464960 | 26248086 | 26248175 | 26248177 | 26248177 | Splice_Site | T | C | . |
| HNSC | TCGA-BA-5558-01 | exon_skip_464964 | 26251282 | 26251376 | 26251377 | 26251377 | Splice_Site | G | C | p.W142_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-BP-5009-01 |
| Cancer type: KIRC | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248013 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248177 | |
| Mutation end: 26248177 | |
| Mutation type: Splice_Site | |
| Reference seq: T | |
| Mutation seq: C | |
| AAchange: . | |
| Sample: TCGA-BP-5009-01 |
| Cancer type: KIRC | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248086 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248177 | |
| Mutation end: 26248177 | |
| Mutation type: Splice_Site | |
| Reference seq: T | |
| Mutation seq: C | |
| AAchange: . | |
exon_skip_385593_KIRC_TCGA-BP-5009-01.png | |
exon_skip_425876_KIRC_TCGA-BP-5009-01.png | |
exon_skip_464960_KIRC_TCGA-BP-5009-01.png | |
 | Sample: TCGA-E9-A229-01 |
| Cancer type: BRCA | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248013 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248161 | |
| Mutation end: 26248165 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: AAGAA | |
| Mutation seq: - | |
| AAchange: p.K107fs | |
| Sample: TCGA-E9-A229-01 |
| Cancer type: BRCA | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248086 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248161 | |
| Mutation end: 26248165 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: AAGAA | |
| Mutation seq: - | |
| AAchange: p.K107fs | |
exon_skip_464960_BRCA_TCGA-E9-A229-01.png | |
 | Sample: TCGA-BP-5009-01 |
| Cancer type: KIRC | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248013 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248177 | |
| Mutation end: 26248177 | |
| Mutation type: Splice_Site | |
| Reference seq: T | |
| Mutation seq: C | |
| AAchange: . | |
| Sample: TCGA-BP-5009-01 |
| Cancer type: KIRC | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248086 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248177 | |
| Mutation end: 26248177 | |
| Mutation type: Splice_Site | |
| Reference seq: T | |
| Mutation seq: C | |
| AAchange: . | |
| exon_skip_385593_KIRC_TCGA-BP-5009-01.png | |
| exon_skip_425876_KIRC_TCGA-BP-5009-01.png | |
| exon_skip_464960_KIRC_TCGA-BP-5009-01.png | |
 | Sample: TCGA-HZ-7919-01 |
| Cancer type: PAAD | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248013 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248012 | |
| Mutation end: 26248012 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: . | |
exon_skip_464958_PAAD_TCGA-HZ-7919-01.png | |
 | Sample: TCGA-S6-A8JY-01 |
| Cancer type: TGCT | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248013 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248012 | |
| Mutation end: 26248012 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: . | |
exon_skip_464958_TGCT_TCGA-S6-A8JY-01.png | |
 | Sample: TCGA-E9-A229-01 |
| Cancer type: BRCA | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248013 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248161 | |
| Mutation end: 26248165 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: AAGAA | |
| Mutation seq: - | |
| AAchange: p.K107fs | |
| Sample: TCGA-E9-A229-01 |
| Cancer type: BRCA | |
| ESID: exon_skip_464960 | |
| Skipped exon start: 26248086 | |
| Skipped exon end: 26248175 | |
| Mutation start: 26248161 | |
| Mutation end: 26248165 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: AAGAA | |
| Mutation seq: - | |
| AAchange: p.K107fs | |
| exon_skip_464960_BRCA_TCGA-E9-A229-01.png | |
 | Sample: TCGA-L5-A8NH-01 |
| Cancer type: ESCA | |
| ESID: exon_skip_464954 | |
| Skipped exon start: 26245988 | |
| Skipped exon end: 26246130 | |
| Mutation start: 26246030 | |
| Mutation end: 26246030 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: T | |
| AAchange: p.E23* | |
exon_skip_17970_ESCA_TCGA-L5-A8NH-01.png | |
exon_skip_313855_ESCA_TCGA-L5-A8NH-01.png | |
exon_skip_37386_ESCA_TCGA-L5-A8NH-01.png | |
exon_skip_37388_ESCA_TCGA-L5-A8NH-01.png | |
exon_skip_455353_ESCA_TCGA-L5-A8NH-01.png | |
exon_skip_464954_ESCA_TCGA-L5-A8NH-01.png | |
 | Sample: TCGA-CG-5726-01 |
| Cancer type: STAD | |
| ESID: exon_skip_464954 | |
| Skipped exon start: 26245988 | |
| Skipped exon end: 26246130 | |
| Mutation start: 26245999 | |
| Mutation end: 26245999 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: A | |
| Mutation seq: - | |
| AAchange: p.G12fs | |
exon_skip_111498_STAD_TCGA-CG-5726-01.png | |
exon_skip_1165_STAD_TCGA-CG-5726-01.png | |
exon_skip_132841_STAD_TCGA-CG-5726-01.png | |
exon_skip_32368_STAD_TCGA-CG-5726-01.png | |
exon_skip_32369_STAD_TCGA-CG-5726-01.png | |
exon_skip_330351_STAD_TCGA-CG-5726-01.png | |
exon_skip_368289_STAD_TCGA-CG-5726-01.png | |
exon_skip_439047_STAD_TCGA-CG-5726-01.png | |
exon_skip_439048_STAD_TCGA-CG-5726-01.png | |
exon_skip_440332_STAD_TCGA-CG-5726-01.png | |
exon_skip_444132_STAD_TCGA-CG-5726-01.png | |
exon_skip_462138_STAD_TCGA-CG-5726-01.png | |
exon_skip_462144_STAD_TCGA-CG-5726-01.png | |
exon_skip_464954_STAD_TCGA-CG-5726-01.png | |
exon_skip_49506_STAD_TCGA-CG-5726-01.png | |
exon_skip_70838_STAD_TCGA-CG-5726-01.png | |
exon_skip_924_STAD_TCGA-CG-5726-01.png | |
exon_skip_94969_STAD_TCGA-CG-5726-01.png | |
| - 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 |
| HEC59_ENDOMETRIUM | 26245988 | 26246130 | 26245999 | 26245999 | Frame_Shift_Del | A | - | p.G12fs |
| LOVO_LARGE_INTESTINE | 26245988 | 26246130 | 26245999 | 26245999 | Frame_Shift_Del | A | - | p.G12fs |
| MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 26245988 | 26246130 | 26246021 | 26246021 | Frame_Shift_Del | A | - | p.K21fs |
| SW1271_LUNG | 26248013 | 26248175 | 26248105 | 26248105 | Frame_Shift_Del | A | - | p.D87fs |
| SW1271_LUNG | 26248086 | 26248175 | 26248105 | 26248105 | Frame_Shift_Del | A | - | p.D87fs |
| MERO84_LUNG | 26245988 | 26246130 | 26245998 | 26245999 | Frame_Shift_Ins | - | A | p.GK12fs |
| HEC251_ENDOMETRIUM | 26245988 | 26246130 | 26246052 | 26246052 | Missense_Mutation | T | G | p.F30C |
| SNU1040_LARGE_INTESTINE | 26245988 | 26246130 | 26246079 | 26246079 | Missense_Mutation | G | A | p.R39H |
| LS411N_LARGE_INTESTINE | 26248013 | 26248175 | 26248020 | 26248020 | Missense_Mutation | A | G | p.N59D |
| MIAPACA2_PANCREAS | 26248013 | 26248175 | 26248047 | 26248047 | Missense_Mutation | G | C | p.D68H |
| 127399_SOFT_TISSUE | 26248013 | 26248175 | 26248138 | 26248138 | Missense_Mutation | A | G | p.E98G |
| 127399_SOFT_TISSUE | 26248086 | 26248175 | 26248138 | 26248138 | Missense_Mutation | A | G | p.E98G |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 26251282 | 26251376 | 26251360 | 26251360 | Missense_Mutation | A | G | p.M137V |
| LS411N_LARGE_INTESTINE | 26245988 | 26246130 | 26245989 | 26245989 | Splice_Site | A | - | p.Q9fs |
| 639V_URINARY_TRACT | 26245988 | 26246130 | 26245989 | 26245989 | Splice_Site | A | - | p.Q9fs |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CBX3 |
| 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 CBX3 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CBX3 |
Top |
RelatedDrugs for CBX3 |
| 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 CBX3 |
| 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)
|