|
||||||
|
 | |
| |
| |
| |
| 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 ELK3 |
 Gene summary |
| Gene information | Gene symbol | ELK3 | Gene ID | 2004 |
| Gene name | ELK3, ETS transcription factor | |
| Synonyms | ERP|NET|SAP-2|SAP2 | |
| Cytomap | 12q23.1 | |
| Type of gene | protein-coding | |
| Description | ETS domain-containing protein Elk-3ELK3, ETS-domain protein (SRF accessory protein 2)ETS-related protein ERPETS-related protein NETSRF accessory protein 2serum response factor accessory protein 2 | |
| Modification date | 20180523 | |
| UniProtAcc | P41970 | |
| Context | PubMed: ELK3 [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 |
| ELK3 | GO:0045892 | negative regulation of transcription, DNA-templated | 12933792 |
| ELK3 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 12788937 |
Top |
Exon skipping events across known transcript of Ensembl for ELK3 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 ELK3 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for ELK3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_85959 | 12 | 96588391:96588483:96591803:96591920:96617342:96617460 | 96591803:96591920 | ENSG00000111145.3 | ENST00000547249.1 |
| exon_skip_85963 | 12 | 96588391:96588483:96617342:96617551:96653508:96653631 | 96617342:96617551 | ENSG00000111145.3 | ENST00000552142.1 |
| exon_skip_85966 | 12 | 96606502:96606619:96607528:96607646:96617342:96617460 | 96607528:96607646 | ENSG00000111145.3 | ENST00000547860.1 |
| exon_skip_85967 | 12 | 96617342:96617551:96640717:96641512:96653508:96653631 | 96640717:96641512 | ENSG00000111145.3 | ENST00000228741.3 |
| exon_skip_85970 | 12 | 96640908:96641061:96641380:96641512:96653508:96653631 | 96641380:96641512 | ENSG00000111145.3 | ENST00000549985.1 |
| exon_skip_85971 | 12 | 96641380:96641512:96653508:96653631:96660859:96661135 | 96653508:96653631 | ENSG00000111145.3 | ENST00000549985.1,ENST00000228741.3 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for ELK3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_85959 | 12 | 96588391:96588483:96591803:96591920:96617342:96617460 | 96591803:96591920 | ENSG00000111145.3 | ENST00000547249.1 |
| exon_skip_85966 | 12 | 96606502:96606619:96607528:96607646:96617342:96617460 | 96607528:96607646 | ENSG00000111145.3 | ENST00000547860.1 |
| exon_skip_85967 | 12 | 96617342:96617551:96640717:96641512:96653508:96653631 | 96640717:96641512 | ENSG00000111145.3 | ENST00000228741.3 |
| exon_skip_85970 | 12 | 96640908:96641061:96641380:96641512:96653508:96653631 | 96641380:96641512 | ENSG00000111145.3 | ENST00000549985.1 |
| exon_skip_85971 | 12 | 96641380:96641512:96653508:96653631:96660859:96661135 | 96653508:96653631 | ENSG00000111145.3 | ENST00000228741.3,ENST00000549985.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for ELK3 |
| 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 |
| ENST00000228741 | 96640717 | 96641512 | In-frame |
| ENST00000228741 | 96653508 | 96653631 | 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 |
| ENST00000228741 | 96640717 | 96641512 | In-frame |
| ENST00000228741 | 96653508 | 96653631 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for ELK3 |
| 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 |
| ENST00000228741 | 4222 | 407 | 96640717 | 96641512 | 534 | 1328 | 69 | 334 |
| ENST00000228741 | 4222 | 407 | 96653508 | 96653631 | 1329 | 1451 | 334 | 375 |
| 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 |
| ENST00000228741 | 4222 | 407 | 96640717 | 96641512 | 534 | 1328 | 69 | 334 |
| ENST00000228741 | 4222 | 407 | 96653508 | 96653631 | 1329 | 1451 | 334 | 375 |
| 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 |
| P41970 | 69 | 334 | 1 | 407 | Chain | ID=PRO_0000204097;Note=ETS domain-containing protein Elk-3 |
| P41970 | 69 | 334 | 207 | 212 | Compositional bias | Note=Poly-Ala |
| P41970 | 69 | 334 | 92 | 92 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P41970 | 69 | 334 | 165 | 165 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P41970 | 69 | 334 | 5 | 85 | DNA binding | Note=ETS;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00237 |
| P41970 | 69 | 334 | 115 | 115 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18691976;Dbxref=PMID:18691976 |
| P41970 | 69 | 334 | 273 | 277 | Motif | Note=CTBP-binding motif |
| P41970 | 69 | 334 | 169 | 169 | Natural variant | ID=VAR_048946;Note=P->L;Dbxref=dbSNP:rs35332676 |
| P41970 | 69 | 334 | 114 | 114 | Sequence conflict | Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 117 | 117 | Sequence conflict | Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 128 | 128 | Sequence conflict | Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 152 | 152 | Sequence conflict | Note=Q->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 163 | 163 | Sequence conflict | Note=T->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 249 | 249 | Sequence conflict | Note=N->K;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 334 | 375 | 1 | 407 | Chain | ID=PRO_0000204097;Note=ETS domain-containing protein Elk-3 |
| 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 |
| P41970 | 69 | 334 | 1 | 407 | Chain | ID=PRO_0000204097;Note=ETS domain-containing protein Elk-3 |
| P41970 | 69 | 334 | 207 | 212 | Compositional bias | Note=Poly-Ala |
| P41970 | 69 | 334 | 92 | 92 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P41970 | 69 | 334 | 165 | 165 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| P41970 | 69 | 334 | 5 | 85 | DNA binding | Note=ETS;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00237 |
| P41970 | 69 | 334 | 115 | 115 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18691976;Dbxref=PMID:18691976 |
| P41970 | 69 | 334 | 273 | 277 | Motif | Note=CTBP-binding motif |
| P41970 | 69 | 334 | 169 | 169 | Natural variant | ID=VAR_048946;Note=P->L;Dbxref=dbSNP:rs35332676 |
| P41970 | 69 | 334 | 114 | 114 | Sequence conflict | Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 117 | 117 | Sequence conflict | Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 128 | 128 | Sequence conflict | Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 152 | 152 | Sequence conflict | Note=Q->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 163 | 163 | Sequence conflict | Note=T->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 69 | 334 | 249 | 249 | Sequence conflict | Note=N->K;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P41970 | 334 | 375 | 1 | 407 | Chain | ID=PRO_0000204097;Note=ETS domain-containing protein Elk-3 |
Top |
SNVs in the skipped exons for ELK3 |
| - 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-A3A0-01 | exon_skip_85967 | 96640718 | 96641512 | 96640748 | 96640748 | Frame_Shift_Del | T | - | p.F80fs |
| UCEC | TCGA-A5-A0GB-01 | exon_skip_85967 | 96640718 | 96641512 | 96641029 | 96641029 | Frame_Shift_Del | C | - | p.S173fs |
| COAD | TCGA-CM-5861-01 | exon_skip_85967 | 96640718 | 96641512 | 96641384 | 96641384 | Frame_Shift_Del | A | - | p.A291fs |
| COAD | TCGA-CM-5861-01 | exon_skip_85970 | 96641381 | 96641512 | 96641384 | 96641384 | Frame_Shift_Del | A | - | p.A291fs |
| COAD | TCGA-AA-A01Q-01 | exon_skip_85963 | 96617343 | 96617551 | 96617494 | 96617495 | Frame_Shift_Ins | - | A | p.N50fs |
| COAD | TCGA-AA-3527-01 | exon_skip_85967 | 96640718 | 96641512 | 96641028 | 96641029 | Frame_Shift_Ins | - | C | p.S173fs |
| COAD | TCGA-AY-6197-01 | exon_skip_85967 | 96640718 | 96641512 | 96641028 | 96641029 | Frame_Shift_Ins | - | C | p.S173fs |
| HNSC | TCGA-CV-5434-01 | exon_skip_85967 | 96640718 | 96641512 | 96641028 | 96641029 | Frame_Shift_Ins | - | C | p.T173fs |
| UCEC | TCGA-D1-A176-01 | exon_skip_85967 | 96640718 | 96641512 | 96641028 | 96641029 | Frame_Shift_Ins | - | C | p.S173fs |
| UCEC | TCGA-D1-A17F-01 | exon_skip_85967 | 96640718 | 96641512 | 96641028 | 96641029 | Frame_Shift_Ins | - | C | p.S173fs |
| STAD | TCGA-BR-6452-01 | exon_skip_85967 | 96640718 | 96641512 | 96641029 | 96641030 | Frame_Shift_Ins | - | C | p.S173fs |
| STAD | TCGA-BR-8361-01 | exon_skip_85967 | 96640718 | 96641512 | 96641029 | 96641030 | Frame_Shift_Ins | - | C | p.S173fs |
| STAD | TCGA-FP-A4BE-01 | exon_skip_85967 | 96640718 | 96641512 | 96641029 | 96641030 | Frame_Shift_Ins | - | C | p.S173fs |
| BLCA | TCGA-R3-A69X-01 | exon_skip_85967 | 96640718 | 96641512 | 96640929 | 96640929 | Nonsense_Mutation | C | G | p.S140* |
| LIHC | TCGA-ZP-A9D2-01 | exon_skip_85967 | 96640718 | 96641512 | 96641039 | 96641039 | Nonsense_Mutation | G | T | p.E177X |
| - 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 |
| GP2D_LARGE_INTESTINE | 96617343 | 96617551 | 96617488 | 96617488 | Frame_Shift_Del | A | - | p.R48fs |
| GP5D_LARGE_INTESTINE | 96617343 | 96617551 | 96617488 | 96617488 | Frame_Shift_Del | A | - | p.R48fs |
| HEC108_ENDOMETRIUM | 96640718 | 96641512 | 96641029 | 96641029 | Frame_Shift_Del | C | - | p.S173fs |
| HEC59_ENDOMETRIUM | 96640718 | 96641512 | 96641029 | 96641029 | Frame_Shift_Del | C | - | p.S173fs |
| RKO_LARGE_INTESTINE | 96640718 | 96641512 | 96641029 | 96641029 | Frame_Shift_Del | C | - | p.S173fs |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96640718 | 96641512 | 96641384 | 96641384 | Frame_Shift_Del | A | - | p.K293fs |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96641381 | 96641512 | 96641384 | 96641384 | Frame_Shift_Del | A | - | p.K293fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 96640718 | 96641512 | 96641014 | 96641016 | In_Frame_Del | GCC | - | p.P170del |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 96640718 | 96641512 | 96641020 | 96641021 | In_Frame_Ins | - | TGT | p.170_171insC |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 96617343 | 96617551 | 96617383 | 96617383 | Missense_Mutation | G | C | p.Q13H |
| SKNSH_AUTONOMIC_GANGLIA | 96617343 | 96617551 | 96617430 | 96617430 | Missense_Mutation | A | T | p.N29I |
| RCCJF_KIDNEY | 96617343 | 96617551 | 96617479 | 96617479 | Missense_Mutation | G | T | p.W45C |
| PACADD135_PANCREAS | 96640718 | 96641512 | 96640851 | 96640851 | Missense_Mutation | C | T | p.A114V |
| SISO_CERVIX | 96640718 | 96641512 | 96640851 | 96640851 | Missense_Mutation | C | T | p.A114V |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96640718 | 96641512 | 96640851 | 96640851 | Missense_Mutation | C | T | p.A114V |
| NBSUSSR_AUTONOMIC_GANGLIA | 96640718 | 96641512 | 96640865 | 96640865 | Missense_Mutation | C | T | p.R119C |
| SNGM_ENDOMETRIUM | 96640718 | 96641512 | 96641018 | 96641018 | Missense_Mutation | C | T | p.P170S |
| HEPG2_LIVER | 96640718 | 96641512 | 96641033 | 96641033 | Missense_Mutation | C | G | p.P175A |
| C3A_LIVER | 96640718 | 96641512 | 96641033 | 96641033 | Missense_Mutation | C | G | p.P175A |
| HAL01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96640718 | 96641512 | 96641060 | 96641060 | Missense_Mutation | A | G | p.R184G |
| TALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96640718 | 96641512 | 96641060 | 96641060 | Missense_Mutation | A | G | p.R184G |
| RMUGS_OVARY | 96640718 | 96641512 | 96641201 | 96641202 | Missense_Mutation | GC | CT | p.A231L |
| RMUGS_OVARY | 96640718 | 96641512 | 96641201 | 96641201 | Missense_Mutation | G | C | p.A231P |
| RMUGS_OVARY | 96640718 | 96641512 | 96641202 | 96641202 | Missense_Mutation | C | T | p.A231V |
| HCT15_LARGE_INTESTINE | 96640718 | 96641512 | 96641216 | 96641216 | Missense_Mutation | G | A | p.A236T |
| A253_SALIVARY_GLAND | 96640718 | 96641512 | 96641250 | 96641250 | Missense_Mutation | C | T | p.S247F |
| HEC59_ENDOMETRIUM | 96640718 | 96641512 | 96641301 | 96641301 | Missense_Mutation | C | T | p.A264V |
| EVSAT_BREAST | 96640718 | 96641512 | 96641367 | 96641367 | Missense_Mutation | C | G | p.S286C |
| SNU1040_LARGE_INTESTINE | 96640718 | 96641512 | 96641453 | 96641453 | Missense_Mutation | G | A | p.A315T |
| SNU1040_LARGE_INTESTINE | 96641381 | 96641512 | 96641453 | 96641453 | Missense_Mutation | G | A | p.A315T |
| HKA1_SKIN | 96640718 | 96641512 | 96641478 | 96641478 | Missense_Mutation | C | T | p.S323L |
| HKA1_SKIN | 96641381 | 96641512 | 96641478 | 96641478 | Missense_Mutation | C | T | p.S323L |
| A549_LUNG | 96653509 | 96653631 | 96653527 | 96653527 | Missense_Mutation | C | A | p.L341M |
| SNU1040_LARGE_INTESTINE | 96653509 | 96653631 | 96653556 | 96653556 | Missense_Mutation | A | G | p.I350M |
| HT115_LARGE_INTESTINE | 96640718 | 96641512 | 96641402 | 96641402 | Nonsense_Mutation | G | T | p.E298* |
| HT115_LARGE_INTESTINE | 96641381 | 96641512 | 96641402 | 96641402 | Nonsense_Mutation | G | T | p.E298* |
| SW1463_LARGE_INTESTINE | 96640718 | 96641512 | 96641478 | 96641478 | Nonsense_Mutation | C | A | p.S323* |
| SW1463_LARGE_INTESTINE | 96641381 | 96641512 | 96641478 | 96641478 | Nonsense_Mutation | C | A | p.S323* |
| MFE319_ENDOMETRIUM | 96617343 | 96617551 | 96617551 | 96617551 | Splice_Site | G | A | p.K69K |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ELK3 |
| 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 ELK3 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ELK3 |
Top |
RelatedDrugs for ELK3 |
| 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 ELK3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ELK3 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|