|
||||||
|
 | |
| |
| |
| |
| 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 ALPK3 |
 Gene summary |
| Gene information | Gene symbol | ALPK3 | Gene ID | 57538 |
| Gene name | alpha kinase 3 | |
| Synonyms | MAK|MIDORI | |
| Cytomap | 15q25.3 | |
| Type of gene | protein-coding | |
| Description | alpha-protein kinase 3muscle alpha-kinasemuscle alpha-protein kinasemyocyte induction differentiation originator | |
| Modification date | 20180523 | |
| UniProtAcc | Q96L96 | |
| Context | PubMed: ALPK3 [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 ALPK3 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 ALPK3 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for ALPK3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_124387 | 15 | 85402473:85402621:85403006:85403134:85403267:85403303 | 85403006:85403134 | ENSG00000136383.6 | ENST00000258888.5 |
| exon_skip_124388 | 15 | 85403006:85403134:85403267:85403303:85405865:85406146 | 85403267:85403303 | ENSG00000136383.6 | ENST00000258888.5 |
| exon_skip_124390 | 15 | 85403267:85403303:85405865:85406146:85406782:85406871 | 85405865:85406146 | ENSG00000136383.6 | ENST00000258888.5 |
| exon_skip_124391 | 15 | 85406782:85406871:85407672:85407896:85410547:85410596 | 85407672:85407896 | ENSG00000136383.6 | ENST00000558077.1,ENST00000258888.5 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for ALPK3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_124387 | 15 | 85402473:85402621:85403006:85403134:85403267:85403303 | 85403006:85403134 | ENSG00000136383.6 | ENST00000258888.5 |
| exon_skip_124388 | 15 | 85403006:85403134:85403267:85403303:85405865:85406146 | 85403267:85403303 | ENSG00000136383.6 | ENST00000258888.5 |
| exon_skip_124390 | 15 | 85403267:85403303:85405865:85406146:85406782:85406871 | 85405865:85406146 | ENSG00000136383.6 | ENST00000258888.5 |
| exon_skip_124391 | 15 | 85406782:85406871:85407672:85407896:85410547:85410596 | 85407672:85407896 | ENSG00000136383.6 | ENST00000258888.5,ENST00000558077.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for ALPK3 |
| 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 |
| ENST00000258888 | 85403006 | 85403134 | Frame-shift |
| ENST00000258888 | 85405865 | 85406146 | Frame-shift |
| ENST00000258888 | 85407672 | 85407896 | Frame-shift |
| ENST00000258888 | 85403267 | 85403303 | 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 |
| ENST00000258888 | 85403006 | 85403134 | Frame-shift |
| ENST00000258888 | 85405865 | 85406146 | Frame-shift |
| ENST00000258888 | 85407672 | 85407896 | Frame-shift |
| ENST00000258888 | 85403267 | 85403303 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for ALPK3 |
| 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 |
| ENST00000258888 | 10934 | 1907 | 85403267 | 85403303 | 4867 | 4902 | 1566 | 1578 |
| 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 |
| ENST00000258888 | 10934 | 1907 | 85403267 | 85403303 | 4867 | 4902 | 1566 | 1578 |
| 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 |
| Q96L96 | 1566 | 1578 | 1 | 1907 | Chain | ID=PRO_0000260031;Note=Alpha-protein kinase 3 |
| Q96L96 | 1566 | 1578 | 1261 | 1907 | Natural variant | ID=VAR_079142;Note=In CMH27. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26846950;Dbxref=PMID:26846950 |
| Q96L96 | 1566 | 1578 | 1264 | 1907 | Natural variant | ID=VAR_079143;Note=In CMH27. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27106955;Dbxref=PMID:27106955 |
| 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 |
| Q96L96 | 1566 | 1578 | 1 | 1907 | Chain | ID=PRO_0000260031;Note=Alpha-protein kinase 3 |
| Q96L96 | 1566 | 1578 | 1261 | 1907 | Natural variant | ID=VAR_079142;Note=In CMH27. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26846950;Dbxref=PMID:26846950 |
| Q96L96 | 1566 | 1578 | 1264 | 1907 | Natural variant | ID=VAR_079143;Note=In CMH27. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27106955;Dbxref=PMID:27106955 |
Top |
SNVs in the skipped exons for ALPK3 |
| - 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_124387 | 85403007 | 85403134 | 85403051 | 85403051 | Frame_Shift_Del | C | - | p.S1539fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_124390 | 85405866 | 85406146 | 85406007 | 85406007 | Frame_Shift_Del | C | - | p.S1626fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_124390 | 85405866 | 85406146 | 85406027 | 85406027 | Frame_Shift_Del | G | - | p.G1633fs |
| KIRC | TCGA-B0-4811-01 | exon_skip_124391 | 85407673 | 85407896 | 85407697 | 85407697 | Frame_Shift_Del | C | - | p.Y1710fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_124391 | 85407673 | 85407896 | 85407726 | 85407726 | Frame_Shift_Del | C | - | p.T1720fs |
| THYM | TCGA-XU-A933-01 | exon_skip_124390 | 85405866 | 85406146 | 85405949 | 85405949 | Nonsense_Mutation | C | T | p.R1607* |
| THYM | TCGA-XU-A933-01 | exon_skip_124390 | 85405866 | 85406146 | 85405949 | 85405949 | Nonsense_Mutation | C | T | p.R1607X |
| UCEC | TCGA-D1-A103-01 | exon_skip_124390 | 85405866 | 85406146 | 85405949 | 85405949 | Nonsense_Mutation | C | T | p.R1607* |
| - 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 |
| SNU520_STOMACH | 85405866 | 85406146 | 85405973 | 85405973 | Frame_Shift_Del | G | - | p.G1617fs |
| IHH4_THYROID | 85403007 | 85403134 | 85403024 | 85403024 | Missense_Mutation | C | T | p.P1530L |
| NCIH1734_LUNG | 85403007 | 85403134 | 85403081 | 85403081 | Missense_Mutation | C | T | p.T1549I |
| HKA1_SKIN | 85405866 | 85406146 | 85405894 | 85405895 | Missense_Mutation | GG | AA | p.1588_1589MV>IM |
| SNU46_UPPER_AERODIGESTIVE_TRACT | 85405866 | 85406146 | 85405920 | 85405920 | Missense_Mutation | C | G | p.S1597C |
| HAL01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 85405866 | 85406146 | 85405920 | 85405920 | Missense_Mutation | C | G | p.S1597C |
| HUPT4_PANCREAS | 85405866 | 85406146 | 85405920 | 85405920 | Missense_Mutation | C | G | p.S1597C |
| HEC251_ENDOMETRIUM | 85405866 | 85406146 | 85405994 | 85405994 | Missense_Mutation | C | A | p.L1622I |
| BC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 85405866 | 85406146 | 85406007 | 85406007 | Missense_Mutation | C | A | p.S1626Y |
| G401_SOFT_TISSUE | 85405866 | 85406146 | 85406054 | 85406054 | Missense_Mutation | C | G | p.R1642G |
| HEC108_ENDOMETRIUM | 85405866 | 85406146 | 85406135 | 85406135 | Missense_Mutation | G | A | p.V1669I |
| HS746T_STOMACH | 85407673 | 85407896 | 85407675 | 85407675 | Missense_Mutation | T | G | p.I1703S |
| TGBC11TKB_STOMACH | 85405866 | 85406146 | 85405949 | 85405949 | Nonsense_Mutation | C | T | p.R1607* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ALPK3 |
| 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 ALPK3 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ALPK3 |
Top |
RelatedDrugs for ALPK3 |
| 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 ALPK3 |
| 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)
|