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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for RSPH4A |
 Gene summary |
| Gene information | Gene symbol | RSPH4A | Gene ID | 345895 |
| Gene name | radial spoke head 4 homolog A | |
| Synonyms | CILD11|RSHL3|RSPH6B|dJ412I7.1 | |
| Cytomap | 6q22.1 | |
| Type of gene | protein-coding | |
| Description | radial spoke head protein 4 homolog Aradial spoke head-like protein 3radial spokehead-like 3 | |
| Modification date | 20180329 | |
| UniProtAcc | Q5TD94 | |
| Context | PubMed: RSPH4A [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 |
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Exon skipping events across known transcript of Ensembl for RSPH4A 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. |
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Gene isoform structures and expression levels for RSPH4A |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for RSPH4A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_453893 | 6 | 116943930:116944165:116948791:116949532:116950729:116950825 | 116948791:116949532 | ENSG00000111834.8 | ENST00000229554.5 |
| exon_skip_453897 | 6 | 116948791:116949532:116950729:116950865:116951597:116951715 | 116950729:116950865 | ENSG00000111834.8 | ENST00000229554.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RSPH4A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_453897 | 6 | 116948791:116949532:116950729:116950865:116951597:116951715 | 116950729:116950865 | ENSG00000111834.8 | ENST00000229554.5 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for RSPH4A |
| 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 |
| ENST00000229554 | 116950729 | 116950865 | Frame-shift |
| ENST00000229554 | 116948791 | 116949532 | 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 |
| ENST00000229554 | 116950729 | 116950865 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for RSPH4A |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
| ENST00000229554 | 2842 | 716 | 116948791 | 116949532 | 1059 | 1799 | 307 | 554 |
| 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 |
| Q5TD94 | 307 | 554 | 308 | 554 | Alternative sequence | ID=VSP_030125;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5TD94 | 307 | 554 | 1 | 716 | Chain | ID=PRO_0000313738;Note=Radial spoke head protein 4 homolog A |
| Q5TD94 | 307 | 554 | 370 | 405 | Compositional bias | Note=Glu-rich |
| Q5TD94 | 307 | 554 | 507 | 586 | Compositional bias | Note=Glu-rich |
| Q5TD94 | 307 | 554 | 396 | 396 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BYM7 |
| Q5TD94 | 307 | 554 | 464 | 464 | Natural variant | ID=VAR_070565;Note=In CILD11%3B unknown pathological significance. G->E;Dbxref=dbSNP:rs753041231 |
| 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 |
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SNVs in the skipped exons for RSPH4A |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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-A39Y-01 | exon_skip_453893 | 116948792 | 116949532 | 116949374 | 116949374 | Frame_Shift_Del | T | - | p.F502fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_453893 | 116948792 | 116949532 | 116949495 | 116949495 | Frame_Shift_Del | C | - | p.S542fs |
| BLCA | TCGA-CF-A9FM-01 | exon_skip_453897 | 116950730 | 116950865 | 116950757 | 116950758 | Frame_Shift_Ins | - | A | p.Q564fs |
| STAD | TCGA-BR-4363-01 | exon_skip_453893 | 116948792 | 116949532 | 116949263 | 116949263 | Nonsense_Mutation | C | T | p.R465* |
| STAD | TCGA-BR-4363-01 | exon_skip_453893 | 116948792 | 116949532 | 116949263 | 116949263 | Nonsense_Mutation | C | T | p.R465X |
| LGG | TCGA-DU-6392-01 | exon_skip_453893 | 116948792 | 116949532 | 116949302 | 116949302 | Nonsense_Mutation | G | T | p.G478* |
| STAD | TCGA-CD-A4MG-01 | exon_skip_453893 | 116948792 | 116949532 | 116949323 | 116949323 | Nonsense_Mutation | C | T | p.R485* |
| STAD | TCGA-CD-A4MG-01 | exon_skip_453893 | 116948792 | 116949532 | 116949323 | 116949323 | Nonsense_Mutation | C | T | p.R485X |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_453893 | 116948792 | 116949532 | 116949323 | 116949323 | Nonsense_Mutation | C | T | p.R485* |
| READ | TCGA-AG-A002-01 | exon_skip_453893 | 116948792 | 116949532 | 116949371 | 116949371 | Nonsense_Mutation | G | T | p.G501X |
| UCS | TCGA-ND-A4WC-01 | exon_skip_453893 | 116948792 | 116949532 | 116949485 | 116949485 | Nonsense_Mutation | G | T | p.E539* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_453893 | 116948792 | 116949532 | 116949485 | 116949485 | Nonsense_Mutation | G | T | p.E539X |
| ESCA | TCGA-XP-A8T6-01 | exon_skip_453893 | 116948792 | 116949532 | 116948791 | 116948791 | Splice_Site | G | T | . |
| ESCA | TCGA-XP-A8T6-01 | exon_skip_453893 | 116948792 | 116949532 | 116948791 | 116948791 | Splice_Site | G | T | e3-1 |
| - 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 |
| HEC108_ENDOMETRIUM | 116950730 | 116950865 | 116950758 | 116950758 | Frame_Shift_Del | A | - | p.Q564fs |
| SNUC4_LARGE_INTESTINE | 116950730 | 116950865 | 116950758 | 116950758 | Frame_Shift_Del | A | - | p.Q564fs |
| TOV21G_OVARY | 116950730 | 116950865 | 116950758 | 116950758 | Frame_Shift_Del | A | - | p.Q564fs |
| LS411N_LARGE_INTESTINE | 116950730 | 116950865 | 116950758 | 116950758 | Frame_Shift_Del | A | - | p.Q564fs |
| KMOE2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 116950730 | 116950865 | 116950828 | 116950828 | Frame_Shift_Del | G | - | p.V587fs |
| HEC6_ENDOMETRIUM | 116950730 | 116950865 | 116950757 | 116950758 | Frame_Shift_Ins | - | A | p.Q564fs |
| SNUC2A_LARGE_INTESTINE | 116950730 | 116950865 | 116950757 | 116950758 | Frame_Shift_Ins | - | A | p.Q564fs |
| SNUC2B_LARGE_INTESTINE | 116950730 | 116950865 | 116950757 | 116950758 | Frame_Shift_Ins | - | A | p.Q564fs |
| 253J_URINARY_TRACT | 116948792 | 116949532 | 116948930 | 116948930 | Missense_Mutation | C | T | p.R354C |
| 253JBV_URINARY_TRACT | 116948792 | 116949532 | 116948930 | 116948930 | Missense_Mutation | C | T | p.R354C |
| SNUC2B_LARGE_INTESTINE | 116948792 | 116949532 | 116948930 | 116948930 | Missense_Mutation | C | T | p.R354C |
| JHUEM7_ENDOMETRIUM | 116948792 | 116949532 | 116948967 | 116948967 | Missense_Mutation | A | T | p.Y366F |
| NCIH650_LUNG | 116948792 | 116949532 | 116949030 | 116949030 | Missense_Mutation | T | A | p.V387E |
| GP5D_LARGE_INTESTINE | 116948792 | 116949532 | 116949036 | 116949036 | Missense_Mutation | A | C | p.E389A |
| KNS42_CENTRAL_NERVOUS_SYSTEM | 116948792 | 116949532 | 116949191 | 116949191 | Missense_Mutation | T | A | p.W441R |
| SIMA_AUTONOMIC_GANGLIA | 116948792 | 116949532 | 116949204 | 116949204 | Missense_Mutation | C | T | p.P445L |
| SNU1041_UPPER_AERODIGESTIVE_TRACT | 116948792 | 116949532 | 116949250 | 116949250 | Missense_Mutation | A | C | p.K460N |
| HKA1_SKIN | 116948792 | 116949532 | 116949276 | 116949276 | Missense_Mutation | C | T | p.P469L |
| HCC4006_LUNG | 116948792 | 116949532 | 116949282 | 116949282 | Missense_Mutation | T | C | p.I471T |
| EW16_BONE | 116948792 | 116949532 | 116949306 | 116949306 | Missense_Mutation | A | G | p.N479S |
| MELHO_SKIN | 116948792 | 116949532 | 116949306 | 116949306 | Missense_Mutation | A | G | p.N479S |
| PC9_LUNG | 116948792 | 116949532 | 116949421 | 116949421 | Missense_Mutation | A | C | p.E517D |
| PC14_LUNG | 116948792 | 116949532 | 116949421 | 116949421 | Missense_Mutation | A | C | p.E517D |
| MDAMB361_BREAST | 116948792 | 116949532 | 116949498 | 116949498 | Missense_Mutation | A | G | p.N543S |
| UMUC5_URINARY_TRACT | 116948792 | 116949532 | 116949511 | 116949511 | Missense_Mutation | T | G | p.H547Q |
| TT_THYROID | 116950730 | 116950865 | 116950767 | 116950767 | Missense_Mutation | A | G | p.E567G |
| ISTMEL1_SKIN | 116950730 | 116950865 | 116950817 | 116950817 | Missense_Mutation | G | A | p.E584K |
| CL34_LARGE_INTESTINE | 116948792 | 116949532 | 116949263 | 116949263 | Nonsense_Mutation | C | T | p.R465* |
| LNCAPCLONEFGC_PROSTATE | 116948792 | 116949532 | 116949323 | 116949323 | Nonsense_Mutation | C | T | p.R485* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RSPH4A |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RSPH4A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RSPH4A |
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RelatedDrugs for RSPH4A |
| 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 |
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RelatedDiseases for RSPH4A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RSPH4A | C2675229 | CILIARY DYSKINESIA, PRIMARY, 11 | 1 | CTD_human;UNIPROT |
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