|
||||||
|
 | |
| |
| |
| |
| 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 RSPH1 |
 Gene summary |
| Gene information | Gene symbol | RSPH1 | Gene ID | 89765 |
| Gene name | radial spoke head 1 homolog | |
| Synonyms | CT79|RSP44|RSPH10A|TSA2|TSGA2 | |
| Cytomap | 21q22.3 | |
| Type of gene | protein-coding | |
| Description | radial spoke head 1 homologcancer/testis antigen 79male meiotic metaphase chromosome-associated acidic proteinmeichroacidintestes specific gene A2 homologtestis specific A2 homolog | |
| Modification date | 20180519 | |
| UniProtAcc | Q8WYR4 | |
| Context | PubMed: RSPH1 [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 RSPH1 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 RSPH1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for RSPH1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_362321 | 21 | 43896007:43896157:43897400:43897554:43902746:43902818 | 43897400:43897554 | ENSG00000160188.5 | ENST00000493019.1,ENST00000291536.3,ENST00000398352.3 |
| exon_skip_362332 | 21 | 43897400:43897554:43902746:43902818:43905778:43905914 | 43902746:43902818 | ENSG00000160188.5 | ENST00000291536.3,ENST00000398352.3 |
| exon_skip_362335 | 21 | 43902746:43902818:43905778:43905914:43906480:43906571 | 43905778:43905914 | ENSG00000160188.5 | ENST00000291536.3,ENST00000398352.3 |
| exon_skip_362339 | 21 | 43906480:43906571:43912867:43912973:43916242:43916296 | 43912867:43912973 | ENSG00000160188.5 | ENST00000398352.3 |
| exon_skip_362341 | 21 | 43912867:43912973:43913075:43913189:43916242:43916296 | 43913075:43913189 | ENSG00000160188.5 | ENST00000291536.3 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for RSPH1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_362321 | 21 | 43896007:43896157:43897400:43897554:43902746:43902818 | 43897400:43897554 | ENSG00000160188.5 | ENST00000493019.1,ENST00000291536.3,ENST00000398352.3 |
| exon_skip_362332 | 21 | 43897400:43897554:43902746:43902818:43905778:43905914 | 43902746:43902818 | ENSG00000160188.5 | ENST00000291536.3,ENST00000398352.3 |
| exon_skip_362335 | 21 | 43902746:43902818:43905778:43905914:43906480:43906571 | 43905778:43905914 | ENSG00000160188.5 | ENST00000291536.3,ENST00000398352.3 |
| exon_skip_362339 | 21 | 43906480:43906571:43912867:43912973:43916242:43916296 | 43912867:43912973 | ENSG00000160188.5 | ENST00000398352.3 |
| exon_skip_362341 | 21 | 43912867:43912973:43913075:43913189:43916242:43916296 | 43913075:43913189 | ENSG00000160188.5 | ENST00000291536.3 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for RSPH1 |
| 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 |
| ENST00000291536 | 43897400 | 43897554 | Frame-shift |
| ENST00000291536 | 43905778 | 43905914 | Frame-shift |
| ENST00000291536 | 43902746 | 43902818 | In-frame |
| ENST00000291536 | 43913075 | 43913189 | 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 |
| ENST00000291536 | 43897400 | 43897554 | Frame-shift |
| ENST00000291536 | 43905778 | 43905914 | Frame-shift |
| ENST00000291536 | 43902746 | 43902818 | In-frame |
| ENST00000291536 | 43913075 | 43913189 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for RSPH1 |
| 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 |
| ENST00000291536 | 1447 | 309 | 43913075 | 43913189 | 223 | 336 | 18 | 56 |
| ENST00000291536 | 1447 | 309 | 43902746 | 43902818 | 670 | 741 | 167 | 191 |
| 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 |
| ENST00000291536 | 1447 | 309 | 43913075 | 43913189 | 223 | 336 | 18 | 56 |
| ENST00000291536 | 1447 | 309 | 43902746 | 43902818 | 670 | 741 | 167 | 191 |
| 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 |
| Q8WYR4 | 18 | 56 | 19 | 56 | Alternative sequence | ID=VSP_055743;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8WYR4 | 18 | 56 | 1 | 309 | Chain | ID=PRO_0000065662;Note=Radial spoke head 1 homolog |
| Q8WYR4 | 18 | 56 | 20 | 43 | Repeat | Note=MORN 1 |
| Q8WYR4 | 18 | 56 | 44 | 66 | Repeat | Note=MORN 2 |
| Q8WYR4 | 167 | 191 | 1 | 309 | Chain | ID=PRO_0000065662;Note=Radial spoke head 1 homolog |
| Q8WYR4 | 167 | 191 | 159 | 181 | Repeat | Note=MORN 6 |
| 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 |
| Q8WYR4 | 18 | 56 | 19 | 56 | Alternative sequence | ID=VSP_055743;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8WYR4 | 18 | 56 | 1 | 309 | Chain | ID=PRO_0000065662;Note=Radial spoke head 1 homolog |
| Q8WYR4 | 18 | 56 | 20 | 43 | Repeat | Note=MORN 1 |
| Q8WYR4 | 18 | 56 | 44 | 66 | Repeat | Note=MORN 2 |
| Q8WYR4 | 167 | 191 | 1 | 309 | Chain | ID=PRO_0000065662;Note=Radial spoke head 1 homolog |
| Q8WYR4 | 167 | 191 | 159 | 181 | Repeat | Note=MORN 6 |
Top |
SNVs in the skipped exons for RSPH1 |
| - 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_362321 | 43897401 | 43897554 | 43897504 | 43897504 | Frame_Shift_Del | T | - | p.K208fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_362335 | 43905779 | 43905914 | 43905780 | 43905780 | Frame_Shift_Del | T | - | p.N167fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_362339 | 43912868 | 43912973 | 43912954 | 43912954 | Frame_Shift_Del | T | - | p.N63fs |
| LUSC | TCGA-66-2795-01 | exon_skip_362341 | 43913076 | 43913189 | 43913095 | 43913095 | Frame_Shift_Del | A | - | p.F50fs |
| COAD | TCGA-AD-5900-01 | exon_skip_362341 | 43913076 | 43913189 | 43913176 | 43913176 | Frame_Shift_Del | C | - | p.G23fs |
| LUAD | TCGA-44-2656-01 | exon_skip_362341 | 43913076 | 43913189 | 43913175 | 43913176 | Frame_Shift_Ins | - | C | p.G23fs |
| SKCM | TCGA-FS-A4F5-06 | exon_skip_362321 | 43897401 | 43897554 | 43897468 | 43897468 | Nonsense_Mutation | C | T | p.W220* |
| SKCM | TCGA-FS-A4F5-06 | exon_skip_362321 | 43897401 | 43897554 | 43897468 | 43897468 | Nonsense_Mutation | C | T | p.W220X |
| - 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 |
| HEC151_ENDOMETRIUM | 43897401 | 43897554 | 43897452 | 43897453 | Frame_Shift_Ins | - | G | p.K226fs |
| MIAPACA2_PANCREAS | 43902747 | 43902818 | 43902769 | 43902769 | Missense_Mutation | C | G | p.G184A |
| YMB1E_BREAST | 43905779 | 43905914 | 43905785 | 43905785 | Missense_Mutation | G | T | p.N165K |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43905779 | 43905914 | 43905861 | 43905861 | Missense_Mutation | G | A | p.T140I |
| NUGC3_STOMACH | 43905779 | 43905914 | 43905864 | 43905864 | Missense_Mutation | C | T | p.G139D |
| ES1_BONE | 43905779 | 43905914 | 43905888 | 43905888 | Missense_Mutation | G | A | p.A131V |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43905779 | 43905914 | 43905889 | 43905889 | Missense_Mutation | C | T | p.A131T |
| PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43912868 | 43912973 | 43912945 | 43912945 | Missense_Mutation | C | T | p.R66Q |
| KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43912868 | 43912973 | 43912968 | 43912968 | Missense_Mutation | G | C | p.I58M |
| GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43913076 | 43913189 | 43913094 | 43913094 | Missense_Mutation | G | T | p.F50L |
| HCC2998_LARGE_INTESTINE | 43913076 | 43913189 | 43913099 | 43913099 | Missense_Mutation | C | T | p.E49K |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RSPH1 |
| 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 RSPH1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RSPH1 |
Top |
RelatedDrugs for RSPH1 |
| 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 RSPH1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RSPH1 | C3809634 | CILIARY DYSKINESIA, PRIMARY, 24 | 1 | UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|