|
||||||
|
 | |
| |
| |
| |
| 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 CYP39A1 |
 Gene summary |
| Gene information | Gene symbol | CYP39A1 | Gene ID | 51302 |
| Gene name | cytochrome P450 family 39 subfamily A member 1 | |
| Synonyms | - | |
| Cytomap | 6p12.3 | |
| Type of gene | protein-coding | |
| Description | 24-hydroxycholesterol 7-alpha-hydroxylasecytochrome P450, family 39, subfamily A, polypeptide 1cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9NYL5 | |
| Context | PubMed: CYP39A1 [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 |
| CYP39A1 | GO:0006699 | bile acid biosynthetic process | 10748047 |
Top |
Exon skipping events across known transcript of Ensembl for CYP39A1 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 CYP39A1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CYP39A1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_459936 | 6 | 46554813:46554902:46555770:46555866:46563723:46563857 | 46555770:46555866 | ENSG00000146233.3 | ENST00000275016.2 |
| exon_skip_459939 | 6 | 46555839:46555866:46563723:46563857:46593154:46593245 | 46563723:46563857 | ENSG00000146233.3 | ENST00000275016.2,ENST00000480804.1 |
| exon_skip_459942 | 6 | 46563723:46563857:46593154:46593245:46598699:46598807 | 46593154:46593245 | ENSG00000146233.3 | ENST00000275016.2 |
| exon_skip_459943 | 6 | 46593154:46593245:46598699:46598807:46604125:46604219 | 46598699:46598807 | ENSG00000146233.3 | ENST00000275016.2 |
| exon_skip_459946 | 6 | 46605565:46605715:46607230:46607405:46609899:46610035 | 46607230:46607405 | ENSG00000146233.3 | ENST00000275016.2 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CYP39A1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_459936 | 6 | 46554813:46554902:46555770:46555866:46563723:46563857 | 46555770:46555866 | ENSG00000146233.3 | ENST00000275016.2 |
| exon_skip_459939 | 6 | 46555839:46555866:46563723:46563857:46593154:46593245 | 46563723:46563857 | ENSG00000146233.3 | ENST00000275016.2,ENST00000480804.1 |
| exon_skip_459942 | 6 | 46563723:46563857:46593154:46593245:46598699:46598807 | 46593154:46593245 | ENSG00000146233.3 | ENST00000275016.2 |
| exon_skip_459943 | 6 | 46593154:46593245:46598699:46598807:46604125:46604219 | 46598699:46598807 | ENSG00000146233.3 | ENST00000275016.2 |
| exon_skip_459946 | 6 | 46605565:46605715:46607230:46607405:46609899:46610035 | 46607230:46607405 | ENSG00000146233.3 | ENST00000275016.2 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CYP39A1 |
| 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 |
| ENST00000275016 | 46563723 | 46563857 | Frame-shift |
| ENST00000275016 | 46593154 | 46593245 | Frame-shift |
| ENST00000275016 | 46607230 | 46607405 | Frame-shift |
| ENST00000275016 | 46555770 | 46555866 | In-frame |
| ENST00000275016 | 46598699 | 46598807 | 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 |
| ENST00000275016 | 46563723 | 46563857 | Frame-shift |
| ENST00000275016 | 46593154 | 46593245 | Frame-shift |
| ENST00000275016 | 46607230 | 46607405 | Frame-shift |
| ENST00000275016 | 46555770 | 46555866 | In-frame |
| ENST00000275016 | 46598699 | 46598807 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for CYP39A1 |
| 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 |
| ENST00000275016 | 2193 | 469 | 46598699 | 46598807 | 937 | 1044 | 244 | 280 |
| ENST00000275016 | 2193 | 469 | 46555770 | 46555866 | 1270 | 1365 | 355 | 387 |
| 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 |
| ENST00000275016 | 2193 | 469 | 46598699 | 46598807 | 937 | 1044 | 244 | 280 |
| ENST00000275016 | 2193 | 469 | 46555770 | 46555866 | 1270 | 1365 | 355 | 387 |
| 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 |
| Q9NYL5 | 244 | 280 | 1 | 469 | Chain | ID=PRO_0000051992;Note=24-hydroxycholesterol 7-alpha-hydroxylase |
| Q9NYL5 | 355 | 387 | 1 | 469 | Chain | ID=PRO_0000051992;Note=24-hydroxycholesterol 7-alpha-hydroxylase |
| 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 |
| Q9NYL5 | 244 | 280 | 1 | 469 | Chain | ID=PRO_0000051992;Note=24-hydroxycholesterol 7-alpha-hydroxylase |
| Q9NYL5 | 355 | 387 | 1 | 469 | Chain | ID=PRO_0000051992;Note=24-hydroxycholesterol 7-alpha-hydroxylase |
Top |
SNVs in the skipped exons for CYP39A1 |
| - 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_459936 | 46555771 | 46555866 | 46555795 | 46555795 | Frame_Shift_Del | A | - | p.F379fs |
| LUAD | TCGA-17-Z042-01 | exon_skip_459946 | 46607231 | 46607405 | 46607308 | 46607308 | Frame_Shift_Del | C | - | p.G137fs |
| STAD | TCGA-CG-5721-01 | exon_skip_459946 | 46607231 | 46607405 | 46607340 | 46607340 | Frame_Shift_Del | T | - | p.M127fs |
| BLCA | TCGA-DK-A3IQ-01 | exon_skip_459946 | 46607231 | 46607405 | 46607286 | 46607286 | Nonsense_Mutation | C | A | p.E145* |
| - 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 |
| NCIH1770_LUNG | 46555771 | 46555866 | 46555794 | 46555794 | Missense_Mutation | G | A | p.P380S |
| NCIH2106_LUNG | 46555771 | 46555866 | 46555794 | 46555794 | Missense_Mutation | G | A | p.P380S |
| HT115_LARGE_INTESTINE | 46563724 | 46563857 | 46563743 | 46563743 | Missense_Mutation | A | G | p.V349A |
| A431_SKIN | 46563724 | 46563857 | 46563810 | 46563810 | Missense_Mutation | G | C | p.L327V |
| RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46563724 | 46563857 | 46563816 | 46563816 | Missense_Mutation | G | T | p.L325I |
| L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 46598700 | 46598807 | 46598731 | 46598731 | Missense_Mutation | A | G | p.L270P |
| HEC251_ENDOMETRIUM | 46607231 | 46607405 | 46607288 | 46607288 | Missense_Mutation | T | C | p.H144R |
| A549_LUNG | 46607231 | 46607405 | 46607353 | 46607353 | Missense_Mutation | C | A | p.M122I |
| HCC15_LUNG | 46607231 | 46607405 | 46607380 | 46607380 | Missense_Mutation | T | A | p.L113F |
| ESO51_OESOPHAGUS | 46563724 | 46563857 | 46563843 | 46563843 | Nonsense_Mutation | T | A | p.K316* |
| HEC251_ENDOMETRIUM | 46607231 | 46607405 | 46607295 | 46607295 | Nonsense_Mutation | C | A | p.E142* |
| OE21_OESOPHAGUS | 46607231 | 46607405 | 46607319 | 46607319 | Nonsense_Mutation | G | A | p.Q134* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CYP39A1 |
| 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 CYP39A1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CYP39A1 |
Top |
RelatedDrugs for CYP39A1 |
| 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 CYP39A1 |
| 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)
|