|
||||||
|
 | |
| |
| |
| |
| 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 ABCF1 |
 Gene summary |
| Gene information | Gene symbol | ABCF1 | Gene ID | 23 |
| Gene name | ATP binding cassette subfamily F member 1 | |
| Synonyms | ABC27|ABC50 | |
| Cytomap | 6p21.33 | |
| Type of gene | protein-coding | |
| Description | ATP-binding cassette sub-family F member 1ATP-binding cassette 50 (TNF-alpha stimulated)ATP-binding cassette, sub-family F (GCN20), member 1TNF-alpha-stimulated ABC proteinTNFalpha-inducible ATP-binding protein | |
| Modification date | 20180519 | |
| UniProtAcc | Q8NE71 | |
| Context | PubMed: ABCF1 [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 ABCF1 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 ABCF1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for ABCF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_449294 | 6 | 30539218:30539337:30545185:30545232:30545594:30545690 | 30545185:30545232 | ENSG00000204574.8 | ENST00000441867.1,ENST00000396515.4,ENST00000376545.3 |
| exon_skip_449299 | 6 | 30546124:30546162:30546246:30546354:30547707:30547782 | 30546246:30546354 | ENSG00000204574.8 | ENST00000468958.1,ENST00000441867.1,ENST00000376545.3,ENST00000326195.8 |
| exon_skip_449302 | 6 | 30546246:30546354:30547707:30547782:30548182:30548225 | 30547707:30547782 | ENSG00000204574.8 | ENST00000468958.1,ENST00000441867.1,ENST00000376545.3,ENST00000326195.8 |
| exon_skip_449303 | 6 | 30547707:30547782:30548182:30548296:30550170:30550284 | 30548182:30548296 | ENSG00000204574.8 | ENST00000441867.1,ENST00000326195.8 |
| exon_skip_449304 | 6 | 30547707:30547782:30548182:30548296:30550842:30550965 | 30548182:30548296 | ENSG00000204574.8 | ENST00000376545.3 |
| exon_skip_449307 | 6 | 30548182:30548296:30550170:30550284:30550842:30550965 | 30550170:30550284 | ENSG00000204574.8 | ENST00000441867.1,ENST00000326195.8 |
| exon_skip_449309 | 6 | 30551581:30551667:30551968:30552108:30552194:30552343 | 30551968:30552108 | ENSG00000204574.8 | ENST00000475993.1,ENST00000376545.3,ENST00000326195.8 |
| exon_skip_449313 | 6 | 30557925:30557990:30558082:30558155:30558311:30558520 | 30558082:30558155 | ENSG00000204574.8 | ENST00000479542.1,ENST00000396515.4,ENST00000475993.1,ENST00000376545.3,ENST00000326195.8 |
| exon_skip_449316 | 6 | 30558082:30558155:30558311:30558938:30564345:30564956 | 30558311:30558938 | ENSG00000204574.8 | ENST00000475993.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for ABCF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_449294 | 6 | 30539218:30539337:30545185:30545232:30545594:30545690 | 30545185:30545232 | ENSG00000204574.8 | ENST00000376545.3,ENST00000396515.4,ENST00000441867.1 |
| exon_skip_449299 | 6 | 30546124:30546162:30546246:30546354:30547707:30547782 | 30546246:30546354 | ENSG00000204574.8 | ENST00000326195.8,ENST00000376545.3,ENST00000441867.1,ENST00000468958.1 |
| exon_skip_449302 | 6 | 30546246:30546354:30547707:30547782:30548182:30548225 | 30547707:30547782 | ENSG00000204574.8 | ENST00000326195.8,ENST00000376545.3,ENST00000441867.1,ENST00000468958.1 |
| exon_skip_449303 | 6 | 30547707:30547782:30548182:30548296:30550170:30550284 | 30548182:30548296 | ENSG00000204574.8 | ENST00000326195.8,ENST00000441867.1 |
| exon_skip_449307 | 6 | 30548182:30548296:30550170:30550284:30550842:30550965 | 30550170:30550284 | ENSG00000204574.8 | ENST00000326195.8,ENST00000441867.1 |
| exon_skip_449309 | 6 | 30551581:30551667:30551968:30552108:30552194:30552343 | 30551968:30552108 | ENSG00000204574.8 | ENST00000326195.8,ENST00000376545.3,ENST00000475993.1 |
| exon_skip_449313 | 6 | 30557925:30557990:30558082:30558155:30558311:30558520 | 30558082:30558155 | ENSG00000204574.8 | ENST00000326195.8,ENST00000376545.3,ENST00000396515.4,ENST00000475993.1,ENST00000479542.1 |
| exon_skip_449316 | 6 | 30558082:30558155:30558311:30558938:30564345:30564956 | 30558311:30558938 | ENSG00000204574.8 | ENST00000475993.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for ABCF1 |
| 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 |
| 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 |
Top |
Infer the effects of exon skipping event on protein functional features for ABCF1 |
| 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 |
| 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 |
| 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 |
Top |
SNVs in the skipped exons for ABCF1 |
| - 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-G3-A3CJ-01 | exon_skip_449294 | 30545186 | 30545232 | 30545224 | 30545224 | Frame_Shift_Del | A | - | p.K39fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_449307 | 30550171 | 30550284 | 30550237 | 30550237 | Frame_Shift_Del | C | - | p.P249fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_449309 | 30551969 | 30552108 | 30552060 | 30552060 | Frame_Shift_Del | G | - | p.Q398fs |
| GBM | TCGA-06-0648-01 | exon_skip_449309 | 30551969 | 30552108 | 30552069 | 30552069 | Frame_Shift_Del | G | - | p.L401fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_449309 | 30551969 | 30552108 | 30552076 | 30552076 | Frame_Shift_Del | G | - | p.G404fs |
| PRAD | TCGA-J9-A52C-01 | exon_skip_449307 | 30550171 | 30550284 | 30550275 | 30550276 | Frame_Shift_Ins | - | A | p.L261fs |
| PRAD | TCGA-J9-A52C-01 | exon_skip_449307 | 30550171 | 30550284 | 30550275 | 30550276 | Frame_Shift_Ins | - | A | p.LK261fs |
| HNSC | TCGA-CV-7097-01 | exon_skip_449309 | 30551969 | 30552108 | 30551996 | 30551997 | Frame_Shift_Ins | - | C | p.A377fs |
| HNSC | TCGA-CV-7097-01 | exon_skip_449309 | 30551969 | 30552108 | 30551996 | 30551997 | Frame_Shift_Ins | - | C | p.V377fs |
| SKCM | TCGA-BF-A5EO-01 | exon_skip_449316 | 30558312 | 30558938 | 30558470 | 30558470 | Nonsense_Mutation | C | T | p.R844* |
| SKCM | TCGA-BF-A5EO-01 | exon_skip_449316 | 30558312 | 30558938 | 30558470 | 30558470 | Nonsense_Mutation | C | T | p.R844X |
| SKCM | TCGA-EB-A3XC-01 | exon_skip_449316 | 30558312 | 30558938 | 30558470 | 30558470 | Nonsense_Mutation | C | T | p.R844* |
| SKCM | TCGA-EB-A3XC-01 | exon_skip_449316 | 30558312 | 30558938 | 30558470 | 30558470 | Nonsense_Mutation | C | T | p.R844X |
| - 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 |
| SNU324_PANCREAS | 30545186 | 30545232 | 30545224 | 30545224 | Frame_Shift_Del | A | - | p.K39fs |
| SNU407_LARGE_INTESTINE | 30545186 | 30545232 | 30545224 | 30545224 | Frame_Shift_Del | A | - | p.K39fs |
| 639V_URINARY_TRACT | 30545186 | 30545232 | 30545224 | 30545224 | Frame_Shift_Del | A | - | p.K39fs |
| EN_ENDOMETRIUM | 30545186 | 30545232 | 30545224 | 30545224 | Frame_Shift_Del | A | - | p.K39fs |
| LS411N_LARGE_INTESTINE | 30546247 | 30546354 | 30546268 | 30546268 | Missense_Mutation | C | A | p.L135M |
| M1203273_SKIN | 30546247 | 30546354 | 30546325 | 30546325 | Missense_Mutation | G | A | p.A154T |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30547708 | 30547782 | 30547711 | 30547711 | Missense_Mutation | G | A | p.V165I |
| HSC3_UPPER_AERODIGESTIVE_TRACT | 30550171 | 30550284 | 30550204 | 30550204 | Missense_Mutation | G | A | p.E238K |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30551969 | 30552108 | 30552024 | 30552024 | Missense_Mutation | G | C | p.K386N |
| LNCAPCLONEFGC_PROSTATE | 30558083 | 30558155 | 30558099 | 30558099 | Missense_Mutation | A | G | p.N772S |
| CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30558083 | 30558155 | 30558107 | 30558107 | Missense_Mutation | A | G | p.I775V |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30558312 | 30558938 | 30558327 | 30558327 | Missense_Mutation | G | A | p.S796N |
| JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30558312 | 30558938 | 30558351 | 30558351 | Missense_Mutation | A | G | p.E804G |
| OVISE_OVARY | 30558312 | 30558938 | 30558368 | 30558368 | Missense_Mutation | T | C | p.W810R |
| HCC2450_LUNG | 30558312 | 30558938 | 30558385 | 30558385 | Missense_Mutation | G | C | p.Q815H |
| RL952_ENDOMETRIUM | 30558312 | 30558938 | 30558423 | 30558423 | Missense_Mutation | A | T | p.K828M |
| KIJK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30558312 | 30558938 | 30558440 | 30558440 | Missense_Mutation | G | A | p.A834T |
| SW872_SOFT_TISSUE | 30558312 | 30558938 | 30558464 | 30558464 | Missense_Mutation | C | T | p.R842W |
| SNU1040_LARGE_INTESTINE | 30548183 | 30548296 | 30548294 | 30548294 | Nonsense_Mutation | C | T | p.Q226* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ABCF1 |
| 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 ABCF1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ABCF1 |
Top |
RelatedDrugs for ABCF1 |
| 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 ABCF1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ABCF1 | C0020517 | Hypersensitivity | 1 | CTD_human |
| ABCF1 | C0032285 | Pneumonia | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|