|
||||||
|
 | |
| |
| |
| |
| 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 RNFT2 |
 Gene summary |
| Gene information | Gene symbol | RNFT2 | Gene ID | 84900 |
| Gene name | ring finger protein, transmembrane 2 | |
| Synonyms | TMEM118 | |
| Cytomap | 12q24.22 | |
| Type of gene | protein-coding | |
| Description | RING finger and transmembrane domain-containing protein 2transmembrane protein 118 | |
| Modification date | 20180329 | |
| UniProtAcc | Q96EX2 | |
| Context | PubMed: RNFT2 [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 RNFT2 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 RNFT2 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for RNFT2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_87453 | 12 | 117178840:117178899:117186466:117186549:117187645:117188112 | 117186466:117186549 | ENSG00000135119.10 | ENST00000547718.1 |
| exon_skip_87454 | 12 | 117178840:117178899:117187645:117188112:117191788:117191865 | 117187645:117188112 | ENSG00000135119.10 | ENST00000319176.7,ENST00000407967.3,ENST00000392549.2,ENST00000257575.4 |
| exon_skip_87456 | 12 | 117271596:117271746:117273764:117273830:117273985:117274087 | 117273764:117273830 | ENSG00000135119.10 | ENST00000407967.3,ENST00000547718.1,ENST00000392549.2,ENST00000257575.4 |
| exon_skip_87458 | 12 | 117273985:117274087:117287118:117287289:117290142:117290509 | 117287118:117287289 | ENSG00000135119.10 | ENST00000392549.2 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for RNFT2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_87453 | 12 | 117178840:117178899:117186466:117186549:117187645:117188112 | 117186466:117186549 | ENSG00000135119.10 | ENST00000547718.1 |
| exon_skip_87454 | 12 | 117178840:117178899:117187645:117188112:117191788:117191865 | 117187645:117188112 | ENSG00000135119.10 | ENST00000257575.4,ENST00000407967.3,ENST00000392549.2,ENST00000319176.7 |
| exon_skip_87456 | 12 | 117271596:117271746:117273764:117273830:117273985:117274087 | 117273764:117273830 | ENSG00000135119.10 | ENST00000257575.4,ENST00000407967.3,ENST00000392549.2,ENST00000547718.1 |
| exon_skip_87458 | 12 | 117273985:117274087:117287118:117287289:117290142:117290509 | 117287118:117287289 | ENSG00000135119.10 | ENST00000392549.2 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for RNFT2 |
| 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 |
| ENST00000392549 | 117287118 | 117287289 | 3UTR-3CDS |
| ENST00000257575 | 117187645 | 117188112 | Frame-shift |
| ENST00000392549 | 117187645 | 117188112 | Frame-shift |
| ENST00000257575 | 117273764 | 117273830 | In-frame |
| ENST00000392549 | 117273764 | 117273830 | 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 |
| ENST00000392549 | 117287118 | 117287289 | 3UTR-3CDS |
| ENST00000257575 | 117187645 | 117188112 | Frame-shift |
| ENST00000392549 | 117187645 | 117188112 | Frame-shift |
| ENST00000257575 | 117273764 | 117273830 | In-frame |
| ENST00000392549 | 117273764 | 117273830 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for RNFT2 |
| 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 |
| ENST00000257575 | 3899 | 444 | 117273764 | 117273830 | 1266 | 1331 | 344 | 366 |
| ENST00000392549 | 2913 | 444 | 117273764 | 117273830 | 1266 | 1331 | 344 | 366 |
| 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 |
| ENST00000257575 | 3899 | 444 | 117273764 | 117273830 | 1266 | 1331 | 344 | 366 |
| ENST00000392549 | 2913 | 444 | 117273764 | 117273830 | 1266 | 1331 | 344 | 366 |
| 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 |
| Q96EX2 | 344 | 366 | 322 | 444 | Alternative sequence | ID=VSP_023466;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96EX2 | 344 | 366 | 322 | 444 | Alternative sequence | ID=VSP_023466;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96EX2 | 344 | 366 | 1 | 444 | Chain | ID=PRO_0000279508;Note=RING finger and transmembrane domain-containing protein 2 |
| Q96EX2 | 344 | 366 | 1 | 444 | Chain | ID=PRO_0000279508;Note=RING finger and transmembrane domain-containing protein 2 |
| Q96EX2 | 344 | 366 | 351 | 444 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96EX2 | 344 | 366 | 351 | 444 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96EX2 | 344 | 366 | 330 | 350 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96EX2 | 344 | 366 | 330 | 350 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q96EX2 | 344 | 366 | 322 | 444 | Alternative sequence | ID=VSP_023466;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96EX2 | 344 | 366 | 322 | 444 | Alternative sequence | ID=VSP_023466;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96EX2 | 344 | 366 | 1 | 444 | Chain | ID=PRO_0000279508;Note=RING finger and transmembrane domain-containing protein 2 |
| Q96EX2 | 344 | 366 | 1 | 444 | Chain | ID=PRO_0000279508;Note=RING finger and transmembrane domain-containing protein 2 |
| Q96EX2 | 344 | 366 | 351 | 444 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96EX2 | 344 | 366 | 351 | 444 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96EX2 | 344 | 366 | 330 | 350 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96EX2 | 344 | 366 | 330 | 350 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for RNFT2 |
| - 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 |
| PCPG | TCGA-S7-A7WV-01 | exon_skip_87454 | 117187646 | 117188112 | 117187692 | 117187692 | Frame_Shift_Del | G | - | p.G44fs |
| UCEC | TCGA-AP-A0LT-01 | exon_skip_87454 | 117187646 | 117188112 | 117187871 | 117187871 | Frame_Shift_Del | G | - | p.E103fs |
| - 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 |
| SNU349_KIDNEY | 117187646 | 117188112 | 117187651 | 117187651 | Missense_Mutation | G | A | p.R30H |
| HT29_LARGE_INTESTINE | 117187646 | 117188112 | 117187658 | 117187658 | Missense_Mutation | G | T | p.Q32H |
| FUOV1_OVARY | 117187646 | 117188112 | 117187699 | 117187699 | Missense_Mutation | T | C | p.F46S |
| SNU1040_LARGE_INTESTINE | 117187646 | 117188112 | 117187711 | 117187711 | Missense_Mutation | A | G | p.K50R |
| MFE319_ENDOMETRIUM | 117187646 | 117188112 | 117187813 | 117187813 | Missense_Mutation | G | A | p.G84D |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 117187646 | 117188112 | 117187869 | 117187869 | Missense_Mutation | G | A | p.E103K |
| SNU1076_UPPER_AERODIGESTIVE_TRACT | 117187646 | 117188112 | 117187873 | 117187873 | Missense_Mutation | G | A | p.G104E |
| NCIH1930_LUNG | 117187646 | 117188112 | 117188010 | 117188010 | Missense_Mutation | G | T | p.A150S |
| CW2_LARGE_INTESTINE | 117187646 | 117188112 | 117188041 | 117188041 | Missense_Mutation | T | A | p.I160N |
| JHH7_LIVER | 117187646 | 117188112 | 117188059 | 117188059 | Missense_Mutation | G | T | p.G166V |
| HSC3_UPPER_AERODIGESTIVE_TRACT | 117187646 | 117188112 | 117188073 | 117188073 | Missense_Mutation | C | A | p.L171M |
| HUPT3_PANCREAS | 117187646 | 117188112 | 117188073 | 117188073 | Missense_Mutation | C | A | p.L171M |
| MS1_SKIN | 117187646 | 117188112 | 117188073 | 117188073 | Missense_Mutation | C | A | p.L171M |
| NKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 117187646 | 117188112 | 117188073 | 117188073 | Missense_Mutation | C | A | p.L171M |
| MS1_LUNG | 117187646 | 117188112 | 117188073 | 117188073 | Missense_Mutation | C | A | p.L171M |
| NCIH1341_LUNG | 117273765 | 117273830 | 117273793 | 117273793 | Missense_Mutation | G | C | p.G354A |
| MDAMB453_BREAST | 117287119 | 117287289 | 117287144 | 117287144 | Missense_Mutation | G | T | p.C409F |
| CAL29_URINARY_TRACT | 117287119 | 117287289 | 117287159 | 117287159 | Missense_Mutation | G | A | p.R414H |
| SNU407_LARGE_INTESTINE | 117287119 | 117287289 | 117287206 | 117287206 | Missense_Mutation | C | T | p.R430C |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RNFT2 |
| 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 RNFT2 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RNFT2 |
Top |
RelatedDrugs for RNFT2 |
| 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 RNFT2 |
| 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)
|