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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 TM9SF4 |
 Gene summary |
| Gene information | Gene symbol | TM9SF4 | Gene ID | 9777 |
| Gene name | transmembrane 9 superfamily member 4 | |
| Synonyms | dJ836N17.2 | |
| Cytomap | 20q11.21 | |
| Type of gene | protein-coding | |
| Description | transmembrane 9 superfamily member 4dinucleotide oxidase disulfide thiol exchanger 3 superfamily member 4transmembrane 9 superfamily protein member 4tumor cannibalism associated protein 1 | |
| Modification date | 20180529 | |
| UniProtAcc | Q92544 | |
| Context | PubMed: TM9SF4 [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 |
| TM9SF4 | GO:0001666 | response to hypoxia | 25961573 |
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Exon skipping events across known transcript of Ensembl for TM9SF4 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 TM9SF4 |
| 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 TM9SF4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_350010 | 20 | 30697530:30697558:30720815:30720929:30723876:30723976 | 30720815:30720929 | ENSG00000101337.11 | ENST00000442842.1,ENST00000450829.1 |
| exon_skip_350018 | 20 | 30697569:30697842:30720815:30720929:30723876:30723976 | 30720815:30720929 | ENSG00000101337.11 | ENST00000417389.1,ENST00000217315.5 |
| exon_skip_350021 | 20 | 30720815:30720929:30723876:30723976:30729299:30729468 | 30723876:30723976 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350023 | 20 | 30720815:30720929:30723876:30723976:30729343:30729409 | 30723876:30723976 | ENSG00000101337.11 | ENST00000417389.1 |
| exon_skip_350025 | 20 | 30723876:30723976:30724679:30724800:30729299:30729468 | 30724679:30724800 | ENSG00000101337.11 | ENST00000442842.1 |
| exon_skip_350027 | 20 | 30723876:30723976:30724679:30724800:30729343:30729409 | 30724679:30724800 | ENSG00000101337.11 | ENST00000450829.1 |
| exon_skip_350028 | 20 | 30729343:30729468:30729568:30729698:30730784:30730880 | 30729568:30729698 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350030 | 20 | 30732893:30733012:30733114:30733226:30734587:30734658 | 30733114:30733226 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350036 | 20 | 30738602:30738678:30742905:30742989:30745596:30745751 | 30742905:30742989 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350045 | 20 | 30742905:30742989:30745596:30745772:30746253:30746317 | 30745596:30745772 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350055 | 20 | 30746253:30746317:30747794:30747914:30749078:30749168 | 30747794:30747914 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for TM9SF4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_350010 | 20 | 30697530:30697558:30720815:30720929:30723876:30723976 | 30720815:30720929 | ENSG00000101337.11 | ENST00000442842.1,ENST00000450829.1 |
| exon_skip_350018 | 20 | 30697569:30697842:30720815:30720929:30723876:30723976 | 30720815:30720929 | ENSG00000101337.11 | ENST00000217315.5,ENST00000417389.1 |
| exon_skip_350021 | 20 | 30720815:30720929:30723876:30723976:30729299:30729468 | 30723876:30723976 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350023 | 20 | 30720815:30720929:30723876:30723976:30729343:30729409 | 30723876:30723976 | ENSG00000101337.11 | ENST00000417389.1 |
| exon_skip_350025 | 20 | 30723876:30723976:30724679:30724800:30729299:30729468 | 30724679:30724800 | ENSG00000101337.11 | ENST00000442842.1 |
| exon_skip_350027 | 20 | 30723876:30723976:30724679:30724800:30729343:30729409 | 30724679:30724800 | ENSG00000101337.11 | ENST00000450829.1 |
| exon_skip_350028 | 20 | 30729343:30729468:30729568:30729698:30730784:30730880 | 30729568:30729698 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350030 | 20 | 30732893:30733012:30733114:30733226:30734587:30734658 | 30733114:30733226 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350036 | 20 | 30738602:30738678:30742905:30742989:30745596:30745751 | 30742905:30742989 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350045 | 20 | 30742905:30742989:30745596:30745772:30746253:30746317 | 30745596:30745772 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| exon_skip_350055 | 20 | 30746253:30746317:30747794:30747914:30749078:30749168 | 30747794:30747914 | ENSG00000101337.11 | ENST00000398022.2,ENST00000217315.5 |
| 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 TM9SF4 |
| 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 |
| ENST00000398022 | 30723876 | 30723976 | Frame-shift |
| ENST00000398022 | 30729568 | 30729698 | Frame-shift |
| ENST00000398022 | 30733114 | 30733226 | Frame-shift |
| ENST00000398022 | 30745596 | 30745772 | Frame-shift |
| ENST00000398022 | 30742905 | 30742989 | In-frame |
| ENST00000398022 | 30747794 | 30747914 | 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 |
| ENST00000398022 | 30723876 | 30723976 | Frame-shift |
| ENST00000398022 | 30729568 | 30729698 | Frame-shift |
| ENST00000398022 | 30733114 | 30733226 | Frame-shift |
| ENST00000398022 | 30745596 | 30745772 | Frame-shift |
| ENST00000398022 | 30742905 | 30742989 | In-frame |
| ENST00000398022 | 30747794 | 30747914 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TM9SF4 |
| 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 |
| ENST00000398022 | 3995 | 642 | 30742905 | 30742989 | 1481 | 1564 | 415 | 443 |
| ENST00000398022 | 3995 | 642 | 30747794 | 30747914 | 1805 | 1924 | 523 | 563 |
| 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 |
| ENST00000398022 | 3995 | 642 | 30742905 | 30742989 | 1481 | 1564 | 415 | 443 |
| ENST00000398022 | 3995 | 642 | 30747794 | 30747914 | 1805 | 1924 | 523 | 563 |
| 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 |
| Q92544 | 415 | 443 | 24 | 642 | Chain | ID=PRO_0000210178;Note=Transmembrane 9 superfamily member 4 |
| Q92544 | 415 | 443 | 398 | 416 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 415 | 443 | 438 | 449 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 415 | 443 | 417 | 437 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 523 | 563 | 24 | 642 | Chain | ID=PRO_0000210178;Note=Transmembrane 9 superfamily member 4 |
| Q92544 | 523 | 563 | 523 | 535 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 523 | 563 | 557 | 570 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 523 | 563 | 536 | 556 | 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 |
| Q92544 | 415 | 443 | 24 | 642 | Chain | ID=PRO_0000210178;Note=Transmembrane 9 superfamily member 4 |
| Q92544 | 415 | 443 | 398 | 416 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 415 | 443 | 438 | 449 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 415 | 443 | 417 | 437 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 523 | 563 | 24 | 642 | Chain | ID=PRO_0000210178;Note=Transmembrane 9 superfamily member 4 |
| Q92544 | 523 | 563 | 523 | 535 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 523 | 563 | 557 | 570 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92544 | 523 | 563 | 536 | 556 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for TM9SF4 |
| - 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. |
TM9SF4_COAD_exon_skip_350036_psi_boxplot.png |
TM9SF4_LIHC_exon_skip_350036_psi_boxplot.png |
TM9SF4_SKCM_exon_skip_350055_psi_boxplot.png |
| - 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 |
| BLCA | TCGA-DK-AA6P-01 | exon_skip_350028 | 30729569 | 30729698 | 30729605 | 30729618 | Frame_Shift_Del | GCTCTACTCCAACC | - | p.LYSNR129fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_350028 | 30729569 | 30729698 | 30729696 | 30729696 | Frame_Shift_Del | A | - | p.K159fs |
| COAD | TCGA-G4-6309-01 | exon_skip_350036 | 30742906 | 30742989 | 30742931 | 30742931 | Frame_Shift_Del | T | - | p.V424fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_350036 | 30742906 | 30742989 | 30742943 | 30742943 | Frame_Shift_Del | G | - | p.C411fs |
| HNSC | TCGA-CQ-6219-01 | exon_skip_350023 exon_skip_350021 | 30723877 | 30723976 | 30723921 | 30723921 | Nonsense_Mutation | C | G | p.Y41* |
| SKCM | TCGA-D9-A1JW-06 | exon_skip_350055 | 30747795 | 30747914 | 30747794 | 30747794 | Splice_Site | G | A | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-D9-A1JW-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_350055 | |
| Skipped exon start: 30747795 | |
| Skipped exon end: 30747914 | |
| Mutation start: 30747794 | |
| Mutation end: 30747794 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: . | |
exon_skip_350055_SKCM_TCGA-D9-A1JW-06.png | |
exon_skip_447531_SKCM_TCGA-D9-A1JW-06.png | |
 | Sample: TCGA-G4-6309-01 |
| Cancer type: COAD | |
| ESID: exon_skip_350036 | |
| Skipped exon start: 30742906 | |
| Skipped exon end: 30742989 | |
| Mutation start: 30742931 | |
| Mutation end: 30742931 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: T | |
| Mutation seq: - | |
| AAchange: p.V424fs | |
exon_skip_143553_COAD_TCGA-G4-6309-01.png | |
exon_skip_350036_COAD_TCGA-G4-6309-01.png | |
exon_skip_384850_COAD_TCGA-G4-6309-01.png | |
| - 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 |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 30729569 | 30729698 | 30729613 | 30729614 | In_Frame_Ins | - | CAG | p.148_149insS |
| HT1080_SOFT_TISSUE | 30720816 | 30720929 | 30720840 | 30720840 | Missense_Mutation | C | T | p.L14F |
| NCIH1435_LUNG | 30720816 | 30720929 | 30720854 | 30720854 | Missense_Mutation | G | T | p.M18I |
| TGBC11TKB_STOMACH | 30720816 | 30720929 | 30720889 | 30720889 | Missense_Mutation | C | T | p.A30V |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 30723877 | 30723976 | 30723947 | 30723947 | Missense_Mutation | G | T | p.S67I |
| SUM159PT_BREAST | 30723877 | 30723976 | 30723956 | 30723956 | Missense_Mutation | C | A | p.T70N |
| MDAPCA2B_PROSTATE | 30729569 | 30729698 | 30729598 | 30729598 | Missense_Mutation | G | A | p.R143Q |
| LIM1215_LARGE_INTESTINE | 30729569 | 30729698 | 30729696 | 30729696 | Missense_Mutation | A | G | p.K176E |
| RCCMF_KIDNEY | 30733115 | 30733226 | 30733139 | 30733139 | Missense_Mutation | C | T | p.R266C |
| KYSE520_OESOPHAGUS | 30733115 | 30733226 | 30733208 | 30733208 | Missense_Mutation | G | T | p.V289L |
| NCIH1339_LUNG | 30742906 | 30742989 | 30742969 | 30742969 | Missense_Mutation | G | A | p.G437R |
| 22RV1_PROSTATE | 30745597 | 30745772 | 30745616 | 30745616 | Missense_Mutation | T | C | p.V450A |
| A375_SKIN | 30745597 | 30745772 | 30745705 | 30745705 | Missense_Mutation | C | T | p.P480S |
| NUGC3_STOMACH | 30745597 | 30745772 | 30745711 | 30745711 | Missense_Mutation | C | T | p.R482C |
| NCIH2804_PLEURA | 30745597 | 30745772 | 30745729 | 30745729 | Missense_Mutation | C | T | p.R488W |
| MKN74_STOMACH | 30745597 | 30745772 | 30745748 | 30745748 | Missense_Mutation | G | A | p.R494Q |
| MKN28_STOMACH | 30745597 | 30745772 | 30745748 | 30745748 | Missense_Mutation | G | A | p.R494Q |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30747795 | 30747914 | 30747819 | 30747819 | Missense_Mutation | T | C | p.Y532H |
| NCIH1299_LUNG | 30742906 | 30742989 | 30742906 | 30742906 | Splice_Site | A | T | p.T416S |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 30742906 | 30742989 | 30742989 | 30742989 | Splice_Site | G | A | p.A443A |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TM9SF4 |
| 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 TM9SF4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TM9SF4 |
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RelatedDrugs for TM9SF4 |
| 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 TM9SF4 |
| 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)
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