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Fusion Protein:CLIP1-TMED2 |
Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: CLIP1-TMED2 | FusionPDB ID: 17171 | FusionGDB2.0 ID: 17171 | Hgene | Tgene | Gene symbol | CLIP1 | TMED2 | Gene ID | 6249 | 10959 |
Gene name | CAP-Gly domain containing linker protein 1 | transmembrane p24 trafficking protein 2 | |
Synonyms | CLIP|CLIP-170|CLIP170|CYLN1|RSN | P24A|RNP24|p24|p24b1|p24beta1 | |
Cytomap | 12q24.31 | 12q24.31 | |
Type of gene | protein-coding | protein-coding | |
Description | CAP-Gly domain-containing linker protein 1cytoplasmic linker protein 1cytoplasmic linker protein 170 alpha-2cytoplasmic linker protein CLIP-170restin (Reed-Steinberg cell-expressed intermediate filament-associated protein) | transmembrane emp24 domain-containing protein 2coated vesicle membrane proteinmembrane protein p24Ap24 family protein beta-1transmembrane emp24 domain trafficking protein 2 | |
Modification date | 20200313 | 20200313 | |
UniProtAcc | P30622 | . | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000302528, ENST00000540338, ENST00000358808, ENST00000361654, ENST00000537178, ENST00000536634, ENST00000540539, ENST00000545889, | ENST00000262225, ENST00000509052, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 22 X 22 X 13=6292 | 6 X 8 X 3=144 |
# samples | 31 | 8 | |
** MAII score | log2(31/6292*10)=-4.34317855014145 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/144*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Context (manual curation of fusion genes in FusionPDB) | PubMed: CLIP1 [Title/Abstract] AND TMED2 [Title/Abstract] AND fusion [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CLIP1(122861936)-TMED2(124081152), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | CLIP1-TMED2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CLIP1-TMED2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CLIP1-TMED2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. CLIP1-TMED2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. CLIP1-TMED2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. CLIP1-TMED2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. CLIP1-TMED2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
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Partner | Gene | GO ID | GO term | PubMed ID |
Tgene | TMED2 | GO:0006886 | intracellular protein transport | 20427317 |
Tgene | TMED2 | GO:0034260 | negative regulation of GTPase activity | 10761932 |
Tgene | TMED2 | GO:0072659 | protein localization to plasma membrane | 20361938 |
![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
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![]() * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
ChimerDB4 | STAD | TCGA-BR-8364-01A | CLIP1 | chr12 | 122861936 | - | TMED2 | chr12 | 124081152 | + |
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Fusion ORF Analysis |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
ENST00000361654 | CLIP1 | chr12 | 122861936 | - | ENST00000262225 | TMED2 | chr12 | 124081152 | + | 2796 | 831 | 174 | 890 | 238 |
ENST00000361654 | CLIP1 | chr12 | 122861936 | - | ENST00000509052 | TMED2 | chr12 | 124081152 | + | 1320 | 831 | 174 | 890 | 238 |
ENST00000358808 | CLIP1 | chr12 | 122861936 | - | ENST00000262225 | TMED2 | chr12 | 124081152 | + | 2777 | 812 | 155 | 871 | 238 |
ENST00000358808 | CLIP1 | chr12 | 122861936 | - | ENST00000509052 | TMED2 | chr12 | 124081152 | + | 1301 | 812 | 155 | 871 | 238 |
ENST00000537178 | CLIP1 | chr12 | 122861936 | - | ENST00000262225 | TMED2 | chr12 | 124081152 | + | 2840 | 875 | 218 | 934 | 238 |
ENST00000537178 | CLIP1 | chr12 | 122861936 | - | ENST00000509052 | TMED2 | chr12 | 124081152 | + | 1364 | 875 | 218 | 934 | 238 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000361654 | ENST00000262225 | CLIP1 | chr12 | 122861936 | - | TMED2 | chr12 | 124081152 | + | 0.001600176 | 0.9983998 |
ENST00000361654 | ENST00000509052 | CLIP1 | chr12 | 122861936 | - | TMED2 | chr12 | 124081152 | + | 0.00783265 | 0.9921673 |
ENST00000358808 | ENST00000262225 | CLIP1 | chr12 | 122861936 | - | TMED2 | chr12 | 124081152 | + | 0.001443552 | 0.99855644 |
ENST00000358808 | ENST00000509052 | CLIP1 | chr12 | 122861936 | - | TMED2 | chr12 | 124081152 | + | 0.008069847 | 0.99193007 |
ENST00000537178 | ENST00000262225 | CLIP1 | chr12 | 122861936 | - | TMED2 | chr12 | 124081152 | + | 0.001370917 | 0.9986291 |
ENST00000537178 | ENST00000509052 | CLIP1 | chr12 | 122861936 | - | TMED2 | chr12 | 124081152 | + | 0.008302568 | 0.99169743 |
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Fusion Amino Acid Sequences |
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>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >17171_17171_1_CLIP1-TMED2_CLIP1_chr12_122861936_ENST00000358808_TMED2_chr12_124081152_ENST00000262225_length(amino acids)=238AA_BP=219 MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS -------------------------------------------------------------- >17171_17171_2_CLIP1-TMED2_CLIP1_chr12_122861936_ENST00000358808_TMED2_chr12_124081152_ENST00000509052_length(amino acids)=238AA_BP=219 MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS -------------------------------------------------------------- >17171_17171_3_CLIP1-TMED2_CLIP1_chr12_122861936_ENST00000361654_TMED2_chr12_124081152_ENST00000262225_length(amino acids)=238AA_BP=219 MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS -------------------------------------------------------------- >17171_17171_4_CLIP1-TMED2_CLIP1_chr12_122861936_ENST00000361654_TMED2_chr12_124081152_ENST00000509052_length(amino acids)=238AA_BP=219 MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS -------------------------------------------------------------- >17171_17171_5_CLIP1-TMED2_CLIP1_chr12_122861936_ENST00000537178_TMED2_chr12_124081152_ENST00000262225_length(amino acids)=238AA_BP=219 MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS -------------------------------------------------------------- >17171_17171_6_CLIP1-TMED2_CLIP1_chr12_122861936_ENST00000537178_TMED2_chr12_124081152_ENST00000509052_length(amino acids)=238AA_BP=219 MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS -------------------------------------------------------------- |
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Fusion Protein Functional Features |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:122861936/chr12:124081152) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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Hgene | Tgene |
CLIP1 | . |
FUNCTION: Binds to the plus end of microtubules and regulates the dynamics of the microtubule cytoskeleton. Promotes microtubule growth and microtubule bundling. Links cytoplasmic vesicles to microtubules and thereby plays an important role in intracellular vesicle trafficking. Plays a role macropinocytosis and endosome trafficking. {ECO:0000269|PubMed:12433698, ECO:0000269|PubMed:17563362, ECO:0000269|PubMed:17889670}. | FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. |
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- Retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000302528 | - | 2 | 24 | 143_204 | 219.0 | 1428.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000358808 | - | 3 | 25 | 143_204 | 219.0 | 1428.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000537178 | - | 3 | 24 | 143_204 | 219.0 | 1393.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000540338 | - | 2 | 25 | 143_204 | 219.0 | 1439.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000302528 | - | 2 | 24 | 78_120 | 219.0 | 1428.0 | Domain | CAP-Gly 1 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000358808 | - | 3 | 25 | 78_120 | 219.0 | 1428.0 | Domain | CAP-Gly 1 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000537178 | - | 3 | 24 | 78_120 | 219.0 | 1393.0 | Domain | CAP-Gly 1 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000540338 | - | 2 | 25 | 78_120 | 219.0 | 1439.0 | Domain | CAP-Gly 1 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000302528 | - | 2 | 24 | 97_101 | 219.0 | 1428.0 | Region | Important for tubulin binding |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000358808 | - | 3 | 25 | 97_101 | 219.0 | 1428.0 | Region | Important for tubulin binding |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000537178 | - | 3 | 24 | 97_101 | 219.0 | 1393.0 | Region | Important for tubulin binding |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000540338 | - | 2 | 25 | 97_101 | 219.0 | 1439.0 | Region | Important for tubulin binding |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 194_201 | 160.33333333333334 | 202.0 | Motif | COPI vesicle coat-binding | |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 190_201 | 160.33333333333334 | 202.0 | Topological domain | Cytoplasmic | |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 169_189 | 160.33333333333334 | 202.0 | Transmembrane | Helical |
- Not-retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000302528 | - | 2 | 24 | 350_1353 | 219.0 | 1428.0 | Coiled coil | Ontology_term=ECO:0000255 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000358808 | - | 3 | 25 | 350_1353 | 219.0 | 1428.0 | Coiled coil | Ontology_term=ECO:0000255 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000537178 | - | 3 | 24 | 350_1353 | 219.0 | 1393.0 | Coiled coil | Ontology_term=ECO:0000255 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000540338 | - | 2 | 25 | 350_1353 | 219.0 | 1439.0 | Coiled coil | Ontology_term=ECO:0000255 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000302528 | - | 2 | 24 | 304_331 | 219.0 | 1428.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000358808 | - | 3 | 25 | 304_331 | 219.0 | 1428.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000537178 | - | 3 | 24 | 304_331 | 219.0 | 1393.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000540338 | - | 2 | 25 | 304_331 | 219.0 | 1439.0 | Compositional bias | Note=Ser-rich |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000302528 | - | 2 | 24 | 232_274 | 219.0 | 1428.0 | Domain | CAP-Gly 2 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000358808 | - | 3 | 25 | 232_274 | 219.0 | 1428.0 | Domain | CAP-Gly 2 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000537178 | - | 3 | 24 | 232_274 | 219.0 | 1393.0 | Domain | CAP-Gly 2 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000540338 | - | 2 | 25 | 232_274 | 219.0 | 1439.0 | Domain | CAP-Gly 2 |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000302528 | - | 2 | 24 | 1417_1434 | 219.0 | 1428.0 | Zinc finger | CCHC-type |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000358808 | - | 3 | 25 | 1417_1434 | 219.0 | 1428.0 | Zinc finger | CCHC-type |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000537178 | - | 3 | 24 | 1417_1434 | 219.0 | 1393.0 | Zinc finger | CCHC-type |
Hgene | CLIP1 | chr12:122861936 | chr12:124081152 | ENST00000540338 | - | 2 | 25 | 1417_1434 | 219.0 | 1439.0 | Zinc finger | CCHC-type |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 117_167 | 160.33333333333334 | 202.0 | Coiled coil | Ontology_term=ECO:0000255 | |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 30_112 | 160.33333333333334 | 202.0 | Domain | GOLD | |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 118_157 | 160.33333333333334 | 202.0 | Region | Note=Required for TMED10 and TMED2 cis-Golgi network localization | |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 21_168 | 160.33333333333334 | 202.0 | Topological domain | Lumenal |
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Fusion Protein-Protein Interaction |
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Gene | PPI interactors |
CLIP1 | MTOR, IQGAP1, CDC42, RAC1, PAFAH1B1, Gorasp1, CALM1, BIN1, MAPRE1, TUBA1A, TUBB, AMOT, BUB3, MAEA, PSMC2, HDAC6, CADPS, CHD4, GPS1, DCTN1, DYNC1H1, Mapre1, Smurf2, PCGF1, DPPA4, NANOG, POU5F1, TSC22D2, GORASP1, BMP1, DAB2IP, RUNDC3A, BRCA1, ZNF598, UBE2M, KIAA1429, DCAF15, BICD1, REL, ORF3a, SERBP1, nsp2, CLIP4, NINL, ORF6, DDX58, AGAP3, CKAP2, CLASP1, CLASP2, DNAJA2, IKBKAP, ELP4, EXOC4, HINT1, HMMR, HNRNPA1L2, IARS2, KIF15, MAP7, MAST4, PLEKHA5, RPS6KA3, SIRT2, SLAIN1, TCHP, TEX9, BIRC6, CAMSAP1, DRG1, KIAA0368, MAP7D1, MAP7D2, MAP7D3, SF3B3, SLAIN2, MAPRE3, TRIM36, PPP2R2B, RABEP1, SRRT, OR2A4, GOT1, RABEP2, SYCE1, MBNL1, SSUH2, C18orf21, AGPAT1, CCR1, FBXO32, CDK1, |
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Gene | STRING network |
CLIP1 | ![]() |
TMED2 |
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Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
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Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
Tgene | TMED2 | chr12:122861936 | chr12:124081152 | ENST00000262225 | 2 | 4 | 1_181 | 160.33333333333334 | 202.0 | F2RL1 |
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Related Drugs to CLIP1-TMED2 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CLIP1-TMED2 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |