![]() |
|||||||
|
Fusion Protein:SDC4-YWHAB |
Fusion Gene and Fusion Protein Summary |
![]() |
Fusion partner gene information | Fusion gene name: SDC4-YWHAB | FusionPDB ID: 79829 | FusionGDB2.0 ID: 79829 | Hgene | Tgene | Gene symbol | SDC4 | YWHAB | Gene ID | 6385 | 7529 |
Gene name | syndecan 4 | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta | |
Synonyms | SYND4 | GW128|HEL-S-1|HS1|KCIP-1|YWHAA | |
Cytomap | 20q13.12 | 20q13.12 | |
Type of gene | protein-coding | protein-coding | |
Description | syndecan-4amphiglycanryudocan amphiglycanryudocan core proteinsyndecan 4 (amphiglycan, ryudocan)syndecan proteoglycan 4 | 14-3-3 protein beta/alpha14-3-3 alphabrain protein 14-3-3, beta isoformepididymis secretory protein Li 1protein 1054protein kinase C inhibitor protein-1tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, alpha polypeptidetyrosin | |
Modification date | 20200313 | 20200327 | |
UniProtAcc | P31431 Main function of 5'-partner protein: FUNCTION: Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413). {ECO:0000269|PubMed:22660413}. | . | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000372733, ENST00000537976, | ENST00000372839, ENST00000479421, ENST00000353703, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 12 X 12 X 10=1440 | 13 X 25 X 12=3900 |
# samples | 21 | 30 | |
** MAII score | log2(21/1440*10)=-2.77760757866355 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(30/3900*10)=-3.70043971814109 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: SDC4 [Title/Abstract] AND YWHAB [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: SDC4 [Title/Abstract] AND YWHAB [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | SDC4(43976965)-YWHAB(43532634), # samples:2 | ||
Anticipated loss of major functional domain due to fusion event. |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
![]() |
Partner | Gene | GO ID | GO term | PubMed ID |
Tgene | YWHAB | GO:0035308 | negative regulation of protein dephosphorylation | 17255105 |
Tgene | YWHAB | GO:0043085 | positive regulation of catalytic activity | 17255105 |
Tgene | YWHAB | GO:0051220 | cytoplasmic sequestering of protein | 10869435 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:43976965/chr20:43532634) - 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. |
![]() |
![]() |
![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
![]() |
![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
![]() |
Top |
Fusion Amino Acid Sequences |
![]() |
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) |
ENST00000372733 | SDC4 | chr20 | 43976964 | - | ENST00000353703 | YWHAB | chr20 | 43532633 | + | 2635 | 100 | 40 | 540 | 166 |
ENST00000372733 | SDC4 | chr20 | 43976965 | - | ENST00000353703 | YWHAB | chr20 | 43532634 | + | 2635 | 100 | 40 | 540 | 166 |
![]() |
Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000372733 | ENST00000353703 | SDC4 | chr20 | 43976964 | - | YWHAB | chr20 | 43532633 | + | 0.000983875 | 0.99901617 |
ENST00000372733 | ENST00000353703 | SDC4 | chr20 | 43976965 | - | YWHAB | chr20 | 43532634 | + | 0.000983875 | 0.99901617 |
![]() |
Get the fusion protein sequences from here. |
Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
Top |
Fusion Protein Breakpoint Sequences for SDC4-YWHAB |
![]() |
Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
SDC4 | chr20 | 43976964 | YWHAB | chr20 | 43532633 | 100 | 20 | ALLLFFVGGVAESELLDKYLIPNATQ |
SDC4 | chr20 | 43976965 | YWHAB | chr20 | 43532634 | 100 | 20 | ALLLFFVGGVAESELLDKYLIPNATQ |
Top |
Potential FusionNeoAntigen Information of SDC4-YWHAB in HLA I |
![]() |
SDC4-YWHAB_43976964_43532633.msa |
![]() * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:03 | AESELLDKY | 0.9992 | 0.9282 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:03 | SELLDKYLI | 0.995 | 0.9489 | 12 | 21 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B45:01 | SELLDKYLI | 0.9841 | 0.6106 | 12 | 21 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:01 | AESELLDKY | 0.9835 | 0.8956 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B45:01 | AESELLDKY | 0.6834 | 0.6282 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B41:01 | SELLDKYLI | 0.413 | 0.8726 | 12 | 21 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:03 | AESELLDKYL | 0.9938 | 0.9542 | 10 | 20 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:03 | VAESELLDKY | 0.5927 | 0.9198 | 9 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:03 | GVAESELLDKY | 0.7988 | 0.963 | 8 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B39:08 | AESELLDKYL | 0.913 | 0.7321 | 10 | 20 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B40:04 | SELLDKYL | 0.9995 | 0.5615 | 12 | 20 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:07 | AESELLDKY | 0.9992 | 0.9282 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:26 | AESELLDKY | 0.9992 | 0.9282 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:13 | AESELLDKY | 0.9992 | 0.9282 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:07 | SELLDKYLI | 0.995 | 0.9489 | 12 | 21 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:13 | SELLDKYLI | 0.995 | 0.9489 | 12 | 21 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:26 | SELLDKYLI | 0.995 | 0.9489 | 12 | 21 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B40:04 | SELLDKYLI | 0.9943 | 0.571 | 12 | 21 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:04 | AESELLDKY | 0.9876 | 0.9039 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:07 | AESELLDKY | 0.9874 | 0.8532 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:05 | AESELLDKY | 0.9835 | 0.8956 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:08 | AESELLDKY | 0.981 | 0.6935 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:06 | AESELLDKY | 0.974 | 0.9122 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:03 | AESELLDKY | 0.9708 | 0.8925 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:11 | AESELLDKY | 0.8858 | 0.8795 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B35:28 | AESELLDKY | 0.6001 | 0.8017 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B40:04 | AESELLDKY | 0.5786 | 0.5492 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B35:20 | AESELLDKY | 0.5389 | 0.8238 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B15:12 | AESELLDKY | 0.533 | 0.7739 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B15:53 | AESELLDKY | 0.2201 | 0.7997 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B48:02 | AESELLDKY | 0.139 | 0.791 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B15:54 | AESELLDKY | 0.0189 | 0.7733 | 10 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:26 | AESELLDKYL | 0.9938 | 0.9542 | 10 | 20 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:13 | AESELLDKYL | 0.9938 | 0.9542 | 10 | 20 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:07 | AESELLDKYL | 0.9938 | 0.9542 | 10 | 20 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B40:04 | AESELLDKYL | 0.9909 | 0.6023 | 10 | 20 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B18:11 | VAESELLDKY | 0.6409 | 0.8973 | 9 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:07 | VAESELLDKY | 0.5927 | 0.9198 | 9 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:13 | VAESELLDKY | 0.5927 | 0.9198 | 9 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:26 | VAESELLDKY | 0.5927 | 0.9198 | 9 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:07 | GVAESELLDKY | 0.7988 | 0.963 | 8 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:26 | GVAESELLDKY | 0.7988 | 0.963 | 8 | 19 |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 | HLA-B44:13 | GVAESELLDKY | 0.7988 | 0.963 | 8 | 19 |
Top |
Potential FusionNeoAntigen Information of SDC4-YWHAB in HLA II |
![]() |
![]() * We used NetMHCIIpan v4.1 (%rank<0.5). |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
Top |
Fusion breakpoint peptide structures of SDC4-YWHAB |
![]() * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
9947 | VGGVAESELLDKYL | SDC4 | YWHAB | chr20 | 43976964 | chr20 | 43532633 | 100 |
Top |
Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SDC4-YWHAB |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
HLA-B14:02 | 3BVN | 9947 | VGGVAESELLDKYL | -7.9962 | -8.1096 |
HLA-B14:02 | 3BVN | 9947 | VGGVAESELLDKYL | -5.70842 | -6.74372 |
HLA-B52:01 | 3W39 | 9947 | VGGVAESELLDKYL | -6.83737 | -6.95077 |
HLA-B52:01 | 3W39 | 9947 | VGGVAESELLDKYL | -4.4836 | -5.5189 |
HLA-A11:01 | 4UQ2 | 9947 | VGGVAESELLDKYL | -10.0067 | -10.1201 |
HLA-A11:01 | 4UQ2 | 9947 | VGGVAESELLDKYL | -9.03915 | -10.0745 |
HLA-A24:02 | 5HGA | 9947 | VGGVAESELLDKYL | -6.56204 | -6.67544 |
HLA-A24:02 | 5HGA | 9947 | VGGVAESELLDKYL | -5.42271 | -6.45801 |
HLA-B44:05 | 3DX8 | 9947 | VGGVAESELLDKYL | -7.85648 | -8.89178 |
HLA-B44:05 | 3DX8 | 9947 | VGGVAESELLDKYL | -5.3978 | -5.5112 |
HLA-A02:01 | 6TDR | 9947 | VGGVAESELLDKYL | -3.37154 | -4.40684 |
Top |
Vaccine Design for the FusionNeoAntigens of SDC4-YWHAB |
![]() |
Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 10 | 19 | AESELLDKY | GCCGAGTCGGAGCTGTTGGACAAATAT |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 10 | 20 | AESELLDKYL | GCCGAGTCGGAGCTGTTGGACAAATATCTT |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 12 | 20 | SELLDKYL | TCGGAGCTGTTGGACAAATATCTT |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 12 | 21 | SELLDKYLI | TCGGAGCTGTTGGACAAATATCTTATT |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 8 | 19 | GVAESELLDKY | GGAGTCGCCGAGTCGGAGCTGTTGGACAAATAT |
SDC4-YWHAB | chr20 | 43976964 | chr20 | 43532633 | 9 | 19 | VAESELLDKY | GTCGCCGAGTCGGAGCTGTTGGACAAATAT |
![]() |
Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
Top |
Information of the samples that have these potential fusion neoantigens of SDC4-YWHAB |
![]() |
Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
LUAD | SDC4-YWHAB | chr20 | 43976964 | ENST00000372733 | chr20 | 43532633 | ENST00000353703 | TCGA-97-8177 |
Top |
Potential target of CAR-T therapy development for SDC4-YWHAB |
![]() |
![]() * Minus value of BPloci means that the break point is located before the CDS. |
- In-frame and retained 'Transmembrane'. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
![]() * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
Top |
Related Drugs to SDC4-YWHAB |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
Top |
Related Diseases to SDC4-YWHAB |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Hgene | SDC4 | C0007131 | Non-Small Cell Lung Carcinoma | 1 | CTD_human |