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Fusion Protein:JMJD6-CD300LF |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: JMJD6-CD300LF | FusionPDB ID: 40989 | FusionGDB2.0 ID: 40989 | Hgene | Tgene | Gene symbol | JMJD6 | CD300LF | Gene ID | 23210 | 146722 |
| Gene name | jumonji domain containing 6, arginine demethylase and lysine hydroxylase | CD300 molecule like family member f | |
| Synonyms | PSR|PTDSR|PTDSR1 | CD300f|CLM-1|CLM1|IREM-1|IREM1|IgSF13|LMIR3|NKIR | |
| Cytomap | 17q25.1 | 17q25.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | bifunctional arginine demethylase and lysyl-hydroxylase JMJD6arginine demethylase and lysine hydroxylasehistone arginine demethylase JMJD6jmjC domain-containing protein 6jumonji domain containing 6jumonji domain-containing protein 6lysyl-hydroxylase | CMRF35-like molecule 1CD300 antigen-like family member FNK inhibitory receptorimmune receptor expressed on myeloid cells 1immunoglobin superfamily member 13immunoglobulin superfamily member 13inhibitory receptor IREM1 | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q6NYC1 Main function of 5'-partner protein: FUNCTION: Dioxygenase that can both act as a arginine demethylase and a lysyl-hydroxylase (PubMed:24498420, PubMed:17947579, PubMed:20684070, PubMed:21060799, PubMed:22189873). Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Regulates RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65 (PubMed:19574390). Hydroxylates its own N-terminus, which is required for homooligomerization (PubMed:22189873). In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA (PubMed:20679243, PubMed:29176719). Also acts as an arginine demethylase which preferentially demethylates asymmetric dimethylation (PubMed:17947579, PubMed:24498420, PubMed:24360279). Demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), including mono-, symmetric di- and asymmetric dimethylated forms, thereby playing a role in histone code (PubMed:17947579, PubMed:24360279). However, histone arginine demethylation may not constitute the primary activity in vivo (PubMed:17947579, PubMed:21060799, PubMed:22189873). In collaboration with BRD4, interacts with the positive transcription elongation factor b (P-TEFb) complex in its active form to regulate polymerase II promoter-proximal pause release for transcriptional activation of a large cohort of genes. On distal enhancers, so called anti-pause enhancers, demethylates both histone H4R3me2 and the methyl cap of 7SKsnRNA leading to the dismissal of the 7SKsnRNA:HEXIM1 inhibitor complex. After removal of repressive marks, the complex BRD4:JMJD6 attract and retain the P-TEFb complex on chromatin, leading to its activation, promoter-proximal polymerase II pause release, and transcriptional activation (PubMed:24360279). Demethylates other arginine methylated-proteins such as ESR1 (PubMed:24498420). Has no histone lysine demethylase activity (PubMed:21060799). Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65 (By similarity). Seems to be necessary for the regulation of macrophage cytokine responses (PubMed:15622002). {ECO:0000250|UniProtKB:Q9ERI5, ECO:0000269|PubMed:15622002, ECO:0000269|PubMed:17947579, ECO:0000269|PubMed:19574390, ECO:0000269|PubMed:20679243, ECO:0000269|PubMed:20684070, ECO:0000269|PubMed:21060799, ECO:0000269|PubMed:22189873, ECO:0000269|PubMed:24360279, ECO:0000269|PubMed:24498420, ECO:0000269|PubMed:29176719}. | Q8TDQ1 Main function of 5'-partner protein: FUNCTION: Acts as an inhibitory receptor for myeloid cells and mast cells (PubMed:15549731). Positively regulates the phagocytosis of apoptotic cells (efferocytosis) via phosphatidylserine (PS) recognition; recognizes and binds PS as a ligand which is expressed on the surface of apoptotic cells. Plays an important role in the maintenance of immune homeostasis, by promoting macrophage-mediated efferocytosis and by inhibiting dendritic cell-mediated efferocytosis (By similarity). Negatively regulates Fc epsilon receptor-dependent mast cell activation and allergic responses via binding to ceramide and sphingomyelin which act as ligands (PubMed:24035150). May act as a coreceptor for interleukin 4 (IL-4). Associates with and regulates IL-4 receptor alpha-mediated responses by augmenting IL-4- and IL-13-induced signaling (By similarity). Negatively regulates the Toll-like receptor (TLR) signaling mediated by MYD88 and TRIF through activation of PTPN6/SHP-1 and PTPN11/SHP-2 (PubMed:22043923). Inhibits osteoclast formation. Induces macrophage cell death upon engagement (By similarity). {ECO:0000250|UniProtKB:Q6SJQ7, ECO:0000269|PubMed:15549731, ECO:0000269|PubMed:22043923, ECO:0000269|PubMed:24035150}. | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000397625, ENST00000445478, ENST00000585429, | ENST00000301573, ENST00000343125, ENST00000361254, ENST00000326165, ENST00000464910, ENST00000469092, ENST00000581500, ENST00000583937, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 4 X 5 X 2=40 | 1 X 1 X 1=1 |
| # samples | 4 | 1 | |
| ** MAII score | log2(4/40*10)=0 | log2(1/1*10)=3.32192809488736 | |
| Fusion gene context | PubMed: JMJD6 [Title/Abstract] AND CD300LF [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: JMJD6 [Title/Abstract] AND CD300LF [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | JMJD6(74719853)-CD300LF(72700955), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | JMJD6-CD300LF 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. JMJD6-CD300LF 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. JMJD6-CD300LF 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. JMJD6-CD300LF 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. JMJD6-CD300LF seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. JMJD6-CD300LF seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. JMJD6-CD300LF seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target 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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | JMJD6 | GO:0006482 | protein demethylation | 24498420 |
| Hgene | JMJD6 | GO:0018395 | peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine | 19574390|22189873 |
| Hgene | JMJD6 | GO:0035513 | oxidative RNA demethylation | 24360279 |
| Hgene | JMJD6 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 24360279 |
| Hgene | JMJD6 | GO:0051260 | protein homooligomerization | 22189873|24360279 |
| Hgene | JMJD6 | GO:0070078 | histone H3-R2 demethylation | 17947579 |
| Hgene | JMJD6 | GO:0070078 | histone H3-R2 demethylation | 22189873 |
| Hgene | JMJD6 | GO:0070079 | histone H4-R3 demethylation | 17947579|24360279|24498420 |
| Hgene | JMJD6 | GO:0070079 | histone H4-R3 demethylation | 22189873 |
| Tgene | CD300LF | GO:0033004 | negative regulation of mast cell activation | 24035150 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:74719853/chr17:72700955) - 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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| Retention analysis results of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features, are available here. |
| Fusion gene breakpoints across JMJD6 (5'-gene) * 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 breakpoints across CD300LF (3'-gene) * 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 Amino Acid Sequences |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| 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) |
| ENST00000445478 | JMJD6 | chr17 | 74719853 | - | ENST00000326165 | CD300LF | chr17 | 72700955 | - | 2618 | 1009 | 108 | 1838 | 576 |
| ENST00000445478 | JMJD6 | chr17 | 74719853 | - | ENST00000469092 | CD300LF | chr17 | 72700955 | - | 2505 | 1009 | 108 | 1541 | 477 |
| ENST00000445478 | JMJD6 | chr17 | 74719853 | - | ENST00000583937 | CD300LF | chr17 | 72700955 | - | 2166 | 1009 | 108 | 1883 | 591 |
| ENST00000445478 | JMJD6 | chr17 | 74719853 | - | ENST00000464910 | CD300LF | chr17 | 72700955 | - | 1898 | 1009 | 108 | 1838 | 576 |
| ENST00000445478 | JMJD6 | chr17 | 74719853 | - | ENST00000581500 | CD300LF | chr17 | 72700955 | - | 1677 | 1009 | 108 | 1676 | 522 |
| ENST00000397625 | JMJD6 | chr17 | 74719853 | - | ENST00000326165 | CD300LF | chr17 | 72700955 | - | 2529 | 920 | 19 | 1749 | 576 |
| ENST00000397625 | JMJD6 | chr17 | 74719853 | - | ENST00000469092 | CD300LF | chr17 | 72700955 | - | 2416 | 920 | 19 | 1452 | 477 |
| ENST00000397625 | JMJD6 | chr17 | 74719853 | - | ENST00000583937 | CD300LF | chr17 | 72700955 | - | 2077 | 920 | 19 | 1794 | 591 |
| ENST00000397625 | JMJD6 | chr17 | 74719853 | - | ENST00000464910 | CD300LF | chr17 | 72700955 | - | 1809 | 920 | 19 | 1749 | 576 |
| ENST00000397625 | JMJD6 | chr17 | 74719853 | - | ENST00000581500 | CD300LF | chr17 | 72700955 | - | 1588 | 920 | 19 | 1587 | 523 |
| ENST00000585429 | JMJD6 | chr17 | 74719853 | - | ENST00000326165 | CD300LF | chr17 | 72700955 | - | 2442 | 833 | 28 | 1662 | 544 |
| ENST00000585429 | JMJD6 | chr17 | 74719853 | - | ENST00000469092 | CD300LF | chr17 | 72700955 | - | 2329 | 833 | 28 | 1365 | 445 |
| ENST00000585429 | JMJD6 | chr17 | 74719853 | - | ENST00000583937 | CD300LF | chr17 | 72700955 | - | 1990 | 833 | 28 | 1707 | 559 |
| ENST00000585429 | JMJD6 | chr17 | 74719853 | - | ENST00000464910 | CD300LF | chr17 | 72700955 | - | 1722 | 833 | 28 | 1662 | 544 |
| ENST00000585429 | JMJD6 | chr17 | 74719853 | - | ENST00000581500 | CD300LF | chr17 | 72700955 | - | 1501 | 833 | 28 | 1500 | 491 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000445478 | ENST00000326165 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.007352324 | 0.99264765 |
| ENST00000445478 | ENST00000469092 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.009955383 | 0.9900446 |
| ENST00000445478 | ENST00000583937 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.014009317 | 0.9859907 |
| ENST00000445478 | ENST00000464910 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.011326707 | 0.98867327 |
| ENST00000445478 | ENST00000581500 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.01329285 | 0.9867071 |
| ENST00000397625 | ENST00000326165 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.00685343 | 0.9931466 |
| ENST00000397625 | ENST00000469092 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.00911626 | 0.99088377 |
| ENST00000397625 | ENST00000583937 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.013235284 | 0.98676467 |
| ENST00000397625 | ENST00000464910 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.010011022 | 0.9899889 |
| ENST00000397625 | ENST00000581500 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.011691291 | 0.98830867 |
| ENST00000585429 | ENST00000326165 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.007450308 | 0.99254966 |
| ENST00000585429 | ENST00000469092 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.009779428 | 0.99022055 |
| ENST00000585429 | ENST00000583937 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.014256421 | 0.9857436 |
| ENST00000585429 | ENST00000464910 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.010716846 | 0.9892832 |
| ENST00000585429 | ENST00000581500 | JMJD6 | chr17 | 74719853 | - | CD300LF | chr17 | 72700955 | - | 0.012517743 | 0.9874822 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
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 |
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Fusion Protein Breakpoint Sequences for JMJD6-CD300LF |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
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Potential FusionNeoAntigen Information of JMJD6-CD300LF in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * 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) |
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Potential FusionNeoAntigen Information of JMJD6-CD300LF in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * 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) |
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Fusion breakpoint peptide structures of JMJD6-CD300LF |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * 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. |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of JMJD6-CD300LF |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
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Vaccine Design for the FusionNeoAntigens of JMJD6-CD300LF |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of JMJD6-CD300LF |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
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Potential target of CAR-T therapy development for JMJD6-CD300LF |
| Predicted 3D structure. We used RoseTTAFold. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * 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 |
| Tgene | CD300LF | chr17:74719853 | chr17:72700955 | ENST00000301573 | 0 | 8 | 157_177 | 0 | 444.6666666666667 | Transmembrane | Helical | |
| Tgene | CD300LF | chr17:74719853 | chr17:72700955 | ENST00000326165 | 0 | 7 | 157_177 | 0 | 291.0 | Transmembrane | Helical | |
| Tgene | CD300LF | chr17:74719853 | chr17:72700955 | ENST00000343125 | 0 | 6 | 157_177 | 0 | 422.6666666666667 | Transmembrane | Helical | |
| Tgene | CD300LF | chr17:74719853 | chr17:72700955 | ENST00000361254 | 0 | 6 | 157_177 | 0 | 467.6666666666667 | Transmembrane | Helical | |
| Tgene | CD300LF | chr17:74719853 | chr17:72700955 | ENST00000464910 | 0 | 7 | 157_177 | 0 | 294.0 | Transmembrane | Helical | |
| Tgene | CD300LF | chr17:74719853 | chr17:72700955 | ENST00000469092 | 1 | 7 | 157_177 | 0 | 442.0 | Transmembrane | Helical | |
| Tgene | CD300LF | chr17:74719853 | chr17:72700955 | ENST00000581500 | 0 | 5 | 157_177 | 0 | 240.0 | Transmembrane | Helical |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * 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 |
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Related Drugs to JMJD6-CD300LF |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to JMJD6-CD300LF |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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