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Fusion Protein:TSKU-KDM5A |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: TSKU-KDM5A | FusionPDB ID: 94635 | FusionGDB2.0 ID: 94635 | Hgene | Tgene | Gene symbol | TSKU | KDM5A | Gene ID | 25987 | 5927 |
| Gene name | tsukushi, small leucine rich proteoglycan | lysine demethylase 5A | |
| Synonyms | E2IG4|LRRC54|TSK | RBBP-2|RBBP2|RBP2 | |
| Cytomap | 11q13.5 | 12p13.33 | |
| Type of gene | protein-coding | protein-coding | |
| Description | tsukushinE2-induced gene 4 proteinleucine rich repeat containing 54leucine-rich repeat-containing protein 54tsukushi homologtsukushi small leucine rich proteoglycan homolog | lysine-specific demethylase 5AJumonji, AT rich interactive domain 1A (RBP2-like)histone demethylase JARID1Ajumonji/ARID domain-containing protein 1Alysine (K)-specific demethylase 5Aretinoblastoma binding protein 2 | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | . | P29375 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000333090, ENST00000527881, | ENST00000382815, ENST00000540838, ENST00000399788, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 9 X 4 X 4=144 | 10 X 11 X 4=440 |
| # samples | 10 | 10 | |
| ** MAII score | log2(10/144*10)=-0.526068811667588 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(10/440*10)=-2.13750352374993 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: TSKU [Title/Abstract] AND KDM5A [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | TSKU(76506776)-KDM5A(495134), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | TSKU-KDM5A 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. TSKU-KDM5A 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. TSKU-KDM5A 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. TSKU-KDM5A 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. TSKU-KDM5A seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. TSKU-KDM5A seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. TSKU-KDM5A seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. TSKU-KDM5A seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. TSKU-KDM5A seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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 |
| Tgene | KDM5A | GO:0034720 | histone H3-K4 demethylation | 18270511 |
| Tgene | KDM5A | GO:0045893 | positive regulation of transcription, DNA-templated | 11358960 |
| Fusion gene breakpoints across TSKU (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 KDM5A (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 Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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 |
| ChiTaRS5.0 | N/A | DA455152 | TSKU | chr11 | 76506776 | + | KDM5A | chr12 | 495134 | - |
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Fusion ORF Analysis |
| 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) |
| ENST00000333090 | TSKU | chr11 | 76506776 | + | ENST00000399788 | KDM5A | chr12 | 495134 | - | 12823 | 2588 | 2651 | 7495 | 1614 |
| 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 |
| ENST00000333090 | ENST00000399788 | TSKU | chr11 | 76506776 | + | KDM5A | chr12 | 495134 | - | 0.001308299 | 0.99869174 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >94635_94635_1_TSKU-KDM5A_TSKU_chr11_76506776_ENST00000333090_KDM5A_chr12_495134_ENST00000399788_length(amino acids)=1614AA_BP= MNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSHYERIL YPYELFQSGVSLMGVQMPNLDLKEKVEPEVLSTDTQTSPEPGTRMNILPKRTRRVKTQSESGDVSRNTELKKLQIFGAGPKVVGLAMGTK DKEDEVTRRRKVTNRSDAFNMQMRQRKGTLSVNFVDLYVCMFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAEECS KPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEE EYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELF ESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCTADWLPIGRQCVNHYRRLRRHCVFSHEEL IFKMAADPECLDVGLAAMVCKELTLMTEEETRLRESVVQMGVLMSEEEVFELVPDDERQCSACRTTCFLSALTCSCNPERLVCLYHPTDL CPCPMQKKCLRYRYPLEDLPSLLYGVKVRAQSYDTWVSRVTEALSANFNHKKDLIELRVMLEDAEDRKYPENDLFRKLRDAVKEAETCAS VAQLLLSKKQKHRQSPDSGRTRTKLTVEELKAFVQQLFSLPCVISQARQVKNLLDDVEEFHERAQEAMMDETPDSSKLQMLIDMGSSLYV ELPELPRLKQELQQARWLDEVRLTLSDPQQVTLDVMKKLIDSGVGLAPHHAVEKAMAELQELLTVSERWEEKAKVCLQARPRHSVASLES IVNEAKNIPAFLPNVLSLKEALQKAREWTAKVEAIQSGSNYAYLEQLESLSAKGRPIPVRLEALPQVESQVAAARAWRERTGRTFLKKNS SHTLLQVLSPRTDIGVYGSGKNRRKKVKELIEKEKEKDLDLEPLSDLEEGLEETRDTAMVVAVFKEREQKEIEAMHSLRAANLAKMTMVD RIEEVKFCICRKTASGFMLQCELCKDWFHNSCVPLPKSSSQKKGSSWQAKEVKFLCPLCMRSRRPRLETILSLLVSLQKLPVRLPEGEAL QCLTERAMSWQDRARQALATDELSSALAKLSVLSQRMVEQAAREKTEKIISAELQKAAANPDLQGHLPSFQQSAFNRVVSSVSSSPRQTM DYDDEETDSDEDIRETYGYDMKDTASVKSSSSLEPNLFCDEEIPIKSEEVVTHMWTAPSFCAEHAYSSASKSCSQGSSTPRKQPRKSPLV PRSLEPPVLELSPGAKAQLEELMMVGDLLEVSLDETQHIWRILQATHPPSEDRFLHIMEDDSMEEKPLKVKGKDSSEKKRKRKLEKVEQL FGEGKQKSKELKKMDKPRKKKLKLGADKSKELNKLAKKLAKEEERKKKKEKAAAAKVELVKESTEKKREKKVLDIPSKYDWSGAEESDDE -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:76506776/chr12:495134) - 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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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | KDM5A |
| 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. | FUNCTION: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Regulates specific gene transcription through DNA-binding on 5'-CCGCCC-3' motif (PubMed:18270511). May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation (PubMed:19430464). May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity). Seems to act as a transcriptional corepressor for some genes such as MT1F and to favor the proliferation of cancer cells (PubMed:27427228). {ECO:0000250|UniProtKB:Q3UXZ9, ECO:0000269|PubMed:11358960, ECO:0000269|PubMed:15949438, ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17320163, ECO:0000269|PubMed:18270511, ECO:0000269|PubMed:19430464, ECO:0000269|PubMed:27427228}. |
| 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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - 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 |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 1492_1587 | 55.0 | 1691.0 | Compositional bias | Note=Lys-rich | |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 437_603 | 55.0 | 1691.0 | Domain | JmjC | |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 84_174 | 55.0 | 1691.0 | Domain | ARID | |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 419_423 | 55.0 | 1691.0 | Motif | GSGFP motif | |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 1161_1218 | 55.0 | 1691.0 | Zinc finger | PHD-type 2 | |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 1607_1661 | 55.0 | 1691.0 | Zinc finger | PHD-type 3 | |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 293_343 | 55.0 | 1691.0 | Zinc finger | PHD-type 1 | |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 676_728 | 55.0 | 1691.0 | Zinc finger | C5HC2 |
| - 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 | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 17_58 | 0 | 354.0 | Domain | Note=LRRNT |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 17_58 | 0 | 354.0 | Domain | Note=LRRNT |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 109_130 | 0 | 354.0 | Repeat | Note=LRR 3 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 132_153 | 0 | 354.0 | Repeat | Note=LRR 4 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 159_179 | 0 | 354.0 | Repeat | Note=LRR 5 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 185_206 | 0 | 354.0 | Repeat | Note=LRR 6 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 207_227 | 0 | 354.0 | Repeat | Note=LRR 7 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 230_249 | 0 | 354.0 | Repeat | Note=LRR 8 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 255_276 | 0 | 354.0 | Repeat | Note=LRR 9 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 280_301 | 0 | 354.0 | Repeat | Note=LRR 10 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 59_80 | 0 | 354.0 | Repeat | Note=LRR 1 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000333090 | + | 1 | 2 | 85_106 | 0 | 354.0 | Repeat | Note=LRR 2 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 109_130 | 0 | 354.0 | Repeat | Note=LRR 3 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 132_153 | 0 | 354.0 | Repeat | Note=LRR 4 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 159_179 | 0 | 354.0 | Repeat | Note=LRR 5 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 185_206 | 0 | 354.0 | Repeat | Note=LRR 6 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 207_227 | 0 | 354.0 | Repeat | Note=LRR 7 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 230_249 | 0 | 354.0 | Repeat | Note=LRR 8 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 255_276 | 0 | 354.0 | Repeat | Note=LRR 9 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 280_301 | 0 | 354.0 | Repeat | Note=LRR 10 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 59_80 | 0 | 354.0 | Repeat | Note=LRR 1 |
| Hgene | TSKU | chr11:76506776 | chr12:495134 | ENST00000527881 | + | 1 | 2 | 85_106 | 0 | 354.0 | Repeat | Note=LRR 2 |
| Tgene | KDM5A | chr11:76506776 | chr12:495134 | ENST00000399788 | 0 | 28 | 19_60 | 55.0 | 1691.0 | Domain | JmjN |
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Fusion Protein-Protein Interaction |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
| Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| TSKU | |
| KDM5A |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to TSKU-KDM5A |
| 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 TSKU-KDM5A |
| 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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