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Fusion gene ID: 42291 |
FusionGeneSummary for YBX1_NCBP2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: YBX1_NCBP2 | Fusion gene ID: 42291 | Hgene | Tgene | Gene symbol | YBX1 | NCBP2 | Gene ID | 4904 | 22916 |
| Gene name | Y-box binding protein 1 | nuclear cap binding protein subunit 2 | |
| Synonyms | BP-8|CBF-A|CSDA2|CSDB|DBPB|EFI-A|MDR-NF1|NSEP-1|NSEP1|YB-1|YB1 | CBC2|CBP20|NIP1|PIG55 | |
| Cytomap | 1p34.2 | 3q29 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nuclease-sensitive element-binding protein 1CCAAT-binding transcription factor I subunit ADNA-binding protein BY-box transcription factorenhancer factor I subunit Amajor histocompatibility complex, class II, Y box-binding protein I | nuclear cap-binding protein subunit 220 kDa nuclear cap-binding proteinNCBP 20 kDa subunitNCBP interacting protein 1cell proliferation-inducing gene 55 proteinnuclear cap binding protein subunit 2, 20kDnuclear cap binding protein subunit 2, 20kDa | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | P67809 | P52298 | |
| Ensembl transtripts involved in fusion gene | ENST00000321358, ENST00000467957, | ENST00000467803, ENST00000447325, ENST00000321256, ENST00000427641, ENST00000452404, ENST00000422610, | |
| Fusion gene scores | * DoF score | 2 X 2 X 1=4 | 1 X 1 X 1=1 |
| # samples | 2 | 1 | |
| ** MAII score | log2(2/4*10)=2.32192809488736 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: YBX1 [Title/Abstract] AND NCBP2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 | YBX1 | GO:0006355 | regulation of transcription, DNA-templated | 18809583 |
| Hgene | YBX1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 18809583 |
| Tgene | NCBP2 | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 11551508 |
| Tgene | NCBP2 | GO:0006446 | regulation of translational initiation | 11551508 |
| Tgene | NCBP2 | GO:0045292 | mRNA cis splicing, via spliceosome | 18426921 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | BU536214 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 5CDS-5UTR | ENST00000321358 | ENST00000467803 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| 5CDS-5UTR | ENST00000321358 | ENST00000447325 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| 5CDS-5UTR | ENST00000321358 | ENST00000321256 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| 5CDS-5UTR | ENST00000321358 | ENST00000427641 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| 5CDS-5UTR | ENST00000321358 | ENST00000452404 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| 5CDS-5UTR | ENST00000321358 | ENST00000422610 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| intron-5UTR | ENST00000467957 | ENST00000467803 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| intron-5UTR | ENST00000467957 | ENST00000447325 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| intron-5UTR | ENST00000467957 | ENST00000321256 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| intron-5UTR | ENST00000467957 | ENST00000427641 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| intron-5UTR | ENST00000467957 | ENST00000452404 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
| intron-5UTR | ENST00000467957 | ENST00000422610 | YBX1 | chr1 | 43148360 | + | NCBP2 | chr3 | 196663955 | - |
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FusionProtFeatures for YBX1_NCBP2 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| YBX1 | NCBP2 |
| Mediates pre-mRNA alternative splicing regulation. Bindsto splice sites in pre-mRNA and regulates splice site selection.Binds and stabilizes cytoplasmic mRNA. Contributes to theregulation of translation by modulating the interaction betweenthe mRNA and eukaryotic initiation factors (By similarity).Regulates the transcription of numerous genes. Its transcriptionalactivity on the multidrug resistance gene MDR1 is enhanced inpresence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'.Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), suchas MDR1 and HLA class II genes. Promotes separation of DNA strandsthat contain mismatches or are modified by cisplatin. Hasendonucleolytic activity and can introduce nicks or breaks intodouble-stranded DNA (in vitro). May play a role in DNA repair.Component of the CRD-mediated complex that promotes MYC mRNAstability. Binds preferentially to the 5'-[CU]CUGCG-3' motif invitro. {ECO:0000250, ECO:0000269|PubMed:10817758,ECO:0000269|PubMed:11698476, ECO:0000269|PubMed:12604611,ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:18335541,ECO:0000269|PubMed:18809583, ECO:0000269|PubMed:19029303,ECO:0000269|PubMed:19483673}. The secreted form acts as an extracellular mitogen andstimulates cell migration and proliferation. | Component of the cap-binding complex (CBC), which bindsco-transcriptionally to the 5' cap of pre-mRNAs and is involved invarious processes such as pre-mRNA splicing, translationregulation, nonsense-mediated mRNA decay, RNA-mediated genesilencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBCcomplex is involved in mRNA export from the nucleus via itsinteraction with ALYREF/THOC4/ALY, leading to the recruitment ofthe mRNA export machinery to the 5' end of mRNA and to mRNA exportin a 5' to 3' direction through the nuclear pore. The CBC complexis also involved in mediating U snRNA and intronless mRNAs exportfrom the nucleus. The CBC complex is essential for a pioneer roundof mRNA translation, before steady state translation when the CBCcomplex is replaced by cytoplasmic cap-binding protein eIF4E. Thepioneer round of mRNA translation mediated by the CBC complexplays a central role in nonsense-mediated mRNA decay (NMD), NMDonly taking place in mRNAs bound to the CBC complex, but not oneIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAscontaining at least one exon-junction complex (EJC) via itsinteraction with UPF1, promoting the interaction between UPF1 andUPF2. The CBC complex is also involved in 'failsafe' NMD, which isindependent of the EJC complex, while it does not participate inStaufen-mediated mRNA decay (SMD). During cell proliferation, theCBC complex is also involved in microRNAs (miRNAs) biogenesis viaits interaction with SRRT/ARS2, thereby being required for miRNA-mediated RNA interference. The CBC complex also acts as a negativeregulator of PARN, thereby acting as an inhibitor of mRNAdeadenylation. In the CBC complex, NCBP2/CBP20 recognizes andbinds capped RNAs (m7GpppG-capped RNA) but requires NCBP1/CBP80 tostabilize the movement of its N-terminal loop and lock the CBCinto a high affinity cap-binding state with the cap structure. Theconventional cap-binding complex with NCBP2 binds both smallnuclear RNA (snRNA) and messenger (mRNA) and is involved in theirexport from the nucleus (PubMed:26382858).{ECO:0000269|PubMed:11551508, ECO:0000269|PubMed:15361857,ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:17363367,ECO:0000269|PubMed:17873884, ECO:0000269|PubMed:18369367,ECO:0000269|PubMed:19632182, ECO:0000269|PubMed:26382858}. |
| 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. |
| - In-frame and 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 |
| - In-frame and 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 |
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FusionGeneSequence for YBX1_NCBP2 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for YBX1_NCBP2 |
| 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 (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for YBX1_NCBP2 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for YBX1_NCBP2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | YBX1 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Hgene | YBX1 | C0027643 | Neoplasm Recurrence, Local | 1 | CTD_human |
| Hgene | YBX1 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
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