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Fusion gene ID: 30963 |
FusionGeneSummary for RER1_DDX21 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RER1_DDX21 | Fusion gene ID: 30963 | Hgene | Tgene | Gene symbol | RER1 | DDX21 | Gene ID | 11079 | 54606 |
| Gene name | retention in endoplasmic reticulum sorting receptor 1 | DEAD-box helicase 56 | |
| Synonyms | - | DDX21|DDX26|NOH61 | |
| Cytomap | 1p36.32 | 7p13 | |
| Type of gene | protein-coding | protein-coding | |
| Description | protein RER1RER1 retention in endoplasmic reticulum 1 homolog | probable ATP-dependent RNA helicase DDX5661-kd nucleolar helicaseATP-dependent 61 kDa nucleolar RNA helicaseDEAD (Asp-Glu-Ala-Asp) box helicase 56DEAD (Asp-Glu-Ala-Asp) box polypeptide 56DEAD box protein 21DEAD box protein 56DEAD-box RNA helicasen | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | O15258 | Q9NR30 | |
| Ensembl transtripts involved in fusion gene | ENST00000378518, ENST00000605895, ENST00000378513, ENST00000378512, ENST00000488353, | ENST00000354185, | |
| Fusion gene scores | * DoF score | 3 X 3 X 3=27 | 33 X 8 X 14=3696 |
| # samples | 3 | 37 | |
| ** MAII score | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(37/3696*10)=-3.32036758089975 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RER1 [Title/Abstract] AND DDX21 [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 | RER1 | GO:0006890 | retrograde vesicle-mediated transport, Golgi to ER | 9309388 |
| 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 |
| TCGA | RV | STAD | TCGA-BR-8679-01A | RER1 | chr1 | 2335188 | + | DDX21 | chr10 | 70723858 | + |
| * 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 |
| intron-intron | ENST00000378518 | ENST00000354185 | RER1 | chr1 | 2335188 | + | DDX21 | chr10 | 70723858 | + |
| 3UTR-intron | ENST00000605895 | ENST00000354185 | RER1 | chr1 | 2335188 | + | DDX21 | chr10 | 70723858 | + |
| 5CDS-intron | ENST00000378513 | ENST00000354185 | RER1 | chr1 | 2335188 | + | DDX21 | chr10 | 70723858 | + |
| 5CDS-intron | ENST00000378512 | ENST00000354185 | RER1 | chr1 | 2335188 | + | DDX21 | chr10 | 70723858 | + |
| intron-intron | ENST00000488353 | ENST00000354185 | RER1 | chr1 | 2335188 | + | DDX21 | chr10 | 70723858 | + |
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FusionProtFeatures for RER1_DDX21 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RER1 | DDX21 |
| Involved in the retrieval of endoplasmic reticulummembrane proteins from the early Golgi compartment. {ECO:0000250}. | RNA helicase that acts as a sensor of thetranscriptional status of both RNA polymerase (Pol) I and II:promotes ribosomal RNA (rRNA) processing and transcription frompolymerase II (Pol II) (PubMed:25470060). Binds various RNAs, suchas rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs(PubMed:25470060). In the nucleolus, localizes to rDNA locus,where it directly binds rRNAs and snoRNAs, and promotes rRNAtranscription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes(PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SKRNA and is recruited to the promoters of Pol II-transcribed genes:acts by facilitating the release of P-TEFb from inhibitory 7SKsnRNP in a manner that is dependent on its helicase activity,thereby promoting transcription of its target genes(PubMed:25470060). Functions as cofactor for JUN-activatedtranscription: required for phosphorylation of JUN at 'Ser-77'(PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA(helicase) and can fold or introduce a secondary structure to asingle-stranded RNA (foldase) (PubMed:9461305). Involved in rRNAprocessing (PubMed:14559904, PubMed:18180292). May bind tospecific miRNA hairpins (PubMed:28431233).{ECO:0000269|PubMed:11823437, ECO:0000269|PubMed:14559904,ECO:0000269|PubMed:18180292, ECO:0000269|PubMed:25260534,ECO:0000269|PubMed:25470060, ECO:0000269|PubMed:25477391,ECO:0000269|PubMed:28431233, ECO:0000269|PubMed:9461305}. |
| 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 RER1_DDX21 |
| 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 RER1_DDX21 |
| 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 |
| RER1 | IMMT, HAP1, SH3GL3, UBL4A, SYVN1, PMP22, RNF2, EGFR, HLA-DPA1, TSPAN5, SLC39A4, POMK, ERGIC3, CHRNA9, UNK, ATP5A1, ATP5H, ATP5I, ATP5L, ATP5O, BCAP31, RAB1A, VDAC2, STX12, HERC2, TCTN2, TCTN3, TMEM17, TMEM216, DPEP1, SLC2A12, UPK1A, SYCE3, TRIM25 | DDX21 | LYAR, PSTPIP1, RTCA, SMNDC1, JUN, RRP1B, SRRM2, SRRM1, CTNNBL1, DOT1L, NPM1, NOP56, TOP1, CALM1, PCK1, HDGF, SIRT7, HNRNPA1, TERF1, TERF2, CUL3, CUL4A, CDK2, GRK5, RPL6, RPL7, RPL31, RPL37A, RPS11, RPS24, RPL5, RSL1D1, RPL19, RPS23, IK, RNPS1, SAP18, SRSF5, SRSF7, HNRNPR, SFPQ, EFTUD2, RBM39, PARP1, RRP7A, RRS1, THRAP3, SON, MYO1C, SSR3, FTSJ3, NFIA, NOP2, SMARCA1, PCDHA2, SUPT16H, PDS5A, LAMP2, LMNB1, S100A9, ESR1, APTX, H2AFX, SMURF1, YWHAE, VCAM1, FN1, CSNK2A1, IL7R, ITGA4, AICDA, PAN2, LYN, SRPK2, SRPK3, FBXO6, TARDBP, WWOX, ERG, LGR4, IVNS1ABP, STAU1, CEP250, HUWE1, PA2G4, KPNA3, CUL7, OBSL1, CCDC8, UBE2I, EED, SUMO2, ILK, MAST3, LUZP4, EBNA1BP2, RPL14, ZC3H3, THUMPD1, NTRK1, DDX50, SCARNA22, HIST1H3E, HNRNPU, RPL10, IBTK, MACROD1, MCM2, MCM5, CDC5L, U2AF2, C1orf131, ZNF746, RBM34, FGF8, WDR46, HIST1H1T, SYNCRIP, ZNF512, RPL30, CNBP, H2AFY2, MECP2, E4F1, GPATCH4, ZCRB1, RBM4, FGF3, NIFK, NCL, INO80B, COX15, DLST, DNM1L, VDAC1, G3BP1, BRCA1, LMNA, RNF168, TES, MTF1 |
| - 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 RER1_DDX21 |
| 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 RER1_DDX21 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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