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Fusion gene ID: 2609 |
FusionGeneSummary for ARID1A_NIPBL |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: ARID1A_NIPBL | Fusion gene ID: 2609 | Hgene | Tgene | Gene symbol | ARID1A | NIPBL | Gene ID | 8289 | 25836 |
| Gene name | AT-rich interaction domain 1A | NIPBL, cohesin loading factor | |
| Synonyms | B120|BAF250|BAF250a|BM029|C1orf4|CSS2|ELD|MRD14|OSA1|P270|SMARCF1|hELD|hOSA1 | CDLS|CDLS1|IDN3|IDN3-B|Scc2 | |
| Cytomap | 1p36.11 | 5p13.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | AT-rich interactive domain-containing protein 1AARID domain-containing protein 1AAT rich interactive domain 1A (SWI-like)BRG1-associated factor 250aOSA1 nuclear proteinSWI-like proteinSWI/SNF complex protein p270SWI/SNF-related, matrix-associated, | nipped-B-like proteinNipped-B homologSCC2 homologdelanginsister chromatid cohesion 2 homolog | |
| Modification date | 20180519 | 20180527 | |
| UniProtAcc | O14497 | Q6KC79 | |
| Ensembl transtripts involved in fusion gene | ENST00000324856, ENST00000457599, ENST00000374152, ENST00000540690, | ENST00000282516, ENST00000448238, ENST00000504430, | |
| Fusion gene scores | * DoF score | 21 X 13 X 13=3549 | 7 X 7 X 4=196 |
| # samples | 31 | 7 | |
| ** MAII score | log2(31/3549*10)=-3.51707245378671 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/196*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: ARID1A [Title/Abstract] AND NIPBL [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain. | ||
| * 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 | ARID1A | GO:0006337 | nucleosome disassembly | 8895581 |
| Hgene | ARID1A | GO:0006338 | chromatin remodeling | 11726552 |
| Hgene | ARID1A | GO:0030520 | intracellular estrogen receptor signaling pathway | 12200431 |
| Hgene | ARID1A | GO:0030521 | androgen receptor signaling pathway | 12200431 |
| Hgene | ARID1A | GO:0042921 | glucocorticoid receptor signaling pathway | 12200431 |
| Hgene | ARID1A | GO:0045893 | positive regulation of transcription, DNA-templated | 12200431 |
| Tgene | NIPBL | GO:0000122 | negative regulation of transcription by RNA polymerase II | 18854353 |
| Tgene | NIPBL | GO:0031065 | positive regulation of histone deacetylation | 18854353 |
| Tgene | NIPBL | GO:0045892 | negative regulation of transcription, DNA-templated | 18854353 |
| Tgene | NIPBL | GO:0071921 | cohesin loading | 22628566 |
| 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 | LUSC | TCGA-18-4083-01A | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| * 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 |
| Frame-shift | ENST00000324856 | ENST00000282516 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| Frame-shift | ENST00000324856 | ENST00000448238 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| 5CDS-3UTR | ENST00000324856 | ENST00000504430 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| Frame-shift | ENST00000457599 | ENST00000282516 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| Frame-shift | ENST00000457599 | ENST00000448238 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| 5CDS-3UTR | ENST00000457599 | ENST00000504430 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| Frame-shift | ENST00000374152 | ENST00000282516 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| Frame-shift | ENST00000374152 | ENST00000448238 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| 5CDS-3UTR | ENST00000374152 | ENST00000504430 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| Frame-shift | ENST00000540690 | ENST00000282516 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| Frame-shift | ENST00000540690 | ENST00000448238 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
| 5CDS-3UTR | ENST00000540690 | ENST00000504430 | ARID1A | chr1 | 27102198 | + | NIPBL | chr5 | 36995724 | + |
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FusionProtFeatures for ARID1A_NIPBL |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| ARID1A | NIPBL |
| Plays an important role in the loading of the cohesincomplex on to DNA. Forms a heterodimeric complex (also known ascohesin loading complex) with MAU2/SCC4 which mediates the loadingof the cohesin complex onto chromatin (PubMed:22628566,PubMed:28914604). Plays a role in cohesin loading at sites of DNAdamage. Its recruitement to double-strand breaks (DSBs) sitesoccurs in a CBX3-, RNF8- and RNF168-dependent manner whereas itsrecruitement to UV irradiation-induced DNA damage sites occurs ina ATM-, ATR-, RNF8- and RNF168-dependent manner (PubMed:28167679).Along with ZNF609, promotes cortical neuron migration during braindevelopment by regulating the transcription of crucial genes inthis process. Preferentially binds promoters containing paused RNApolymerase II. Up-regulates the expression of SEMA3A, NRP1, PLXND1and GABBR2 genes, among others (By similarity).{ECO:0000250|UniProtKB:Q6KCD5, ECO:0000269|PubMed:22628566,ECO:0000269|PubMed:28167679, ECO:0000269|PubMed:28914604}. |
| 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 ARID1A_NIPBL |
| 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 ARID1A_NIPBL |
| 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 |
| ARID1A | KLF1, GATA1, SMARCB1, SMARCA4, SMARCA2, ING1, SMARCE1, PBRM1, SMARCC2, SMARCC1, PGR, BCL7C, HIC1, CUL2, ARID1B, SMAD2, SMAD3, CARM1, ADNP, RARA, SOX2, CHD7, SMARCD1, TP53, ELAVL1, SIRT7, TFAP4, CUL3, SMARCD2, ACTL6A, SMARCD3, PHF10, ECT2, YAP1, ITCH, NEDD4, SHMT2, MOV10, NXF1, EED, DPF3, DPF2, SS18, UNK, BCL7A, BCL7B, ESR1, NCOA1, RARB, RARG, EWSR1, SNW1, CDC5L, CUL1, SKP1, NFATC1, NFATC2, TOP1, CHEK1, VHL, EYA2, NR3C1, AR, ALDH2, TRIM25 | NIPBL | PRSS23, CBX5, SP100, CBX3, MLLT3, SMC1A, SMC3, MED23, CDK8, SIRT7, HINFP, TOMM40, PPT1, SF3A2, RAD21, MAU2, CDK6, RPA3, RPA2, RPA1, BRCA1, OBSL1, CCDC8, EED, EWSR1, RPL10, TFG, LDHD, SUCO, USP37, SNW1, CDC5L, ARFGAP1, TRIM25 |
| - 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 ARID1A_NIPBL |
| 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 ARID1A_NIPBL |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | ARID1A | C0038356 | Stomach Neoplasms | 3 | CTD_human |
| Hgene | ARID1A | C2239176 | Liver carcinoma | 3 | CTD_human |
| Hgene | ARID1A | C0001418 | Adenocarcinoma | 1 | CTD_human |
| Hgene | ARID1A | C0005695 | Bladder Neoplasm | 1 | CTD_human |
| Hgene | ARID1A | C0006413 | Burkitt Lymphoma | 1 | CTD_human |
| Hgene | ARID1A | C0007138 | Carcinoma, Transitional Cell | 1 | CTD_human |
| Hgene | ARID1A | C0010606 | Adenoid Cystic Carcinoma | 1 | CTD_human |
| Hgene | ARID1A | C0014170 | Endometrial Neoplasms | 1 | CTD_human |
| Hgene | ARID1A | C0027819 | Neuroblastoma | 1 | CTD_human |
| Hgene | ARID1A | C0036920 | Sezary Syndrome | 1 | CTD_human |
| Hgene | ARID1A | C0079772 | T-Cell Lymphoma | 1 | CTD_human |
| Hgene | ARID1A | C0079773 | Lymphoma, T-Cell, Cutaneous | 1 | CTD_human |
| Hgene | ARID1A | C0206698 | Cholangiocarcinoma | 1 | CTD_human |
| Hgene | ARID1A | C0265338 | Coffin-Siris syndrome | 1 | CTD_human;ORPHANET |
| Hgene | ARID1A | C0279628 | Adenocarcinoma Of Esophagus | 1 | CTD_human |
| Hgene | ARID1A | C0920269 | Microsatellite Instability | 1 | CTD_human |
| Hgene | ARID1A | C2931822 | Nasopharyngeal carcinoma | 1 | CTD_human |
| Tgene | NIPBL | C0270972 | Cornelia De Lange Syndrome | 9 | CTD_human;ORPHANET;UNIPROT |
| Tgene | NIPBL | C0005941 | Bone Diseases, Developmental | 1 | CTD_human |
| Tgene | NIPBL | C0018798 | Congenital Heart Defects | 1 | CTD_human |
| Tgene | NIPBL | C0260662 | Hearing problem | 1 | CTD_human |
| Tgene | NIPBL | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
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