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Fusion gene ID: 24395 |
FusionGeneSummary for NIPBL_SLC1A3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NIPBL_SLC1A3 | Fusion gene ID: 24395 | Hgene | Tgene | Gene symbol | NIPBL | SLC1A3 | Gene ID | 25836 | 6507 |
| Gene name | NIPBL, cohesin loading factor | solute carrier family 1 member 3 | |
| Synonyms | CDLS|CDLS1|IDN3|IDN3-B|Scc2 | EA6|EAAT1|GLAST|GLAST1 | |
| Cytomap | 5p13.2 | 5p13.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nipped-B-like proteinNipped-B homologSCC2 homologdelanginsister chromatid cohesion 2 homolog | excitatory amino acid transporter 1GLAST-1sodium-dependent glutamate/aspartate transporter 1solute carrier family 1 (glial high affinity glutamate transporter), member 3 | |
| Modification date | 20180527 | 20180519 | |
| UniProtAcc | Q6KC79 | P43003 | |
| Ensembl transtripts involved in fusion gene | ENST00000282516, ENST00000448238, ENST00000504430, | ENST00000265113, ENST00000506725, ENST00000381918, | |
| Fusion gene scores | * DoF score | 18 X 9 X 11=1782 | 10 X 9 X 6=540 |
| # samples | 24 | 12 | |
| ** MAII score | log2(24/1782*10)=-2.8923910259134 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(12/540*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: NIPBL [Title/Abstract] AND SLC1A3 [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 | NIPBL | GO:0000122 | negative regulation of transcription by RNA polymerase II | 18854353 |
| Hgene | NIPBL | GO:0031065 | positive regulation of histone deacetylation | 18854353 |
| Hgene | NIPBL | GO:0045892 | negative regulation of transcription, DNA-templated | 18854353 |
| Hgene | NIPBL | GO:0071921 | cohesin loading | 22628566 |
| Tgene | SLC1A3 | GO:0015813 | L-glutamate transmembrane transport | 26690923 |
| Tgene | SLC1A3 | GO:0051938 | L-glutamate import | 7521911 |
| Tgene | SLC1A3 | GO:0070779 | D-aspartate import across plasma membrane | 7521911 |
| Tgene | SLC1A3 | GO:0071805 | potassium ion transmembrane transport | 20477940 |
| Tgene | SLC1A3 | GO:0098712 | L-glutamate import across plasma membrane | 26690923 |
| Tgene | SLC1A3 | GO:0140009 | L-aspartate import across plasma membrane | 20477940 |
| Tgene | SLC1A3 | GO:1902476 | chloride transmembrane transport | 20477940 |
| 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 | LUAD | TCGA-50-5946-01A | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| TCGA | RV | SKCM | TCGA-EE-A2MJ-06A | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| * 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 |
| 5UTR-3CDS | ENST00000282516 | ENST00000265113 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| 5UTR-intron | ENST00000282516 | ENST00000506725 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| 5UTR-intron | ENST00000282516 | ENST00000381918 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| 5UTR-3CDS | ENST00000448238 | ENST00000265113 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| 5UTR-intron | ENST00000448238 | ENST00000506725 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| 5UTR-intron | ENST00000448238 | ENST00000381918 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| intron-3CDS | ENST00000504430 | ENST00000265113 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| intron-intron | ENST00000504430 | ENST00000506725 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| intron-intron | ENST00000504430 | ENST00000381918 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36671131 | + |
| 5UTR-5UTR | ENST00000282516 | ENST00000265113 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| 5UTR-3UTR | ENST00000282516 | ENST00000506725 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| 5UTR-3UTR | ENST00000282516 | ENST00000381918 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| 5UTR-5UTR | ENST00000448238 | ENST00000265113 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| 5UTR-3UTR | ENST00000448238 | ENST00000506725 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| 5UTR-3UTR | ENST00000448238 | ENST00000381918 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| intron-5UTR | ENST00000504430 | ENST00000265113 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| intron-3UTR | ENST00000504430 | ENST00000506725 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
| intron-3UTR | ENST00000504430 | ENST00000381918 | NIPBL | chr5 | 36877280 | + | SLC1A3 | chr5 | 36608431 | + |
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FusionProtFeatures for NIPBL_SLC1A3 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| NIPBL | SLC1A3 |
| 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}. | Sodium-dependent, high-affinity amino acid transporterthat mediates the uptake of L-glutamate and also L-aspartate andD-aspartate (PubMed:7521911, PubMed:8123008, PubMed:20477940,PubMed:26690923, PubMed:28032905, PubMed:28424515). Functions as asymporter that transports one amino acid molecule together withtwo or three Na(+) ions and one proton, in parallel with thecounter-transport of one K(+) ion (PubMed:20477940). MediatesCl(-) flux that is not coupled to amino acid transport; thisavoids the accumulation of negative charges due to aspartate andNa(+) symport (PubMed:20477940). Plays a redundant role in therapid removal of released glutamate from the synaptic cleft, whichis essential for terminating the postsynaptic action of glutamate(By similarity). {ECO:0000250|UniProtKB:P56564,ECO:0000269|PubMed:20477940, ECO:0000269|PubMed:26690923,ECO:0000269|PubMed:28032905, ECO:0000269|PubMed:28424515,ECO:0000269|PubMed:7521911, ECO:0000269|PubMed:8123008}. |
| 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 NIPBL_SLC1A3 |
| 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 NIPBL_SLC1A3 |
| 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 |
| 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 | SLC1A3 | CUL3, ZDHHC17, LGALS3, TCTN3, TMEM17, PDZK1 |
| - 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 NIPBL_SLC1A3 |
| 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 |
| Tgene | SLC1A3 | P43003 | DB00142 | Glutamic Acid | Excitatory amino acid transporter 1 {ECO:0000303|PubMed:16042756, ECO:0000303|PubMed:8647279} | small molecule | approved|nutraceutical |
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RelatedDiseases for NIPBL_SLC1A3 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | NIPBL | C0270972 | Cornelia De Lange Syndrome | 9 | CTD_human;ORPHANET;UNIPROT |
| Hgene | NIPBL | C0005941 | Bone Diseases, Developmental | 1 | CTD_human |
| Hgene | NIPBL | C0018798 | Congenital Heart Defects | 1 | CTD_human |
| Hgene | NIPBL | C0260662 | Hearing problem | 1 | CTD_human |
| Hgene | NIPBL | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| Tgene | SLC1A3 | C0036341 | Schizophrenia | 4 | PSYGENET |
| Tgene | SLC1A3 | C0004352 | Autistic Disorder | 1 | CTD_human |
| Tgene | SLC1A3 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| Tgene | SLC1A3 | C0014544 | Epilepsy | 1 | CTD_human;HPO |
| Tgene | SLC1A3 | C0178417 | Anhedonia | 1 | PSYGENET |
| Tgene | SLC1A3 | C2675211 | EPISODIC ATAXIA, TYPE 6 (disorder) | 1 | CTD_human;ORPHANET;UNIPROT |
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