|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 34853 |
FusionGeneSummary for SMC1A_UBQLN2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SMC1A_UBQLN2 | Fusion gene ID: 34853 | Hgene | Tgene | Gene symbol | SMC1A | UBQLN2 | Gene ID | 8243 | 29978 |
| Gene name | structural maintenance of chromosomes 1A | ubiquilin 2 | |
| Synonyms | CDLS2|DXS423E|SB1.8|SMC1|SMC1L1|SMC1alpha|SMCB | ALS15|CHAP1|DSK2|HRIHFB2157|N4BP4|PLIC2 | |
| Cytomap | Xp11.22 | Xp11.21 | |
| Type of gene | protein-coding | protein-coding | |
| Description | structural maintenance of chromosomes protein 1ASMC protein 1ASMC-1-alphaSMC1 (structural maintenance of chromosomes 1, yeast)-like 1segregation of mitotic chromosomes 1 | ubiquilin-2Nedd4 binding protein 4protein linking IAP with cytoskeleton 2ubiquitin-like product Chap1/Dsk2 | |
| Modification date | 20180522 | 20180519 | |
| UniProtAcc | Q14683 | Q9UHD9 | |
| Ensembl transtripts involved in fusion gene | ENST00000322213, ENST00000469129, ENST00000375340, | ENST00000338222, | |
| Fusion gene scores | * DoF score | 5 X 5 X 4=100 | 2 X 3 X 2=12 |
| # samples | 6 | 3 | |
| ** MAII score | log2(6/100*10)=-0.736965594166206 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/12*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SMC1A [Title/Abstract] AND UBQLN2 [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 | SMC1A | GO:0072423 | response to DNA damage checkpoint signaling | 11877377 |
| 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 | LD | LUSC | TCGA-60-2709-01A | SMC1A | chrX | 53431924 | - | UBQLN2 | chrX | 56591222 | + |
| * 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-3CDS | ENST00000322213 | ENST00000338222 | SMC1A | chrX | 53431924 | - | UBQLN2 | chrX | 56591222 | + |
| intron-3CDS | ENST00000469129 | ENST00000338222 | SMC1A | chrX | 53431924 | - | UBQLN2 | chrX | 56591222 | + |
| intron-3CDS | ENST00000375340 | ENST00000338222 | SMC1A | chrX | 53431924 | - | UBQLN2 | chrX | 56591222 | + |
Top |
FusionProtFeatures for SMC1A_UBQLN2 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SMC1A | UBQLN2 |
| Involved in chromosome cohesion during cell cycle and inDNA repair. Central component of cohesin complex. The cohesincomplex is required for the cohesion of sister chromatids afterDNA replication. The cohesin complex apparently forms a largeproteinaceous ring within which sister chromatids can be trapped.At anaphase, the complex is cleaved and dissociates fromchromatin, allowing sister chromatids to segregate. The cohesincomplex may also play a role in spindle pole assembly duringmitosis. Involved in DNA repair via its interaction with BRCA1 andits related phosphorylation by ATM, or via its phosphorylation byATR. Works as a downstream effector both in the ATM/NBS1 branchand in the ATR/MSH2 branch of S-phase checkpoint.{ECO:0000269|PubMed:11877377}. | Plays an important role in the regulation of differentprotein degradation mechanisms and pathways including ubiquitin-proteasome system (UPS), autophagy and the endoplasmic reticulum-associated protein degradation (ERAD) pathway. Mediates theproteasomal targeting of misfolded or accumulated proteins fordegradation by binding (via UBA domain) to their polyubiquitinchains and by interacting (via ubiquitin-like domain) with thesubunits of the proteasome (PubMed:10983987). Plays a role in theERAD pathway via its interaction with ER-localized proteinsFAF2/UBXD8 and HERPUD1 and may form a link between thepolyubiquitinated ERAD substrates and the proteasome(PubMed:24215460, PubMed:18307982). Involved in the regulation ofmacroautophagy and autophagosome formation; required formaturation of autophagy-related protein LC3 from the cytosolicform LC3-I to the membrane-bound form LC3-II and may assist in thematuration of autophagosomes to autolysosomes by mediatingautophagosome-lysosome fusion (PubMed:19148225, PubMed:20529957).Negatively regulates the endocytosis of GPCR receptors: AVPR2 andADRB2, by specifically reducing the rate at which receptor-arrestin complexes concentrate in clathrin-coated pits (CCPs)(PubMed:18199683). {ECO:0000269|PubMed:10983987,ECO:0000269|PubMed:18199683, ECO:0000269|PubMed:18307982,ECO:0000269|PubMed:19148225, ECO:0000269|PubMed:20529957,ECO:0000269|PubMed:24215460}. |
| 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 |
Top |
FusionGeneSequence for SMC1A_UBQLN2 |
| 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). |
Top |
FusionGenePPI for SMC1A_UBQLN2 |
| 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 |
| SMC1A | STYXL1, CASP4, CDK4, ATM, SMC3, MSH6, CHTF18, SYCP3, SMARCA5, RAD21, NUMA1, STAG1, STAG3, RAE1, SMC1A, USP13, USP32, MLH1, ATRX, AIRE, ATG2A, ATG4C, BECN1, CAMKK2, PRKAA2, MGMT, SRRM1, RPGR, ATR, PHF1, CTCF, PAXIP1, THRA, THRB, KDM1B, EHMT2, SSU72, STAG2, PDS5A, PDS5B, WFDC5, BRCA1, HDAC5, WAPAL, BARD1, SMARCAD1, POLR2A, NIPBL, CDK8, CEBPA, MDC1, CUL3, CDK2, NSMCE2, FBXO6, MCM7, SF3B3, SMC2, RBM14, ACIN1, NOTCH1, METTL21B, MCM6, RFC1, POLA1, HDAC8, HDAC11, CDK20, ANKRD28, ARMCX3, KIF13A, RPA3, RPA2, RPA1, STAU1, CUL7, OBSL1, CCDC8, EED, RNF2, EGFR, SIRT6, ABCE1, ESR1, CDCA5, SDF4, PSMC2, NDC80, PLK1, POLE, SF3A2, SMC4, NTRK1, SCARNA22, HIST1H3E, BPTF, GANC, PEX1, HLTF, YWHAZ, SNX3, MRPL50, AKR7A2, SAP30, KCTD2, OSBPL3, PRPF19, KIAA1191, MTUS1, HAUS3, GCC1, NUF2, MGME1, LSM14B, DDI1, IRF3, TEAD2, FOXB1, FOXG1, FOXJ2, EP300, BRD4, FOXL1, FOXQ1, NF2, USP37, SNW1, CDC5L, RNF126, DERL1, USP15, SPAG9, MCM2, MCM4, EPS15L1, IVNS1ABP, GTF3C4, HSF1, NCL, MTF1 | UBQLN2 | UBE3A, HSPA13, PSMA6, HERC6, HERC3, HERPUD1, PSMA2, RNF185, ATXN7, INSIG2, ELAVL1, BCL2L11, UBQLN1, UBQLN2, EPS15, EPN1, EPN2, UBQLN4, UBA2, SSSCA1, YAP1, ZRANB2, USP34, USP9X, IGBP1, SNAP23, ZFYVE19, UBE2A, RNH1, STAM, UBL7, PLAUR, TTC1, SEC23A, BID, EEF1B2, PRPF40A, RNF11, TARDBP, FBXO25, C1QA, CD93, FAF2, AARSD1, ADSL, CALU, MARCKS, P4HB, PDE12, PFDN2, CUL5, DNAJB1, NPLOC4, PRKACA, RNASEH2B, RPA2, TPD52L2, VBP1, WDR4, SHFM1, EMC7, EMC8, EMC3, MMGT1, EDEM1, PSMC2, PSMC1, RAD23A, RAD23B, C12orf10, ZMYM3, NTRK1, TP53, PSMA5, UBC, HTT, HNRNPA1, HNRNPA3, HNRNPU, SMURF1, ADRM1, SLC17A2, MTNR1B, HSPA1A, HSPA8, HSPA1B |
| - 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 |
Top |
RelatedDrugs for SMC1A_UBQLN2 |
| 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 |
Top |
RelatedDiseases for SMC1A_UBQLN2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SMC1A | C1802395 | Congenital muscular hypertrophy-cerebral syndrome | 5 | UNIPROT |
| Hgene | SMC1A | C0005695 | Bladder Neoplasm | 1 | CTD_human |
| Hgene | SMC1A | C0010606 | Adenoid Cystic Carcinoma | 1 | CTD_human |
| Hgene | SMC1A | C0023470 | Myeloid Leukemia | 1 | CTD_human |
| Tgene | UBQLN2 | C3275459 | AMYOTROPHIC LATERAL SCLEROSIS 15, WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA | 3 | UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|