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Fusion gene ID: 19633 |
FusionGeneSummary for LETM1_NELFA |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LETM1_NELFA | Fusion gene ID: 19633 | Hgene | Tgene | Gene symbol | LETM1 | NELFA | Gene ID | 3954 | 7469 |
| Gene name | leucine zipper and EF-hand containing transmembrane protein 1 | negative elongation factor complex member A | |
| Synonyms | SLC55A1 | NELF-A|P/OKcl.15|WHSC2 | |
| Cytomap | 4p16.3 | 4p16.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | mitochondrial proton/calcium exchanger proteinLETM1 and EF-hand domain-containing protein 1, mitochondrialMdm38 homologleucine zipper-EF-hand containing transmembrane protein 1 | negative elongation factor Awolf-Hirschhorn syndrome candidate 2 protein | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | O95202 | Q9H3P2 | |
| Ensembl transtripts involved in fusion gene | ENST00000302787, ENST00000512189, | ENST00000382882, ENST00000411638, ENST00000542778, | |
| Fusion gene scores | * DoF score | 5 X 5 X 4=100 | 1 X 1 X 1=1 |
| # samples | 6 | 1 | |
| ** MAII score | log2(6/100*10)=-0.736965594166206 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: LETM1 [Title/Abstract] AND NELFA [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 | LETM1 | GO:0006851 | mitochondrial calcium ion transmembrane transport | 19797662 |
| Hgene | LETM1 | GO:0051560 | mitochondrial calcium ion homeostasis | 19797662 |
| Hgene | LETM1 | GO:0099093 | calcium export from the mitochondrion | 19797662 |
| 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 | UCEC | TCGA-PG-A914-01A | LETM1 | chr4 | 1823908 | - | NELFA | chr4 | 2025263 | - |
| * 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-intron | ENST00000302787 | ENST00000382882 | LETM1 | chr4 | 1823908 | - | NELFA | chr4 | 2025263 | - |
| 5CDS-intron | ENST00000302787 | ENST00000411638 | LETM1 | chr4 | 1823908 | - | NELFA | chr4 | 2025263 | - |
| 5CDS-intron | ENST00000302787 | ENST00000542778 | LETM1 | chr4 | 1823908 | - | NELFA | chr4 | 2025263 | - |
| intron-intron | ENST00000512189 | ENST00000382882 | LETM1 | chr4 | 1823908 | - | NELFA | chr4 | 2025263 | - |
| intron-intron | ENST00000512189 | ENST00000411638 | LETM1 | chr4 | 1823908 | - | NELFA | chr4 | 2025263 | - |
| intron-intron | ENST00000512189 | ENST00000542778 | LETM1 | chr4 | 1823908 | - | NELFA | chr4 | 2025263 | - |
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FusionProtFeatures for LETM1_NELFA |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LETM1 | NELFA |
| Mitochondrial proton/calcium antiporter that mediatesproton-dependent calcium efflux from mitochondrion(PubMed:19797662). Crucial for the maintenance of mitochondrialtubular networks and for the assembly of the supercomplexes of therespiratory chain (PubMed:18628306). Required for the maintenanceof the tubular shape and cristae organization (PubMed:18628306).In contrast to SLC8B1/NCLX, does not constitute the major factorfor mitochondrial calcium extrusion (PubMed:24898248).{ECO:0000269|PubMed:18628306, ECO:0000269|PubMed:19797662,ECO:0000269|PubMed:24898248}. | Essential component of the NELF complex, a complex thatnegatively regulates the elongation of transcription by RNApolymerase II. The NELF complex, which acts via an associationwith the DSIF complex and causes transcriptional pausing, iscounteracted by the P-TEFb kinase complex. The NELF complex isinvolved in HIV-1 latency possibly involving recruitment of PCF11to paused RNA polymerase II. In vitro, the NELFA:NELFCD subcomplexbinds to ssDNA and ssRNA in a sequence- and structure-dependentmanner. Probably required to interact with the RNA polymerase IIcomplex. {ECO:0000269|PubMed:10199401,ECO:0000269|PubMed:12563561, ECO:0000269|PubMed:12612062,ECO:0000305}. |
| 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 LETM1_NELFA |
| 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 LETM1_NELFA |
| 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 |
| LETM1 | ICT1, TBK1, ILF3, C12orf57, SYNCRIP, LATS2, PSMA3, CYP1A1, NTRK1, NDUFA4, COQ9, PTPMT1, C15orf48, PPM1A, USP47, SNRNP27, PCDHGB4, HSD3B2, FGB, MRPS11, LYPD4, RNF19B, ATP6V0D1 | NELFA | NELFE, NELFB, NELFCD, POLR2A, TCEA2, ATP1A1, APP, POLR2C, YWHAB, HECW2, SIAH1, PRR22, NXF1, NTRK1, POLR2B, SUPT5H, NCBP1, ATL2, INTS12, WIBG, FEZ1, PROSER2, MCM9, IGHMBP2, TMOD4 |
| - 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 LETM1_NELFA |
| 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 LETM1_NELFA |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LETM1 | C0026827 | Muscle hypotonia | 1 | CTD_human;HPO |
| Hgene | LETM1 | C0036572 | Seizures | 1 | CTD_human;HPO |
| Hgene | LETM1 | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| Hgene | LETM1 | C1956097 | Wolf-Hirschhorn Syndrome | 1 | CTD_human;ORPHANET |
| Hgene | LETM1 | C2239176 | Liver carcinoma | 1 | CTD_human |
| Hgene | LETM1 | C3714756 | Intellectual Disability | 1 | CTD_human |
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