|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 19635 |
FusionGeneSummary for LETM1_SLBP |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LETM1_SLBP | Fusion gene ID: 19635 | Hgene | Tgene | Gene symbol | LETM1 | SLBP | Gene ID | 3954 | 7884 |
| Gene name | leucine zipper and EF-hand containing transmembrane protein 1 | stem-loop binding protein | |
| Synonyms | SLC55A1 | HBP | |
| 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 | histone RNA hairpin-binding proteinhairpin binding protein, histonehistone binding proteinhistone stem-loop binding proteinstem-loop (histone) binding protein | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | O95202 | Q14493 | |
| Ensembl transtripts involved in fusion gene | ENST00000302787, ENST00000512189, | ENST00000429429, ENST00000489418, ENST00000318386, ENST00000488267, | |
| Fusion gene scores | * DoF score | 5 X 5 X 4=100 | 3 X 3 X 2=18 |
| # 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(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: LETM1 [Title/Abstract] AND SLBP [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 |
| Tgene | SLBP | GO:0051028 | mRNA transport | 19155325 |
| 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 | STAD | TCGA-VQ-A8PE-01A | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| * 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 | ENST00000302787 | ENST00000429429 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| Frame-shift | ENST00000302787 | ENST00000489418 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| Frame-shift | ENST00000302787 | ENST00000318386 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| 5CDS-intron | ENST00000302787 | ENST00000488267 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| intron-3CDS | ENST00000512189 | ENST00000429429 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| intron-3CDS | ENST00000512189 | ENST00000489418 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| intron-3CDS | ENST00000512189 | ENST00000318386 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
| intron-intron | ENST00000512189 | ENST00000488267 | LETM1 | chr4 | 1821065 | - | SLBP | chr4 | 1705427 | - |
Top |
FusionProtFeatures for LETM1_SLBP |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LETM1 | SLBP |
| 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}. | RNA-binding protein involved in the histone pre-mRNAprocessing. Binds the stem-loop structure of replication-dependenthistone pre-mRNAs and contributes to efficient 3'-end processingby stabilizing the complex between histone pre-mRNA and U7 smallnuclear ribonucleoprotein (snRNP), via the histone downstreamelement (HDE). Plays an important role in targeting mature histonemRNA from the nucleus to the cytoplasm and to the translationmachinery. Stabilizes mature histone mRNA and could be involved incell-cycle regulation of histone gene expression. Involved in themechanism by which growing oocytes accumulate histone proteinsthat support early embryogenesis. Binds to the 5' side of thestem-loop structure of histone pre-mRNAs.{ECO:0000269|PubMed:12588979, ECO:0000269|PubMed:19155325}. |
| 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 LETM1_SLBP |
| 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 LETM1_SLBP |
| 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 | SLBP | ERI1, ZNF473, UPF1, CDK4, CDK6, GSTM3, HIST1H2BG, TACC3, FEM1A, FEM1B, FEM1C, CUL2, NCBP1, CTIF, CCNF, CCNA2, DCAF11, CUL4A, SKP1, CDK1, CDK2, EIF4G1, ZCCHC6, MIF4GD, CSNK2A1, CSNK2A2, CUL1, P4HA3, ZFC3H1 |
| - 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 LETM1_SLBP |
| 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 LETM1_SLBP |
| 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 |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|