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Fusion gene ID: 33177 |
FusionGeneSummary for SEMA6A_LSM6 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SEMA6A_LSM6 | Fusion gene ID: 33177 | Hgene | Tgene | Gene symbol | SEMA6A | LSM6 | Gene ID | 57556 | 11157 |
| Gene name | semaphorin 6A | LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated | |
| Synonyms | HT018|SEMA|SEMA6A1|SEMAQ|VIA | YDR378C | |
| Cytomap | 5q23.1 | 4q31.22 | |
| Type of gene | protein-coding | protein-coding | |
| Description | semaphorin-6ASEMA6A-1sema VIasema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Asemaphorin 6A-1semaphorin VIA | U6 snRNA-associated Sm-like protein LSm6LSM6 U6 small nuclear RNA and mRNA degradation associatedLSM6 homolog, U6 small nuclear RNA associatedSm protein F | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q9H2E6 | P62312 | |
| Ensembl transtripts involved in fusion gene | ENST00000343348, ENST00000257414, ENST00000510263, ENST00000513137, ENST00000282394, ENST00000503865, ENST00000503962, | ENST00000296581, ENST00000503982, ENST00000502781, | |
| Fusion gene scores | * DoF score | 6 X 6 X 2=72 | 1 X 1 X 1=1 |
| # samples | 11 | 1 | |
| ** MAII score | log2(11/72*10)=0.611434712082347 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: SEMA6A [Title/Abstract] AND LSM6 [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 | SEMA6A | GO:1903671 | negative regulation of sprouting angiogenesis | 22184411 |
| 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 | BRCA | TCGA-A8-A08I-01A | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| * 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-5UTR | ENST00000343348 | ENST00000296581 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-3UTR | ENST00000343348 | ENST00000503982 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-5UTR | ENST00000343348 | ENST00000502781 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-5UTR | ENST00000257414 | ENST00000296581 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-3UTR | ENST00000257414 | ENST00000503982 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-5UTR | ENST00000257414 | ENST00000502781 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-5UTR | ENST00000510263 | ENST00000296581 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-3UTR | ENST00000510263 | ENST00000503982 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| 5CDS-5UTR | ENST00000510263 | ENST00000502781 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000513137 | ENST00000296581 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-3UTR | ENST00000513137 | ENST00000503982 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000513137 | ENST00000502781 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000282394 | ENST00000296581 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-3UTR | ENST00000282394 | ENST00000503982 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000282394 | ENST00000502781 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000503865 | ENST00000296581 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-3UTR | ENST00000503865 | ENST00000503982 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000503865 | ENST00000502781 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000503962 | ENST00000296581 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-3UTR | ENST00000503962 | ENST00000503982 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
| intron-5UTR | ENST00000503962 | ENST00000502781 | SEMA6A | chr5 | 115822445 | - | LSM6 | chr4 | 147104064 | + |
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FusionProtFeatures for SEMA6A_LSM6 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SEMA6A | LSM6 |
| Cell surface receptor for PLXNA2 that plays an importantrole in cell-cell signaling. Required for normal granule cellmigration in the developing cerebellum. Promotes reorganization ofthe actin cytoskeleton and plays an important role in axonguidance in the developing central nervous system. Can act asrepulsive axon guidance cue. Has repulsive action towardsmigrating granular neurons. May play a role in channelingsympathetic axons into the sympathetic chains and controlling thetemporal sequence of sympathetic target innervation (Bysimilarity). {ECO:0000250}. | Component of LSm protein complexes, which are involvedin RNA processing and may function in a chaperone-like manner,facilitating the efficient association of RNA processing factorswith their substrates. Component of the cytoplasmic LSM1-LSM7complex, which is thought to be involved in mRNA degradation byactivating the decapping step in the 5'-to-3' mRNA decay pathway.Component of the nuclear LSM2-LSM8 complex, which is involved insplicing of nuclear mRNAs. LSM2-LSM8 associates with multiplesnRNP complexes containing the U6 snRNA (U4/U6 di-snRNP,spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It bindsdirectly to the 3'-terminal U-tract of U6 snRNA and plays a rolein the biogenesis and stability of the U6 snRNP and U4/U6 snRNPcomplexes. LSM2-LSM8 probably also is involved degradation ofnuclear pre-mRNA by targeting them for decapping, and inprocessing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity).{ECO:0000250}. |
| 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 SEMA6A_LSM6 |
| 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 SEMA6A_LSM6 |
| 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 |
| SEMA6A | EVL, SORBS2, ITSN2, SORBS1, SH3RF1, UBE2I, ITM2B, NCK2, PTCH1, TMEM17, TMEM216, MPPE1, PCDHGA5, INSL5, ADAM30 | LSM6 | SNRPD2, MCRS1, POLD2, LSM4, SMN1, USP15, USP4, PRPF4, SART3, APP, LSM3, LSM5, LSM8, LSM2, LSM7, DHX16, NAPG, SNRPF, CLNS1A, SOX2, LSM1, TARDBP, SDCBP, HERC4, CWC27, PKN2, PPP2R5C, SNRPD3, ZMAT2, NAA38, PATL1, TUT1, AKAP7, PRPF3, RIOK1, COPRS, MEPCE, WBP4, PRMT5, ZNF511, LSM10, SNRPE, SNRPD1, SNRPN, WDR77, PRPF31, GEMIN2, PPIH, ALYREF |
| - 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 SEMA6A_LSM6 |
| 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 | LSM6 | P62312 | DB04272 | Citric Acid | U6 snRNA-associated Sm-like protein LSm6 | small molecule | approved|nutraceutical|vet_approved |
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RelatedDiseases for SEMA6A_LSM6 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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