|
||||||
|
 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:LSM6-COL5A2 (FusionGDB2 ID:HG11157TG1290) |
Fusion Gene Summary for LSM6-COL5A2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LSM6-COL5A2 | Fusion gene ID: hg11157tg1290 | Hgene | Tgene | Gene symbol | LSM6 | COL5A2 | Gene ID | 11157 | 1290 |
| Gene name | LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated | collagen type V alpha 2 chain | |
| Synonyms | YDR378C | EDSC|EDSCL2 | |
| Cytomap | ('LSM6')('COL5A2') 4q31.22 | 2q32.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | U6 snRNA-associated Sm-like protein LSm6LSM6 U6 small nuclear RNA and mRNA degradation associatedLSM6 homolog, U6 small nuclear RNA associatedSm protein F | collagen alpha-2(V) chainAB collagencollagen, fetal membrane, A polypeptidetype V preprocollagen alpha 2 chain | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P62312 | P05997 | |
| Ensembl transtripts involved in fusion gene | ENST00000296581, ENST00000502781, ENST00000503982, | ||
| Fusion gene scores | * DoF score | 3 X 3 X 1=9 | 8 X 9 X 4=288 |
| # samples | 3 | 9 | |
| ** MAII score | log2(3/9*10)=1.73696559416621 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(9/288*10)=-1.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LSM6 [Title/Abstract] AND COL5A2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | LSM6(147118319)-COL5A2(189897240), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | LSM6 | GO:0000398 | mRNA splicing, via spliceosome | 28781166 |
| Hgene | LSM6 | GO:0006402 | mRNA catabolic process | 12515382 |
| Tgene | COL5A2 | GO:1903225 | negative regulation of endodermal cell differentiation | 23154389 |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS5.0 | N/A | BI491243 | LSM6 | chr4 | 147118319 | + | COL5A2 | chr2 | 189897240 | + |
Top |
Fusion Gene ORF analysis for LSM6-COL5A2 |
| 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-3UTR | ENST00000296581 | ENST00000374866 | LSM6 | chr4 | 147118319 | + | COL5A2 | chr2 | 189897240 | + |
| intron-3UTR | ENST00000502781 | ENST00000374866 | LSM6 | chr4 | 147118319 | + | COL5A2 | chr2 | 189897240 | + |
| intron-3UTR | ENST00000503982 | ENST00000374866 | LSM6 | chr4 | 147118319 | + | COL5A2 | chr2 | 189897240 | + |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
Top |
Fusion Genomic Features for LSM6-COL5A2 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
Top |
Fusion Protein Features for LSM6-COL5A2 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:147118319/:189897240) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LSM6 | COL5A2 |
| FUNCTION: Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320). Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway (Probable). {ECO:0000269|PubMed:10523320, ECO:0000269|PubMed:28781166, ECO:0000305|PubMed:12515382}. | FUNCTION: Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin. Type V collagen is a key determinant in the assembly of tissue-specific matrices (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 |
Top |
Fusion Gene Sequence for LSM6-COL5A2 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
Top |
Fusion Gene PPI Analysis for LSM6-COL5A2 |
| 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 |
| - 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 |
Related Drugs for LSM6-COL5A2 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | LSM6 | P62312 | DB04272 | Citric acid | Small molecule | Approved|Nutraceutical|Vet_approved |
Top |
Related Diseases for LSM6-COL5A2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | C4538407 | EHLERS-DANLOS SYNDROME, CLASSIC TYPE, 2 | 4 | GENOMICS_ENGLAND;UNIPROT | |
| Tgene | C4552122 | EHLERS-DANLOS SYNDROME, CLASSIC TYPE, 1 | 3 | GENOMICS_ENGLAND | |
| Tgene | C0220679 | Ehlers-Danlos Syndrome, Autosomal Dominant, Type Unspecified | 2 | ORPHANET | |
| Tgene | C3151201 | MULTISYSTEMIC SMOOTH MUSCLE DYSFUNCTION SYNDROME | 2 | GENOMICS_ENGLAND | |
| Tgene | C0000786 | Spontaneous abortion | 1 | CTD_human | |
| Tgene | C0000822 | Abortion, Tubal | 1 | CTD_human | |
| Tgene | C0005779 | Blood Coagulation Disorders | 1 | GENOMICS_ENGLAND | |
| Tgene | C0023890 | Liver Cirrhosis | 1 | CTD_human | |
| Tgene | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human | |
| Tgene | C0239946 | Fibrosis, Liver | 1 | CTD_human | |
| Tgene | C0268335 | Ehlers-Danlos syndrome type 1 | 1 | GENOMICS_ENGLAND | |
| Tgene | C0268336 | Ehlers-Danlos syndrome type 2 | 1 | GENOMICS_ENGLAND | |
| Tgene | C1458140 | Bleeding tendency | 1 | GENOMICS_ENGLAND | |
| Tgene | C1846545 | Autoimmune Lymphoproliferative Syndrome Type 2B | 1 | GENOMICS_ENGLAND | |
| Tgene | C3830362 | Early Pregnancy Loss | 1 | CTD_human | |
| Tgene | C4225429 | Ehlers-Danlos syndrome classic type | 1 | GENOMICS_ENGLAND | |
| Tgene | C4552766 | Miscarriage | 1 | CTD_human |
Copyright 2021-Present -The University of Texas Health Science Center at Houston (UTHealth)
Web File Viewing | Emergency Information |Campus Carry|Site Policies