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 | 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:COL5A1-DDX21 (FusionGDB2 ID:HG1289TG9188) |
Fusion Gene Summary for COL5A1-DDX21 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: COL5A1-DDX21 | Fusion gene ID: hg1289tg9188 | Hgene | Tgene | Gene symbol | COL5A1 | DDX21 | Gene ID | 1289 | 9188 |
| Gene name | collagen type V alpha 1 chain | DExD-box helicase 21 | |
| Synonyms | EDSC|EDSCL1 | GUA|GURDB|RH-II/GU|RH-II/GuA | |
| Cytomap | ('COL5A1')('DDX21') 9q34.3 | 10q22.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | collagen alpha-1(V) chaincollagen, type V, alpha 1 | nucleolar RNA helicase 2DEAD (Asp-Glu-Ala-Asp) box helicase 21DEAD (Asp-Glu-Ala-Asp) box polypeptide 21DEAD box protein 21DEAD-box helicase 21DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21Gu proteinRH II/GuRNA helicase II/Gu alphagu-alphanucleo | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P20908 | Q9NR30 | |
| Ensembl transtripts involved in fusion gene | ENST00000371817, ENST00000464187, | ||
| Fusion gene scores | * DoF score | 11 X 10 X 8=880 | 36 X 11 X 14=5544 |
| # samples | 12 | 37 | |
| ** MAII score | log2(12/880*10)=-2.87446911791614 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(37/5544*10)=-3.9053300816209 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: COL5A1 [Title/Abstract] AND DDX21 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | COL5A1(137736686)-DDX21(70723858), # samples:1 COL5A1(137734719)-DDX21(70723858), # 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 | COL5A1 | GO:1903225 | negative regulation of endodermal cell differentiation | 23154389 |
| Fusion gene information * 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 |
| ChimerDB4 | ACC | TCGA-P6-A5OG-01A | COL5A1 | chr9 | 137734719 | - | DDX21 | chr10 | 70723858 | + |
| ChimerDB4 | UCS | TCGA-N6-A4VG-01A | COL5A1 | chr9 | 137736686 | - | DDX21 | chr10 | 70723858 | + |
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Fusion Gene ORF analysis for COL5A1-DDX21 |
| 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 |
| 3UTR-intron | ENST00000371817 | ENST00000354185 | COL5A1 | chr9 | 137734719 | - | DDX21 | chr10 | 70723858 | + |
| 5CDS-intron | ENST00000371817 | ENST00000354185 | COL5A1 | chr9 | 137736686 | - | DDX21 | chr10 | 70723858 | + |
| intron-intron | ENST00000464187 | ENST00000354185 | COL5A1 | chr9 | 137734719 | - | DDX21 | chr10 | 70723858 | + |
| intron-intron | ENST00000464187 | ENST00000354185 | COL5A1 | chr9 | 137736686 | - | DDX21 | chr10 | 70723858 | + |
| 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 |
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Fusion Genomic Features for COL5A1-DDX21 |
| 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) |
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Fusion Protein Features for COL5A1-DDX21 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:137736686/:70723858) - 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. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| COL5A1 | DDX21 |
| 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. | FUNCTION: RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060, PubMed:28790157). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Together with SIRT7, required to prevent R-loop-associated DNA damage and transcription-associated genomic instability: deacetylation by SIRT7 activates the helicase activity, thereby overcoming R-loop-mediated stalling of RNA polymerases (PubMed:28790157). Involved in rRNA processing (PubMed:14559904, PubMed:18180292). May bind to specific miRNA hairpins (PubMed:28431233). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines via the adapter molecule TICAM1 (By similarity). {ECO:0000250|UniProtKB:Q9JIK5, ECO:0000269|PubMed:11823437, ECO:0000269|PubMed:14559904, ECO:0000269|PubMed:18180292, ECO:0000269|PubMed:25260534, ECO:0000269|PubMed:25470060, ECO:0000269|PubMed:25477391, ECO:0000269|PubMed:28431233, ECO:0000269|PubMed:28790157, ECO:0000269|PubMed:9461305}. |
| 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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Fusion Gene Sequence for COL5A1-DDX21 |
| 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. |
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Fusion Gene PPI Analysis for COL5A1-DDX21 |
| 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 |
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Related Drugs for COL5A1-DDX21 |
| 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 |
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Related Diseases for COL5A1-DDX21 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | COL5A1 | C4552122 | EHLERS-DANLOS SYNDROME, CLASSIC TYPE, 1 | 7 | GENOMICS_ENGLAND;UNIPROT |
| Hgene | COL5A1 | C0268335 | Ehlers-Danlos syndrome type 1 | 3 | CTD_human;GENOMICS_ENGLAND |
| Hgene | COL5A1 | C0220679 | Ehlers-Danlos Syndrome, Autosomal Dominant, Type Unspecified | 2 | ORPHANET |
| Hgene | COL5A1 | C0268336 | Ehlers-Danlos syndrome type 2 | 2 | CTD_human;GENOMICS_ENGLAND |
| Hgene | COL5A1 | C0000786 | Spontaneous abortion | 1 | CTD_human |
| Hgene | COL5A1 | C0000822 | Abortion, Tubal | 1 | CTD_human |
| Hgene | COL5A1 | C0005779 | Blood Coagulation Disorders | 1 | GENOMICS_ENGLAND |
| Hgene | COL5A1 | C0007097 | Carcinoma | 1 | CTD_human |
| Hgene | COL5A1 | C0022548 | Keloid | 1 | CTD_human |
| Hgene | COL5A1 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Hgene | COL5A1 | C0024667 | Animal Mammary Neoplasms | 1 | CTD_human |
| Hgene | COL5A1 | C0024668 | Mammary Neoplasms, Experimental | 1 | CTD_human |
| Hgene | COL5A1 | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| Hgene | COL5A1 | C0205696 | Anaplastic carcinoma | 1 | CTD_human |
| Hgene | COL5A1 | C0205697 | Carcinoma, Spindle-Cell | 1 | CTD_human |
| Hgene | COL5A1 | C0205698 | Undifferentiated carcinoma | 1 | CTD_human |
| Hgene | COL5A1 | C0205699 | Carcinomatosis | 1 | CTD_human |
| Hgene | COL5A1 | C0376358 | Malignant neoplasm of prostate | 1 | CTD_human |
| Hgene | COL5A1 | C1257925 | Mammary Carcinoma, Animal | 1 | CTD_human |
| Hgene | COL5A1 | C1458140 | Bleeding tendency | 1 | GENOMICS_ENGLAND |
| Hgene | COL5A1 | C1846545 | Autoimmune Lymphoproliferative Syndrome Type 2B | 1 | GENOMICS_ENGLAND |
| Hgene | COL5A1 | C3830362 | Early Pregnancy Loss | 1 | CTD_human |
| Hgene | COL5A1 | C4225429 | Ehlers-Danlos syndrome classic type | 1 | GENOMICS_ENGLAND |
| Hgene | COL5A1 | C4552766 | Miscarriage | 1 | CTD_human |
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