|
||||||
|
 | 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:CALM1-NRDE2 (FusionGDB2 ID:12538) |
Fusion Gene Summary for CALM1-NRDE2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CALM1-NRDE2 | Fusion gene ID: 12538 | Hgene | Tgene | Gene symbol | CALM1 | NRDE2 | Gene ID | 801 | 55051 |
| Gene name | calmodulin 1 | NRDE-2, necessary for RNA interference, domain containing | |
| Synonyms | CALML2|CAM2|CAM3|CAMB|CAMC|CAMI|CAMIII|CPVT4|DD132|LQT14|PHKD|caM | C14orf102 | |
| Cytomap | 14q32.11 | 14q32.11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | calmodulin-1Calmodulin-2Calmodulin-3calmodulin 1 (phosphorylase kinase, delta)phosphorylase kinase subunit deltaphosphorylase kinase, delta subunitprepro-calmodulin 1 | nuclear exosome regulator NRDE2UPF0614 protein C14orf102protein NRDE2 homolog | |
| Modification date | 20200329 | 20200313 | |
| UniProtAcc | P0DP23 | Q9H7Z3 | |
| Ensembl transtripts involved in fusion gene | ENST00000356978, ENST00000447653, ENST00000544280, ENST00000553542, ENST00000555132, | ENST00000557106, ENST00000357904, ENST00000354366, | |
| Fusion gene scores | * DoF score | 13 X 13 X 3=507 | 3 X 3 X 2=18 |
| # samples | 15 | 3 | |
| ** MAII score | log2(15/507*10)=-1.75702324650746 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: CALM1 [Title/Abstract] AND NRDE2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CALM1(90870858)-NRDE2(90784457), # 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 | CALM1 | GO:0010880 | regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum | 20226167 |
| Hgene | CALM1 | GO:0032516 | positive regulation of phosphoprotein phosphatase activity | 8631777 |
| Hgene | CALM1 | GO:0035307 | positive regulation of protein dephosphorylation | 8631777 |
| Hgene | CALM1 | GO:0051343 | positive regulation of cyclic-nucleotide phosphodiesterase activity | 8631777 |
| Hgene | CALM1 | GO:0051592 | response to calcium ion | 7607248 |
| Hgene | CALM1 | GO:0060314 | regulation of ryanodine-sensitive calcium-release channel activity | 22067155 |
| Hgene | CALM1 | GO:0060315 | negative regulation of ryanodine-sensitive calcium-release channel activity | 26164367 |
| Hgene | CALM1 | GO:0060316 | positive regulation of ryanodine-sensitive calcium-release channel activity | 20226167 |
| Fusion gene breakpoints across CALM1 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
 |
| Fusion gene breakpoints across NRDE2 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
 |
| 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 |
| ChimerDB4 | STAD | TCGA-BR-A4PE-01A | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
Top |
Fusion Gene ORF analysis for CALM1-NRDE2 |
| 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 | ENST00000356978 | ENST00000557106 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 5CDS-5UTR | ENST00000447653 | ENST00000557106 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 5CDS-5UTR | ENST00000544280 | ENST00000557106 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 5CDS-5UTR | ENST00000553542 | ENST00000557106 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 5CDS-intron | ENST00000356978 | ENST00000357904 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 5CDS-intron | ENST00000447653 | ENST00000357904 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 5CDS-intron | ENST00000544280 | ENST00000357904 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 5CDS-intron | ENST00000553542 | ENST00000357904 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| In-frame | ENST00000356978 | ENST00000354366 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| In-frame | ENST00000447653 | ENST00000354366 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| In-frame | ENST00000544280 | ENST00000354366 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| In-frame | ENST00000553542 | ENST00000354366 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| intron-3CDS | ENST00000555132 | ENST00000354366 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| intron-5UTR | ENST00000555132 | ENST00000557106 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| intron-intron | ENST00000555132 | ENST00000357904 | CALM1 | chr14 | 90870858 | + | NRDE2 | chr14 | 90784457 | - |
| 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 CALM1-NRDE2 |
| 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) |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
 |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
Top |
Fusion Protein Features for CALM1-NRDE2 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr14:90870858/chr14:90784457) - 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 |
| CALM1 | NRDE2 |
| FUNCTION: Calmodulin mediates the control of a large number of enzymes, ion channels, aquaporins and other proteins through calcium-binding. Among the enzymes to be stimulated by the calmodulin-calcium complex are a number of protein kinases and phosphatases. Together with CCP110 and centrin, is involved in a genetic pathway that regulates the centrosome cycle and progression through cytokinesis (PubMed:16760425). Is a regulator of voltage-dependent L-type calcium channels (PubMed:31454269). Mediates calcium-dependent inactivation of CACNA1C (PubMed:26969752). Positively regulates calcium-activated potassium channel activity of KCNN2 (PubMed:27165696). Forms a potassium channel complex with KCNQ1 and regulates electrophysiological activity of the channel via calcium-binding (PubMed:25441029). Acts as a sensor to modulate the endomplasmic reticulum contacts with other organelles mediated by VMP1:ATP2A2 (PubMed:28890335). {ECO:0000269|PubMed:16760425, ECO:0000269|PubMed:23893133, ECO:0000269|PubMed:26969752, ECO:0000269|PubMed:27165696, ECO:0000269|PubMed:28890335, ECO:0000269|PubMed:31454269}.; FUNCTION: (Microbial infection) Required for Legionella pneumophila SidJ glutamylase activity. {ECO:0000269|PubMed:31330532}. | FUNCTION: Protein of the nuclear speckles that regulates RNA degradation and export from the nucleus through its interaction with MTREX an essential factor directing various RNAs to exosomal degradation (PubMed:30842217). Changes the conformation of MTREX, precluding its association with the nuclear exosome and interaction with proteins required for its function in RNA exosomal degradation (PubMed:30842217). Negatively regulates, for instance, the degradation of mRNAs and lncRNAs by inhibiting their MTREX-mediated recruitment to nuclear exosome (PubMed:30842217). By preventing the degradation of RNAs in the nucleus, it promotes their export to the cytoplasm (PubMed:30842217). U5 snRNP-associated RNA splicing factor which is required for efficient splicing of CEP131 pre-mRNA and plays an important role in centrosome maturation, integrity and function during mitosis (PubMed:30538148). Suppresses intron retention in a subset of pre-mRNAs containing short, GC-rich introns with relatively weak 5' and 3' splice sites (PubMed:30538148). Plays a role in DNA damage response (PubMed:29902117). {ECO:0000269|PubMed:29902117, ECO:0000269|PubMed:30538148, ECO:0000269|PubMed:30842217}. |
| 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 |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 61_383 | 21 | 1165.0 | Coiled coil | Ontology_term=ECO:0000255 | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 105_110 | 21 | 1165.0 | Compositional bias | Note=Poly-Ser | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 73_101 | 21 | 1165.0 | Compositional bias | Note=Lys-rich | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 81_91 | 21 | 1165.0 | Compositional bias | Note=Poly-Lys | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 163_266 | 21 | 1165.0 | Region | MID/MTR4-interacting domain | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 1067_1101 | 21 | 1165.0 | Repeat | Note=HAT 5 | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 305_337 | 21 | 1165.0 | Repeat | Note=HAT 1 | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 395_427 | 21 | 1165.0 | Repeat | Note=HAT 2 | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 758_792 | 21 | 1165.0 | Repeat | Note=HAT 3 | |
| Tgene | NRDE2 | chr14:90870858 | chr14:90784457 | ENST00000354366 | 0 | 14 | 978_1010 | 21 | 1165.0 | Repeat | Note=HAT 4 |
| - 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 CALM1-NRDE2 |
| 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 CALM1-NRDE2 |
| 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 CALM1-NRDE2 |
| 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 |
Top |
Related Diseases for CALM1-NRDE2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2021-Present -The University of Texas Health Science Center at Houston (UTHealth)
Web File Viewing | Emergency Information |Campus Carry|Site Policies