|
||||||
|
 | 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:LARP7-ALPK1 (FusionGDB2 ID:43921) |
Fusion Gene Summary for LARP7-ALPK1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LARP7-ALPK1 | Fusion gene ID: 43921 | Hgene | Tgene | Gene symbol | LARP7 | ALPK1 | Gene ID | 51574 | 80216 |
| Gene name | La ribonucleoprotein 7, transcriptional regulator | alpha kinase 1 | |
| Synonyms | ALAZS|HDCMA18P|PIP7S | 8430410J10Rik|LAK | |
| Cytomap | 4q25 | 4q25 | |
| Type of gene | protein-coding | protein-coding | |
| Description | la-related protein 7La ribonucleoprotein domain family member 7P-TEFb-interaction protein for 7SK stability | alpha-protein kinase 1chromosome 4 kinaselymphocyte alpha-kinaselymphocyte alpha-protein kinase | |
| Modification date | 20200313 | 20200320 | |
| UniProtAcc | Q4G0J3 | Q96QP1 | |
| Ensembl transtripts involved in fusion gene | ENST00000344442, ENST00000509061, ENST00000324052, ENST00000503898, | ENST00000458497, ENST00000177648, ENST00000504176, ENST00000505912, | |
| Fusion gene scores | * DoF score | 2 X 2 X 2=8 | 3 X 5 X 4=60 |
| # samples | 2 | 5 | |
| ** MAII score | log2(2/8*10)=1.32192809488736 | log2(5/60*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LARP7 [Title/Abstract] AND ALPK1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | ALPK1(113245232)-LARP7(113560614), # samples:2 LARP7(113558759)-ALPK1(113332983), # samples:2 | ||
| 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 |
| Tgene | ALPK1 | GO:0002753 | cytoplasmic pattern recognition receptor signaling pathway | 28222186|28877472|30111836 |
| Tgene | ALPK1 | GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB signaling | 28222186|28877472|30111836 |
| Tgene | ALPK1 | GO:0045087 | innate immune response | 28222186|28877472|30111836 |
| Fusion gene breakpoints across LARP7 (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 ALPK1 (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 | BRCA | TCGA-A8-A09N-01A | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| ChimerDB4 | BRCA | TCGA-A8-A09N-01A | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
Top |
Fusion Gene ORF analysis for LARP7-ALPK1 |
| 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-3CDS | ENST00000344442 | ENST00000458497 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000344442 | ENST00000177648 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000344442 | ENST00000504176 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3UTR | ENST00000344442 | ENST00000505912 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000509061 | ENST00000458497 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000509061 | ENST00000177648 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000509061 | ENST00000504176 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3UTR | ENST00000509061 | ENST00000505912 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| 5UTR-3CDS | ENST00000324052 | ENST00000458497 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| 5UTR-3CDS | ENST00000324052 | ENST00000177648 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| 5UTR-3CDS | ENST00000324052 | ENST00000504176 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| 5UTR-3UTR | ENST00000324052 | ENST00000505912 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000503898 | ENST00000458497 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000503898 | ENST00000177648 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3CDS | ENST00000503898 | ENST00000504176 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| intron-3UTR | ENST00000503898 | ENST00000505912 | LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332983 | + |
| 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 LARP7-ALPK1 |
| 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) |
| LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332982 | + | 3.38E-06 | 0.99999666 |
| LARP7 | chr4 | 113558759 | + | ALPK1 | chr4 | 113332982 | + | 3.38E-06 | 0.99999666 |
| 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 LARP7-ALPK1 |
| Go to FGviewer for the breakpoints of :-: - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LARP7 | ALPK1 |
| FUNCTION: RNA-binding protein that specifically binds distinct small nuclear RNA (snRNAs) and regulates their processing and function (PubMed:18249148, PubMed:32017898). Specifically binds the 7SK snRNA (7SK RNA) and acts as a core component of the 7SK ribonucleoprotein (RNP) complex, thereby acting as a negative regulator of transcription elongation by RNA polymerase II (PubMed:18249148, PubMed:18483487). The 7SK RNP complex sequesters the positive transcription elongation factor b (P-TEFb) in a large inactive 7SK RNP complex preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation (PubMed:18249148, PubMed:18483487). The 7SK RNP complex also promotes snRNA gene transcription by RNA polymerase II via interaction with the little elongation complex (LEC) (PubMed:28254838). LARP7 specifically binds to the highly conserved 3'-terminal U-rich stretch of 7SK RNA; on stimulation, remains associated with 7SK RNA, whereas P-TEFb is released from the complex (PubMed:18483487, PubMed:18281698). LARP7 also acts as a regulator of mRNA splicing fidelity by promoting U6 snRNA processing (PubMed:32017898). Specifically binds U6 snRNAs and associates with a subset of box C/D RNP complexes: promotes U6 snRNA 2'-O-methylation by facilitating U6 snRNA loading into box C/D RNP complexes (PubMed:32017898). U6 snRNA 2'-O-methylation is required for mRNA splicing fidelity (PubMed:32017898). Binds U6 snRNAs with a 5'-CAGGG-3' sequence motif (PubMed:32017898). U6 snRNA processing is required for spermatogenesis (By similarity). {ECO:0000250|UniProtKB:Q05CL8, ECO:0000269|PubMed:18249148, ECO:0000269|PubMed:18281698, ECO:0000269|PubMed:18483487, ECO:0000269|PubMed:28254838, ECO:0000269|PubMed:32017898}. | FUNCTION: Serine/threonine-protein kinase that detects bacterial pathogen-associated molecular pattern metabolites (PAMPs) and initiates an innate immune response, a critical step for pathogen elimination and engagement of adaptive immunity (PubMed:28877472, PubMed:28222186, PubMed:30111836). Specifically recognizes and binds ADP-D-glycero-beta-D-manno-heptose (ADP-Heptose), a potent PAMP present in all Gram-negative and some Gram-positive bacteria (PubMed:30111836). ADP-Heptose-binding stimulates its kinase activity to phosphorylate and activate TIFA, triggering proinflammatory NF-kappa-B signaling (PubMed:30111836). May be involved in monosodium urate monohydrate (MSU)-induced inflammation by mediating phosphorylation of unconventional myosin MYO9A (PubMed:27169898). May also play a role in apical protein transport by mediating phosphorylation of unconventional myosin MYO1A (PubMed:15883161). {ECO:0000269|PubMed:15883161, ECO:0000269|PubMed:27169898, ECO:0000269|PubMed:28222186, ECO:0000269|PubMed:28877472, ECO:0000269|PubMed:30111836}. |
| 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 LARP7-ALPK1 |
| 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 LARP7-ALPK1 |
| 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 LARP7-ALPK1 |
| 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 LARP7-ALPK1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LARP7 | C3554439 | Microcephalic primordial dwarfism Alazami type | 3 | CTD_human;GENOMICS_ENGLAND;ORPHANET |
| Hgene | LARP7 | C0013336 | Dwarfism | 1 | GENOMICS_ENGLAND |
| Hgene | LARP7 | C0020796 | Profound Mental Retardation | 1 | CTD_human |
| Hgene | LARP7 | C0025363 | Mental Retardation, Psychosocial | 1 | CTD_human |
| Hgene | LARP7 | C0342573 | PITUITARY DWARFISM I | 1 | GENOMICS_ENGLAND |
| Hgene | LARP7 | C0917816 | Mental deficiency | 1 | CTD_human |
| Hgene | LARP7 | C3714756 | Intellectual Disability | 1 | CTD_human |
| Tgene | ALPK1 | C0011849 | Diabetes Mellitus | 1 | CTD_human |
| Tgene | ALPK1 | C0011881 | Diabetic Nephropathy | 1 | CTD_human |
| Tgene | ALPK1 | C0017667 | Nodular glomerulosclerosis | 1 | CTD_human |
| Tgene | ALPK1 | C0018099 | Gout | 1 | CTD_human |
| Tgene | ALPK1 | C0027719 | Nephrosclerosis | 1 | CTD_human |
| Tgene | ALPK1 | C1262477 | Weight decreased | 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