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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:GLI3-GLI3 (FusionGDB2 ID:HG2737TG2737) |
Fusion Gene Summary for GLI3-GLI3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: GLI3-GLI3 | Fusion gene ID: hg2737tg2737 | Hgene | Tgene | Gene symbol | GLI3 | GLI3 | Gene ID | 2737 | 2737 |
| Gene name | GLI family zinc finger 3 | GLI family zinc finger 3 | |
| Synonyms | ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV | ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV | |
| Cytomap | ('GLI3')('GLI3') 7p14.1 | 7p14.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | transcriptional activator GLI3GLI-Kruppel family member GLI3glioma-associated oncogene family zinc finger 3oncogene GLI3zinc finger protein GLI3 | transcriptional activator GLI3GLI-Kruppel family member GLI3glioma-associated oncogene family zinc finger 3oncogene GLI3zinc finger protein GLI3 | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P10071 | P10071 | |
| Ensembl transtripts involved in fusion gene | ENST00000395925, ENST00000479210, ENST00000437480, | ENST00000479210, ENST00000437480, ENST00000395925, | |
| Fusion gene scores | * DoF score | 11 X 11 X 8=968 | 7 X 7 X 5=245 |
| # samples | 14 | 8 | |
| ** MAII score | log2(14/968*10)=-2.78958022032963 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/245*10)=-1.61470984411521 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: GLI3 [Title/Abstract] AND GLI3 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | GLI3(42034993)-GLI3(42035984), # samples:1 GLI3(42063066)-GLI3(42088295), # samples:1 GLI3(42048577)-GLI3(42050811), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | GLI3-GLI3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. GLI3-GLI3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. GLI3-GLI3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. GLI3-GLI3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. | ||
| * 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 | GLI3 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 10693759|12435627|19084012 |
| Hgene | GLI3 | GO:0045892 | negative regulation of transcription, DNA-templated | 12435627|16254602|19084012 |
| Hgene | GLI3 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 17000779 |
| Hgene | GLI3 | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 17331723 |
| Tgene | GLI3 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 10693759|12435627|19084012 |
| Tgene | GLI3 | GO:0045892 | negative regulation of transcription, DNA-templated | 12435627|16254602|19084012 |
| Tgene | GLI3 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 17000779 |
| Tgene | GLI3 | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 17331723 |
| Fusion gene breakpoints across GLI3 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across GLI3 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| 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 |
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Fusion Gene ORF analysis for GLI3-GLI3 |
| 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 |
| 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 GLI3-GLI3 |
| 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. |
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Fusion Protein Features for GLI3-GLI3 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:42034993/chr7:42035984) - 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 |
| GLI3 | GLI3 |
| FUNCTION: Has a dual function as a transcriptional activator and a repressor of the sonic hedgehog (Shh) pathway, and plays a role in limb development. The full-length GLI3 form (GLI3FL) after phosphorylation and nuclear translocation, acts as an activator (GLI3A) while GLI3R, its C-terminally truncated form, acts as a repressor. A proper balance between the GLI3 activator and the repressor GLI3R, rather than the repressor gradient itself or the activator/repressor ratio gradient, specifies limb digit number and identity. In concert with TRPS1, plays a role in regulating the size of the zone of distal chondrocytes, in restricting the zone of PTHLH expression in distal cells and in activating chondrocyte proliferation. Binds to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'. {ECO:0000269|PubMed:10693759, ECO:0000269|PubMed:11238441, ECO:0000269|PubMed:17764085}. | FUNCTION: Has a dual function as a transcriptional activator and a repressor of the sonic hedgehog (Shh) pathway, and plays a role in limb development. The full-length GLI3 form (GLI3FL) after phosphorylation and nuclear translocation, acts as an activator (GLI3A) while GLI3R, its C-terminally truncated form, acts as a repressor. A proper balance between the GLI3 activator and the repressor GLI3R, rather than the repressor gradient itself or the activator/repressor ratio gradient, specifies limb digit number and identity. In concert with TRPS1, plays a role in regulating the size of the zone of distal chondrocytes, in restricting the zone of PTHLH expression in distal cells and in activating chondrocyte proliferation. Binds to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'. {ECO:0000269|PubMed:10693759, ECO:0000269|PubMed:11238441, ECO:0000269|PubMed:17764085}. |
| 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 | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | 3 | 15 | 1492_1512 | 157 | 1581.0 | Compositional bias | Note=Asp/Glu-rich (acidic) | |
| Tgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | 3 | 15 | 480_505 | 157 | 1581.0 | Zinc finger | C2H2-type 1 | |
| Tgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | 3 | 15 | 513_540 | 157 | 1581.0 | Zinc finger | C2H2-type 2 | |
| Tgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | 3 | 15 | 546_570 | 157 | 1581.0 | Zinc finger | C2H2-type 3 | |
| Tgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | 3 | 15 | 576_601 | 157 | 1581.0 | Zinc finger | C2H2-type 4 | |
| Tgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | 3 | 15 | 607_632 | 157 | 1581.0 | Zinc finger | C2H2-type 5 |
| - 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 |
| Hgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | - | 10 | 15 | 1492_1512 | 499 | 1581.0 | Compositional bias | Note=Asp/Glu-rich (acidic) |
| Hgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | - | 10 | 15 | 480_505 | 499 | 1581.0 | Zinc finger | C2H2-type 1 |
| Hgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | - | 10 | 15 | 513_540 | 499 | 1581.0 | Zinc finger | C2H2-type 2 |
| Hgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | - | 10 | 15 | 546_570 | 499 | 1581.0 | Zinc finger | C2H2-type 3 |
| Hgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | - | 10 | 15 | 576_601 | 499 | 1581.0 | Zinc finger | C2H2-type 4 |
| Hgene | GLI3 | chr7:42063066 | chr7:42088295 | ENST00000395925 | - | 10 | 15 | 607_632 | 499 | 1581.0 | Zinc finger | C2H2-type 5 |
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Fusion Gene Sequence for GLI3-GLI3 |
| 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 GLI3-GLI3 |
| 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 GLI3-GLI3 |
| 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 GLI3-GLI3 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | GLI3 | C0265306 | Greig cephalopolysyndactyly syndrome | 13 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
| Hgene | GLI3 | C0265220 | Pallister-Hall syndrome | 6 | CTD_human;GENOMICS_ENGLAND |
| Hgene | GLI3 | C0152427 | Polydactyly | 2 | CTD_human;GENOMICS_ENGLAND |
| Hgene | GLI3 | C0796147 | Acrocallosal Syndrome | 2 | ORPHANET |
| Hgene | GLI3 | C1868111 | Polydactyly, preaxial 4 | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET |
| Hgene | GLI3 | C1868120 | POSTAXIAL POLYDACTYLY, TYPE B | 2 | CTD_human;ORPHANET |
| Hgene | GLI3 | C2931760 | Acrocallosal syndrome, Schinzel type | 2 | ORPHANET |
| Hgene | GLI3 | C3887487 | Postaxial polydactyly type A | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET |
| Hgene | GLI3 | C4282400 | Polydactyly, Postaxial, Type A1 | 2 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
| Hgene | GLI3 | C0011999 | Diastematomyelia | 1 | CTD_human |
| Hgene | GLI3 | C0024623 | Malignant neoplasm of stomach | 1 | CTD_human |
| Hgene | GLI3 | C0027794 | Neural Tube Defects | 1 | CTD_human |
| Hgene | GLI3 | C0027806 | Neurenteric Cyst | 1 | CTD_human |
| Hgene | GLI3 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| Hgene | GLI3 | C0080218 | Tethered Cord Syndrome | 1 | CTD_human |
| Hgene | GLI3 | C0152234 | Iniencephaly | 1 | CTD_human |
| Hgene | GLI3 | C0152426 | Craniorachischisis | 1 | CTD_human |
| Hgene | GLI3 | C0162835 | Hypopigmentation disorder | 1 | CTD_human |
| Hgene | GLI3 | C0238198 | Gastrointestinal Stromal Tumors | 1 | CTD_human |
| Hgene | GLI3 | C0265553 | Polysyndactyly | 1 | ORPHANET |
| Hgene | GLI3 | C0265633 | Congenital absence of tibia | 1 | ORPHANET |
| Hgene | GLI3 | C0266453 | Exencephaly | 1 | CTD_human |
| Hgene | GLI3 | C0342418 | Hypothalamic hamartomas | 1 | CTD_human;GENOMICS_ENGLAND |
| Hgene | GLI3 | C0344479 | Spinal Cord Myelodysplasia | 1 | CTD_human |
| Hgene | GLI3 | C0702169 | Acrania | 1 | CTD_human |
| Hgene | GLI3 | C1708349 | Hereditary Diffuse Gastric Cancer | 1 | CTD_human |
| Hgene | GLI3 | C3179349 | Gastrointestinal Stromal Sarcoma | 1 | CTD_human |
| Hgene | GLI3 | C3495676 | Anorectal Malformations | 1 | GENOMICS_ENGLAND |
| Tgene | C0265306 | Greig cephalopolysyndactyly syndrome | 13 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT | |
| Tgene | C0265220 | Pallister-Hall syndrome | 6 | CTD_human;GENOMICS_ENGLAND | |
| Tgene | C0152427 | Polydactyly | 2 | CTD_human;GENOMICS_ENGLAND | |
| Tgene | C0796147 | Acrocallosal Syndrome | 2 | ORPHANET | |
| Tgene | C1868111 | Polydactyly, preaxial 4 | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET | |
| Tgene | C1868120 | POSTAXIAL POLYDACTYLY, TYPE B | 2 | CTD_human;ORPHANET | |
| Tgene | C2931760 | Acrocallosal syndrome, Schinzel type | 2 | ORPHANET | |
| Tgene | C3887487 | Postaxial polydactyly type A | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET | |
| Tgene | C4282400 | Polydactyly, Postaxial, Type A1 | 2 | CTD_human;GENOMICS_ENGLAND;UNIPROT | |
| Tgene | C0011999 | Diastematomyelia | 1 | CTD_human | |
| Tgene | C0024623 | Malignant neoplasm of stomach | 1 | CTD_human | |
| Tgene | C0027794 | Neural Tube Defects | 1 | CTD_human | |
| Tgene | C0027806 | Neurenteric Cyst | 1 | CTD_human | |
| Tgene | C0038356 | Stomach Neoplasms | 1 | CTD_human | |
| Tgene | C0080218 | Tethered Cord Syndrome | 1 | CTD_human | |
| Tgene | C0152234 | Iniencephaly | 1 | CTD_human | |
| Tgene | C0152426 | Craniorachischisis | 1 | CTD_human | |
| Tgene | C0162835 | Hypopigmentation disorder | 1 | CTD_human | |
| Tgene | C0238198 | Gastrointestinal Stromal Tumors | 1 | CTD_human | |
| Tgene | C0265553 | Polysyndactyly | 1 | ORPHANET | |
| Tgene | C0265633 | Congenital absence of tibia | 1 | ORPHANET | |
| Tgene | C0266453 | Exencephaly | 1 | CTD_human | |
| Tgene | C0342418 | Hypothalamic hamartomas | 1 | CTD_human;GENOMICS_ENGLAND | |
| Tgene | C0344479 | Spinal Cord Myelodysplasia | 1 | CTD_human | |
| Tgene | C0702169 | Acrania | 1 | CTD_human | |
| Tgene | C1708349 | Hereditary Diffuse Gastric Cancer | 1 | CTD_human | |
| Tgene | C3179349 | Gastrointestinal Stromal Sarcoma | 1 | CTD_human | |
| Tgene | C3495676 | Anorectal Malformations | 1 | GENOMICS_ENGLAND |
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