|
||||||
|
 | 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:GADD45GIP1-CSTF1 (FusionGDB2 ID:32156) |
Fusion Gene Summary for GADD45GIP1-CSTF1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: GADD45GIP1-CSTF1 | Fusion gene ID: 32156 | Hgene | Tgene | Gene symbol | GADD45GIP1 | CSTF1 | Gene ID | 90480 | 1477 |
| Gene name | GADD45G interacting protein 1 | cleavage stimulation factor subunit 1 | |
| Synonyms | CKBBP2|CKbetaBP2|CRIF1|MRP-L59|PLINP|PLINP-1|PRG6|Plinp1 | CstF-50|CstFp50 | |
| Cytomap | 19p13.13 | 20q13.2-q13.31 | |
| Type of gene | protein-coding | protein-coding | |
| Description | growth arrest and DNA damage-inducible proteins-interacting protein 139S ribosomal protein L59, mitochondrialCKII beta binding protein 2CKII beta-associating proteinCR6 interacting factor 1growth arrest and DNA-damage-inducible, gamma interacting pro | cleavage stimulation factor subunit 1CF-1 50 kDa subunitCSTF 50 kDa subunitcleavage stimulation factor 50 kDa subunitcleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDcleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q8TAE8 | Q05048 | |
| Ensembl transtripts involved in fusion gene | ENST00000316939, | ENST00000493039, ENST00000217109, | |
| Fusion gene scores | * DoF score | 4 X 5 X 4=80 | 3 X 4 X 2=24 |
| # samples | 6 | 4 | |
| ** MAII score | log2(6/80*10)=-0.415037499278844 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/24*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: GADD45GIP1 [Title/Abstract] AND CSTF1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | GADD45GIP1(13067676)-CSTF1(54978523), # samples:1 GADD45GIP1(13067677)-CSTF1(54978524), # 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 | GADD45GIP1 | GO:0071850 | mitotic cell cycle arrest | 24520316 |
| Fusion gene breakpoints across GADD45GIP1 (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 CSTF1 (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 | UCEC | TCGA-D1-A17K-01A | GADD45GIP1 | chr19 | 13067677 | - | CSTF1 | chr20 | 54978524 | + |
| ChimerDB4 | UCEC | TCGA-D1-A17K | GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + |
Top |
Fusion Gene ORF analysis for GADD45GIP1-CSTF1 |
| 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-3UTR | ENST00000316939 | ENST00000493039 | GADD45GIP1 | chr19 | 13067677 | - | CSTF1 | chr20 | 54978524 | + |
| 5CDS-3UTR | ENST00000316939 | ENST00000493039 | GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + |
| In-frame | ENST00000316939 | ENST00000217109 | GADD45GIP1 | chr19 | 13067677 | - | CSTF1 | chr20 | 54978524 | + |
| In-frame | ENST00000316939 | ENST00000217109 | GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + |
| 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) |
| ENST00000316939 | GADD45GIP1 | chr19 | 13067676 | - | ENST00000217109 | CSTF1 | chr20 | 54978523 | + | 1369 | 374 | 837 | 382 | 151 |
| ENST00000316939 | GADD45GIP1 | chr19 | 13067677 | - | ENST00000217109 | CSTF1 | chr20 | 54978524 | + | 1369 | 374 | 837 | 382 | 151 |
| 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 |
| ENST00000316939 | ENST00000217109 | GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + | 0.22306034 | 0.77693963 |
| ENST00000316939 | ENST00000217109 | GADD45GIP1 | chr19 | 13067677 | - | CSTF1 | chr20 | 54978524 | + | 0.22306034 | 0.77693963 |
Top |
Fusion Genomic Features for GADD45GIP1-CSTF1 |
| 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) |
| GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + | 1.82E-06 | 0.9999982 |
| GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + | 1.82E-06 | 0.9999982 |
| GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + | 1.82E-06 | 0.9999982 |
| GADD45GIP1 | chr19 | 13067676 | - | CSTF1 | chr20 | 54978523 | + | 1.82E-06 | 0.9999982 |
| 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 GADD45GIP1-CSTF1 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:13067676/chr20:54978523) - 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 |
| GADD45GIP1 | CSTF1 |
| FUNCTION: Acts as a negative regulator of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occurs also in the absence of GADD45 proteins. Acts as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity. May be involved in the hormone-mediated regulation of NR4A1 transcriptional activity. May play a role in mitochondrial protein synthesis. | FUNCTION: One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs (PubMed:10669729). May be responsible for the interaction of CSTF with other factors to form a stable complex on the pre-mRNA (PubMed:10669729). {ECO:0000303|PubMed:10669729}. |
| 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 | CSTF1 | chr19:13067676 | chr20:54978523 | ENST00000217109 | 4 | 6 | 395_430 | 345 | 432.0 | Repeat | Note=WD 6 | |
| Tgene | CSTF1 | chr19:13067677 | chr20:54978524 | ENST00000217109 | 4 | 6 | 395_430 | 345 | 432.0 | Repeat | Note=WD 6 |
| - 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 | GADD45GIP1 | chr19:13067676 | chr20:54978523 | ENST00000316939 | - | 1 | 2 | 99_212 | 116 | 223.0 | Coiled coil | Ontology_term=ECO:0000255 |
| Hgene | GADD45GIP1 | chr19:13067677 | chr20:54978524 | ENST00000316939 | - | 1 | 2 | 99_212 | 116 | 223.0 | Coiled coil | Ontology_term=ECO:0000255 |
| Hgene | GADD45GIP1 | chr19:13067676 | chr20:54978523 | ENST00000316939 | - | 1 | 2 | 136_139 | 116 | 223.0 | Compositional bias | Note=Poly-Gln |
| Hgene | GADD45GIP1 | chr19:13067677 | chr20:54978524 | ENST00000316939 | - | 1 | 2 | 136_139 | 116 | 223.0 | Compositional bias | Note=Poly-Gln |
| Hgene | GADD45GIP1 | chr19:13067676 | chr20:54978523 | ENST00000316939 | - | 1 | 2 | 184_200 | 116 | 223.0 | Motif | Nuclear localization signal |
| Hgene | GADD45GIP1 | chr19:13067677 | chr20:54978524 | ENST00000316939 | - | 1 | 2 | 184_200 | 116 | 223.0 | Motif | Nuclear localization signal |
| Tgene | CSTF1 | chr19:13067676 | chr20:54978523 | ENST00000217109 | 4 | 6 | 14_35 | 345 | 432.0 | Region | Note=Hydrophobic | |
| Tgene | CSTF1 | chr19:13067677 | chr20:54978524 | ENST00000217109 | 4 | 6 | 14_35 | 345 | 432.0 | Region | Note=Hydrophobic | |
| Tgene | CSTF1 | chr19:13067676 | chr20:54978523 | ENST00000217109 | 4 | 6 | 106_145 | 345 | 432.0 | Repeat | Note=WD 1 | |
| Tgene | CSTF1 | chr19:13067676 | chr20:54978523 | ENST00000217109 | 4 | 6 | 171_210 | 345 | 432.0 | Repeat | Note=WD 2 | |
| Tgene | CSTF1 | chr19:13067676 | chr20:54978523 | ENST00000217109 | 4 | 6 | 215_254 | 345 | 432.0 | Repeat | Note=WD 3 | |
| Tgene | CSTF1 | chr19:13067676 | chr20:54978523 | ENST00000217109 | 4 | 6 | 260_301 | 345 | 432.0 | Repeat | Note=WD 4 | |
| Tgene | CSTF1 | chr19:13067676 | chr20:54978523 | ENST00000217109 | 4 | 6 | 303_343 | 345 | 432.0 | Repeat | Note=WD 5 | |
| Tgene | CSTF1 | chr19:13067677 | chr20:54978524 | ENST00000217109 | 4 | 6 | 106_145 | 345 | 432.0 | Repeat | Note=WD 1 | |
| Tgene | CSTF1 | chr19:13067677 | chr20:54978524 | ENST00000217109 | 4 | 6 | 171_210 | 345 | 432.0 | Repeat | Note=WD 2 | |
| Tgene | CSTF1 | chr19:13067677 | chr20:54978524 | ENST00000217109 | 4 | 6 | 215_254 | 345 | 432.0 | Repeat | Note=WD 3 | |
| Tgene | CSTF1 | chr19:13067677 | chr20:54978524 | ENST00000217109 | 4 | 6 | 260_301 | 345 | 432.0 | Repeat | Note=WD 4 | |
| Tgene | CSTF1 | chr19:13067677 | chr20:54978524 | ENST00000217109 | 4 | 6 | 303_343 | 345 | 432.0 | Repeat | Note=WD 5 |
Top |
Fusion Gene Sequence for GADD45GIP1-CSTF1 |
| 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. |
| >32156_32156_1_GADD45GIP1-CSTF1_GADD45GIP1_chr19_13067676_ENST00000316939_CSTF1_chr20_54978523_ENST00000217109_length(transcript)=1369nt_BP=374nt CTGTGAGGACCCCGCACAGCCAAGATGGCGGCGTCCGTGCGACAGGCACGCAGCCTACTAGGTGTGGCGGCGACCCTGGCCCCGGGTTCC CGTGGCTACCGGGCGCGGCCGCCCCCGCGCCGCAGGCCGGGACCCCGGTGGCCAGACCCCGAGGACCTCCTGACCCCGCGGTGGCAGCTG GGACCGCGCTACGCGGCTAAGCAGTTCGCGCGTTACGGCGCCGCCTCCGGGGTGGTCCCCGGTTCGTTATGGCCGTCGCCGGAGCAGCTG CGGGAGCTGGAGGCCGAAGAACGCGAATGGTACCCGAGCCTGGCGACCATGCAGGAGTCGCTGCGGGTGAAGCAGCTGGCCGAAGAGCAG AAGCGTCGGGAGAGGCGCGGGTTTAAGTGGACGCCAGGTGCACCGGACACAGGCTGTGTTTAACCACACCGAGGACTATGTGTTGCTGCC CGACGAGAGGACGATCAGTCTTTGCTGCTGGGACTCGAGGACAGCCGAGCGGAGAAACCTGCTGTCGTTGGGGCACAACAATATTGTACG CTGCATAGTGCACTCCCCCACCAACCCCGGGTTCATGACGTGCAGCGATGACTTCAGAGCGCGGTTTTGGTACCGGAGATCGACCACTGA CTGAGCCACCCTCTCCGTAGGGTTCTTTCTCGAGGACTCTACCCTCCTCCCCCACGTCCTGTCTCAGCTGCAGTCGTAAGTCCGTGCACC ATCCTTGACGTTTTGCTGCCACCTCTGTCCACATTCTTCTTGGATTTGTATAAAAGAATCTTTTTTTACCTTGATGTAGAATCATGGTGG AAAAAGTTGGAAACACAGATCTGTGCAGTTCTACATTCACTGATTATTACAGTGTGATTTTCATCGGTTTTGTAAGTACAGGACTTGCCG TTTCTTTTGATCTCTTGATTGAAGGAGGATAGGGCATTAAAGTGCTTTTGACATGAGGAATTTTCATTTGGTTCTTCTGTCAACTTTCTT GCTTATTCTGCTGAACCCTCTGTGTATTTCCCTTCCAGGTATATTTGAACAGATAAGCAGGCATGCAGCTCTGAGACTCCTGAGTTTTAT GCCATTATCAAAAGCATTTTCAAGAATCCCTCAATTCTATCCTGAAATGATGTTATTCTGATAATAAAGCTCAGATCTGCAACTTTATTG TTATATATTTTTCACTTCTGTAAAATTAATGGCCAGTTTTTCCTGACAATTTATAGGAACAGTATCTTTCAACATACTCCCTACATTATC CTTCAATATCTGCAATACTTGTCTTTAGTAACTGTATTTCTGGTAAGATTATGATTTCATGAGAAACAATTGAAAATATATCCGATCTAA >32156_32156_1_GADD45GIP1-CSTF1_GADD45GIP1_chr19_13067676_ENST00000316939_CSTF1_chr20_54978523_ENST00000217109_length(amino acids)=151AA_BP= MHRSVFPTFSTMILHQGKKRFFYTNPRRMWTEVAAKRQGWCTDLRLQLRQDVGEEGRVLEKEPYGEGGSVSGRSPVPKPRSEVIAARHEP -------------------------------------------------------------- >32156_32156_2_GADD45GIP1-CSTF1_GADD45GIP1_chr19_13067677_ENST00000316939_CSTF1_chr20_54978524_ENST00000217109_length(transcript)=1369nt_BP=374nt CTGTGAGGACCCCGCACAGCCAAGATGGCGGCGTCCGTGCGACAGGCACGCAGCCTACTAGGTGTGGCGGCGACCCTGGCCCCGGGTTCC CGTGGCTACCGGGCGCGGCCGCCCCCGCGCCGCAGGCCGGGACCCCGGTGGCCAGACCCCGAGGACCTCCTGACCCCGCGGTGGCAGCTG GGACCGCGCTACGCGGCTAAGCAGTTCGCGCGTTACGGCGCCGCCTCCGGGGTGGTCCCCGGTTCGTTATGGCCGTCGCCGGAGCAGCTG CGGGAGCTGGAGGCCGAAGAACGCGAATGGTACCCGAGCCTGGCGACCATGCAGGAGTCGCTGCGGGTGAAGCAGCTGGCCGAAGAGCAG AAGCGTCGGGAGAGGCGCGGGTTTAAGTGGACGCCAGGTGCACCGGACACAGGCTGTGTTTAACCACACCGAGGACTATGTGTTGCTGCC CGACGAGAGGACGATCAGTCTTTGCTGCTGGGACTCGAGGACAGCCGAGCGGAGAAACCTGCTGTCGTTGGGGCACAACAATATTGTACG CTGCATAGTGCACTCCCCCACCAACCCCGGGTTCATGACGTGCAGCGATGACTTCAGAGCGCGGTTTTGGTACCGGAGATCGACCACTGA CTGAGCCACCCTCTCCGTAGGGTTCTTTCTCGAGGACTCTACCCTCCTCCCCCACGTCCTGTCTCAGCTGCAGTCGTAAGTCCGTGCACC ATCCTTGACGTTTTGCTGCCACCTCTGTCCACATTCTTCTTGGATTTGTATAAAAGAATCTTTTTTTACCTTGATGTAGAATCATGGTGG AAAAAGTTGGAAACACAGATCTGTGCAGTTCTACATTCACTGATTATTACAGTGTGATTTTCATCGGTTTTGTAAGTACAGGACTTGCCG TTTCTTTTGATCTCTTGATTGAAGGAGGATAGGGCATTAAAGTGCTTTTGACATGAGGAATTTTCATTTGGTTCTTCTGTCAACTTTCTT GCTTATTCTGCTGAACCCTCTGTGTATTTCCCTTCCAGGTATATTTGAACAGATAAGCAGGCATGCAGCTCTGAGACTCCTGAGTTTTAT GCCATTATCAAAAGCATTTTCAAGAATCCCTCAATTCTATCCTGAAATGATGTTATTCTGATAATAAAGCTCAGATCTGCAACTTTATTG TTATATATTTTTCACTTCTGTAAAATTAATGGCCAGTTTTTCCTGACAATTTATAGGAACAGTATCTTTCAACATACTCCCTACATTATC CTTCAATATCTGCAATACTTGTCTTTAGTAACTGTATTTCTGGTAAGATTATGATTTCATGAGAAACAATTGAAAATATATCCGATCTAA >32156_32156_2_GADD45GIP1-CSTF1_GADD45GIP1_chr19_13067677_ENST00000316939_CSTF1_chr20_54978524_ENST00000217109_length(amino acids)=151AA_BP= MHRSVFPTFSTMILHQGKKRFFYTNPRRMWTEVAAKRQGWCTDLRLQLRQDVGEEGRVLEKEPYGEGGSVSGRSPVPKPRSEVIAARHEP -------------------------------------------------------------- |
Top |
Fusion Gene PPI Analysis for GADD45GIP1-CSTF1 |
| 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 GADD45GIP1-CSTF1 |
| 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 GADD45GIP1-CSTF1 |
| 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