Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CCL4-PRPF38A (FusionGDB2 ID:HG6351TG84950)

Fusion Gene Summary for CCL4-PRPF38A

check button Fusion gene summary
Fusion gene informationFusion gene name: CCL4-PRPF38A
Fusion gene ID: hg6351tg84950
HgeneTgene
Gene symbol

CCL4

PRPF38A

Gene ID

6351

84950

Gene nameC-C motif chemokine ligand 4pre-mRNA processing factor 38A
SynonymsACT2|AT744.1|G-26|HC21|LAG-1|LAG1|MIP-1-beta|MIP1B|MIP1B1|SCYA2|SCYA4PRP38A|Prp38
Cytomap('CCL4')('PRPF38A')

17q12

1p32.3

Type of geneprotein-codingprotein-coding
DescriptionC-C motif chemokine 4G-26 T-lymphocyte-secreted proteinMIP-1-beta(1-69)PAT 744SIS-gammaT-cell activation protein 2chemokine (C-C motif) ligand 4lymphocyte activation gene 1 proteinmacrophage inflammatory protein 1-betasecreted protein G-26small pre-mRNA-splicing factor 38APRP38 pre-mRNA processing factor 38 domain containing A
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000250151, ENST00000394495, 
Fusion gene scores* DoF score1 X 1 X 1=11 X 1 X 1=1
# samples 11
** MAII scorelog2(1/1*10)=3.32192809488736log2(1/1*10)=3.32192809488736
Context

PubMed: CCL4 [Title/Abstract] AND PRPF38A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCL4(34432864)-PRPF38A(52882577), # 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCCL4

GO:0009636

response to toxic substance

10841574

HgeneCCL4

GO:0043922

negative regulation by host of viral transcription

10841574

HgeneCCL4

GO:0051928

positive regulation of calcium ion transport

8699119

HgeneCCL4

GO:2000503

positive regulation of natural killer cell chemotaxis

7545673

TgenePRPF38A

GO:0000398

mRNA splicing, via spliceosome

28781166



check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand


Top

Fusion Gene ORF analysis for CCL4-PRPF38A

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

Top

Fusion Genomic Features for CCL4-PRPF38A


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


Top

Fusion Protein Features for CCL4-PRPF38A


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:34432864/:52882577)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention 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

download page


* 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


Top

Fusion Gene Sequence for CCL4-PRPF38A


check button 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 CCL4-PRPF38A


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


Top

Related Drugs for CCL4-PRPF38A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for CCL4-PRPF38A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCCL4C0020517Hypersensitivity2CTD_human
HgeneCCL4C1527304Allergic Reaction2CTD_human
HgeneCCL4C0004153Atherosclerosis1CTD_human
HgeneCCL4C0007786Brain Ischemia1CTD_human
HgeneCCL4C0017658Glomerulonephritis1CTD_human
HgeneCCL4C0021368Inflammation1CTD_human
HgeneCCL4C0032285Pneumonia1CTD_human
HgeneCCL4C0032300Lobar Pneumonia1CTD_human
HgeneCCL4C0034069Pulmonary Fibrosis1CTD_human
HgeneCCL4C0037274Dermatologic disorders1CTD_human
HgeneCCL4C0151744Myocardial Ischemia1CTD_human
HgeneCCL4C0273115Lung Injury1CTD_human
HgeneCCL4C0274861Arsenic Poisoning, Inorganic1CTD_human
HgeneCCL4C0274862Nervous System, Organic Arsenic Poisoning1CTD_human
HgeneCCL4C0311375Arsenic Poisoning1CTD_human
HgeneCCL4C0751851Arsenic Encephalopathy1CTD_human
HgeneCCL4C0751852Arsenic Induced Polyneuropathy1CTD_human
HgeneCCL4C0887898Experimental Lung Inflammation1CTD_human
HgeneCCL4C0917798Cerebral Ischemia1CTD_human
HgeneCCL4C0949804Polyomavirus Infections1CTD_human
HgeneCCL4C1563937Atherogenesis1CTD_human
HgeneCCL4C1704377Bright Disease1CTD_human
HgeneCCL4C2350344Chronic Lung Injury1CTD_human
HgeneCCL4C3714636Pneumonitis1CTD_human
HgeneCCL4C4721507Alveolitis, Fibrosing1CTD_human