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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CFTR-RAN (FusionGDB2 ID:16186)

Fusion Gene Summary for CFTR-RAN

check button Fusion gene summary
Fusion gene informationFusion gene name: CFTR-RAN
Fusion gene ID: 16186
HgeneTgene
Gene symbol

CFTR

RAN

Gene ID

1080

5901

Gene nameCF transmembrane conductance regulatorRAN, member RAS oncogene family
SynonymsABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1ARA24|Gsp1|TC4
Cytomap

7q31.2

12q24.33

Type of geneprotein-codingprotein-coding
Descriptioncystic fibrosis transmembrane conductance regulatorcAMP-dependent chloride channelchannel conductance-controlling ATPasecystic fibrosis transmembrane conductance regulatingcystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-fGTP-binding nuclear protein RanGTPase RanOK/SW-cl.81RanGTPaseandrogen receptor-associated protein 24guanosine triphosphatase Ranmember RAS oncogene familyras-like protein TC4ras-related nuclear protein
Modification date2020032920200313
UniProtAcc

P13569

RGPD8

Ensembl transtripts involved in fusion geneENST00000003084, ENST00000454343, 
ENST00000608965, 		ENST00000543796, 
ENST00000541630, ENST00000392369, 
ENST00000254675, ENST00000392367, 
Fusion gene scores* DoF score6 X 5 X 3=903 X 3 X 2=18
# samples 63
** MAII scorelog2(6/90*10)=-0.584962500721156
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: CFTR [Title/Abstract] AND RAN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCFTR(117267200)-RAN(131360154), # 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
HgeneCFTR

GO:0015701

bicarbonate transport

15010471|19019741

HgeneCFTR

GO:0034976

response to endoplasmic reticulum stress

21884936|28067262

HgeneCFTR

GO:1902476

chloride transmembrane transport

11524016|11707463|19019741

HgeneCFTR

GO:1902943

positive regulation of voltage-gated chloride channel activity

22006324

HgeneCFTR

GO:1904322

cellular response to forskolin

15010471|19621064

TgeneRAN

GO:0006606

protein import into nucleus

9822603

TgeneRAN

GO:0006611

protein export from nucleus

16449645|31075303

TgeneRAN

GO:0032092

positive regulation of protein binding

16449645

TgeneRAN

GO:0046039

GTP metabolic process

26272610


check buttonFusion gene breakpoints across CFTR (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across RAN (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ABP428521CFTRchr7

117267200

+RANchr12

131360154

+


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Fusion Gene ORF analysis for CFTR-RAN

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
intron-3CDSENST00000003084ENST00000543796CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000003084ENST00000541630CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000003084ENST00000392369CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000003084ENST00000254675CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000003084ENST00000392367CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000454343ENST00000543796CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000454343ENST00000541630CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000454343ENST00000392369CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000454343ENST00000254675CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000454343ENST00000392367CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000608965ENST00000543796CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000608965ENST00000541630CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000608965ENST00000392369CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000608965ENST00000254675CFTRchr7

117267200

+RANchr12

131360154

+
intron-3CDSENST00000608965ENST00000392367CFTRchr7

117267200

+RANchr12

131360154

+

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

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Fusion Genomic Features for CFTR-RAN


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)

check buttonDistribution 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.

check buttonDistribution 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.

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Fusion Protein Features for CFTR-RAN


check button 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CFTR

P13569

RAN

RGPD8

FUNCTION: Epithelial ion channel that plays an important role in the regulation of epithelial ion and water transport and fluid homeostasis (PubMed:26823428). Mediates the transport of chloride ions across the cell membrane (PubMed:10792060, PubMed:11524016, PubMed:11707463, PubMed:12519745, PubMed:15010471, PubMed:12588899, PubMed:17036051, PubMed:19398555, PubMed:19621064, PubMed:22178883, PubMed:25330774, PubMed:1712898, PubMed:8910473, PubMed:9804160, PubMed:12529365, PubMed:17182731, PubMed:26846474, PubMed:28087700). Channel activity is coupled to ATP hydrolysis (PubMed:8910473). The ion channel is also permeable to HCO(3-); selectivity depends on the extracellular chloride concentration (PubMed:15010471, PubMed:19019741). Exerts its function also by modulating the activity of other ion channels and transporters (PubMed:12403779, PubMed:22178883, PubMed:22121115, PubMed:27941075). Plays an important role in airway fluid homeostasis (PubMed:16645176, PubMed:19621064, PubMed:26823428). Contributes to the regulation of the pH and the ion content of the airway surface fluid layer and thereby plays an important role in defense against pathogens (PubMed:14668433, PubMed:16645176, PubMed:26823428). Modulates the activity of the epithelial sodium channel (ENaC) complex, in part by regulating the cell surface expression of the ENaC complex (PubMed:17434346, PubMed:27941075, PubMed:17182731). Inhibits the activity of the ENaC channel containing subunits SCNN1A, SCNN1B and SCNN1G (PubMed:17182731). Inhibits the activity of the ENaC channel containing subunits SCNN1D, SCNN1B and SCNN1G, but not of the ENaC channel containing subunits SCNN1A, SCNN1B and SCNN1G (PubMed:27941075). May regulate bicarbonate secretion and salvage in epithelial cells by regulating the transporter SLC4A7 (PubMed:12403779). Can inhibit the chloride channel activity of ANO1 (PubMed:22178883). Plays a role in the chloride and bicarbonate homeostasis during sperm epididymal maturation and capacitation (PubMed:19923167, PubMed:27714810). {ECO:0000269|PubMed:10792060, ECO:0000269|PubMed:11524016, ECO:0000269|PubMed:11707463, ECO:0000269|PubMed:12403779, ECO:0000269|PubMed:12519745, ECO:0000269|PubMed:12529365, ECO:0000269|PubMed:12588899, ECO:0000269|PubMed:14668433, ECO:0000269|PubMed:15010471, ECO:0000269|PubMed:16645176, ECO:0000269|PubMed:17036051, ECO:0000269|PubMed:1712898, ECO:0000269|PubMed:17182731, ECO:0000269|PubMed:19019741, ECO:0000269|PubMed:19398555, ECO:0000269|PubMed:19621064, ECO:0000269|PubMed:22178883, ECO:0000269|PubMed:25330774, ECO:0000269|PubMed:26627831, ECO:0000269|PubMed:26823428, ECO:0000269|PubMed:26846474, ECO:0000269|PubMed:27714810, ECO:0000269|PubMed:27941075, ECO:0000269|PubMed:28087700, ECO:0000269|PubMed:8910473, ECO:0000269|PubMed:9804160, ECO:0000305|PubMed:19923167}.1765

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


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Fusion Gene Sequence for CFTR-RAN


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.

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Fusion Gene PPI Analysis for CFTR-RAN


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


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Related Drugs for CFTR-RAN


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCFTRP13569DB00887BumetanideAntagonistSmall moleculeApproved
HgeneCFTRP13569DB00887BumetanideAntagonistSmall moleculeApproved
HgeneCFTRP13569DB01016GlyburideAntagonistSmall moleculeApproved
HgeneCFTRP13569DB01016GlyburideAntagonistSmall moleculeApproved
HgeneCFTRP13569DB01050IbuprofenInhibitorSmall moleculeApproved
HgeneCFTRP13569DB01050IbuprofenInhibitorSmall moleculeApproved
HgeneCFTRP13569DB04941CrofelemerAntagonistSmall moleculeApproved
HgeneCFTRP13569DB04941CrofelemerAntagonistSmall moleculeApproved
HgeneCFTRP13569DB08820IvacaftorPotentiatorSmall moleculeApproved
HgeneCFTRP13569DB08820IvacaftorPotentiatorSmall moleculeApproved
HgeneCFTRP13569DB09280LumacaftorModulatorSmall moleculeApproved
HgeneCFTRP13569DB09280LumacaftorModulatorSmall moleculeApproved
HgeneCFTRP13569DB09213DexibuprofenInhibitorSmall moleculeApproved|Investigational
HgeneCFTRP13569DB09213DexibuprofenInhibitorSmall moleculeApproved|Investigational
HgeneCFTRP13569DB11712TezacaftorActivatorSmall moleculeApproved|Investigational
HgeneCFTRP13569DB11712TezacaftorActivatorSmall moleculeApproved|Investigational
HgeneCFTRP13569DB15444ElexacaftorModulatorSmall moleculeApproved|Investigational
HgeneCFTRP13569DB15444ElexacaftorModulatorSmall moleculeApproved|Investigational

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Related Diseases for CFTR-RAN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCFTRC0010674Cystic Fibrosis91CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCFTRC0392164Pulmonary Cystic Fibrosis15CTD_human
HgeneCFTRC1527396Fibrocystic Disease of Pancreas15CTD_human
HgeneCFTRC0403814Congenital bilateral aplasia of vas deferens8CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCFTRC0238339Hereditary pancreatitis3CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneCFTRC0021364Male infertility2CTD_human
HgeneCFTRC0030305Pancreatitis2CTD_human
HgeneCFTRC0267937Acute recurrent pancreatitis2ORPHANET
HgeneCFTRC0339985Idiopathic bronchiectasis2ORPHANET
HgeneCFTRC0848676Subfertility, Male2CTD_human
HgeneCFTRC0917731Male sterility2CTD_human
HgeneCFTRC0001973Alcoholic Intoxication, Chronic1PSYGENET
HgeneCFTRC0004509Azoospermia1CTD_human
HgeneCFTRC0008340Choledochal Cyst1CTD_human
HgeneCFTRC0008370Cholestasis1GENOMICS_ENGLAND
HgeneCFTRC0009402Colorectal Carcinoma1CTD_human
HgeneCFTRC0009404Colorectal Neoplasms1CTD_human
HgeneCFTRC0009439Choledochal Cyst, Type I1CTD_human
HgeneCFTRC0013146Drug abuse1CTD_human
HgeneCFTRC0013170Drug habituation1CTD_human
HgeneCFTRC0013222Drug Use Disorders1CTD_human
HgeneCFTRC0019284Diaphragmatic Hernia1CTD_human
HgeneCFTRC0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneCFTRC0035455Rhinitis1CTD_human
HgeneCFTRC0037199Sinusitis1CTD_human
HgeneCFTRC0038580Substance Dependence1CTD_human
HgeneCFTRC0038586Substance Use Disorders1CTD_human
HgeneCFTRC0085548Autosomal Recessive Polycystic Kidney Disease1CTD_human
HgeneCFTRC0149521Pancreatitis, Chronic1CTD_human
HgeneCFTRC0236969Substance-Related Disorders1CTD_human
HgeneCFTRC0740858Substance abuse problem1CTD_human
HgeneCFTRC1257796Choledochal Cyst, Type II1CTD_human
HgeneCFTRC1257797Choledochal Cyst, Type III1CTD_human
HgeneCFTRC1257798Choledochal Cyst, Type IV1CTD_human
HgeneCFTRC1257799Choledochal Cyst, Type V1CTD_human
HgeneCFTRC1510472Drug Dependence1CTD_human
HgeneCFTRC4316881Prescription Drug Abuse1CTD_human
TgeneRANC0007097Carcinoma2CTD_human
TgeneRANC0024667Animal Mammary Neoplasms2CTD_human
TgeneRANC0024668Mammary Neoplasms, Experimental2CTD_human
TgeneRANC0205696Anaplastic carcinoma2CTD_human
TgeneRANC0205697Carcinoma, Spindle-Cell2CTD_human
TgeneRANC0205698Undifferentiated carcinoma2CTD_human
TgeneRANC0205699Carcinomatosis2CTD_human
TgeneRANC1257925Mammary Carcinoma, Animal2CTD_human
TgeneRANC0019693HIV Infections1CTD_human
TgeneRANC0022548Keloid1CTD_human
TgeneRANC0029408Degenerative polyarthritis1CTD_human
TgeneRANC0086743Osteoarthrosis Deformans1CTD_human
TgeneRANC4505456HIV Coinfection1CTD_human