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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 7768

FusionGeneSummary for CNTLN_RFX3

check button Fusion gene summary
Fusion gene informationFusion gene name: CNTLN_RFX3
Fusion gene ID: 7768
HgeneTgene
Gene symbol

CNTLN

RFX3

Gene ID

54875

5991

Gene namecentleinregulatory factor X3
SynonymsC9orf101|C9orf39|bA340N12.1-
Cytomap

9p22.2

9p24.2

Type of geneprotein-codingprotein-coding
Descriptioncentleincentlein, centrosomal proteincentrosomal proteintranscription factor RFX3DNA binding protein RFX3regulatory factor X, 3 (influences HLA class II expression)
Modification date2018051920180523
UniProtAcc

Q9NXG0

P48380

Ensembl transtripts involved in fusion geneENST00000380647, ENST00000262360, 
ENST00000425824, ENST00000380641, 
ENST00000484374, 
ENST00000382004, 
ENST00000358730, ENST00000302303, 
ENST00000381984, 
Fusion gene scores* DoF score3 X 3 X 3=273 X 3 X 2=18
# samples 42
** MAII scorelog2(4/27*10)=0.567040592723894
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(2/18*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CNTLN [Title/Abstract] AND RFX3 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
TgeneRFX3

GO:0045892

negative regulation of transcription, DNA-templated

12411430

TgeneRFX3

GO:0045893

positive regulation of transcription, DNA-templated

20148032


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVKIRCTCGA-B0-4696-01ACNTLNchr9

17226285

+RFX3chr9

3248185

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shitENST00000380647ENST00000382004CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000380647ENST00000358730CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000380647ENST00000302303CNTLNchr9

17226285

+RFX3chr9

3248185

-
5CDS-intronENST00000380647ENST00000381984CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000262360ENST00000382004CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000262360ENST00000358730CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000262360ENST00000302303CNTLNchr9

17226285

+RFX3chr9

3248185

-
5CDS-intronENST00000262360ENST00000381984CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000425824ENST00000382004CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000425824ENST00000358730CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000425824ENST00000302303CNTLNchr9

17226285

+RFX3chr9

3248185

-
5CDS-intronENST00000425824ENST00000381984CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000380641ENST00000382004CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000380641ENST00000358730CNTLNchr9

17226285

+RFX3chr9

3248185

-
Frame-shitENST00000380641ENST00000302303CNTLNchr9

17226285

+RFX3chr9

3248185

-
5CDS-intronENST00000380641ENST00000381984CNTLNchr9

17226285

+RFX3chr9

3248185

-
intron-3CDSENST00000484374ENST00000382004CNTLNchr9

17226285

+RFX3chr9

3248185

-
intron-3CDSENST00000484374ENST00000358730CNTLNchr9

17226285

+RFX3chr9

3248185

-
intron-3CDSENST00000484374ENST00000302303CNTLNchr9

17226285

+RFX3chr9

3248185

-
intron-intronENST00000484374ENST00000381984CNTLNchr9

17226285

+RFX3chr9

3248185

-

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FusionProtFeatures for CNTLN_RFX3


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

Q9NXG0

RFX3

P48380

Required for centrosome cohesion and recruitment ofCEP68 to centrosomes. {ECO:0000269|PubMed:24554434}.

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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FusionGeneSequence for CNTLN_RFX3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for CNTLN_RFX3


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
CNTLNSP1, BRCA1, HDAC6, TPM1, C9orf41, PRSS12, GOPCRFX3TRAF2, RFX6, RFX4, BIN1, CREB1, EWSR1, IRF6, PKNOX1, SOX2, FHL2, FHL3, TRIP6, SEC63, PABPC5, FOXJ1, FOXJ2, FOXN3, FAM188A, IGSF8, RFX1, HDAC1, XYLT2, RTCB, MTA2, PTOV1, DDX1, TBC1D32, VPS45, TAF6L, MBD2, CDK20, ACAD9, HDAC2, TMED4, CFAP20, PLK1


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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RelatedDrugs for CNTLN_RFX3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CNTLN_RFX3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneRFX3C0037274Dermatologic disorders1CTD_human
TgeneRFX3C0311375Arsenic Poisoning1CTD_human