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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: 31077

FusionGeneSummary for RFXAP_SMAD9

check button Fusion gene summary
Fusion gene informationFusion gene name: RFXAP_SMAD9
Fusion gene ID: 31077
HgeneTgene
Gene symbol

RFXAP

SMAD9

Gene ID

5994

4093

Gene nameregulatory factor X associated proteinSMAD family member 9
Synonyms-MADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B
Cytomap

13q13.3

13q13.3

Type of geneprotein-codingprotein-coding
Descriptionregulatory factor X-associated proteinRFX DNA-binding complex 36 kDa subunitRFX-associated proteinmothers against decapentaplegic homolog 9MAD homolog 9Mothers against decapentaplegic, drosophila, homolog of, 9SMAD, mothers against DPP homolog 9
Modification date2018052320180519
UniProtAcc

O00287

O15198

Ensembl transtripts involved in fusion geneENST00000255476, ENST00000472888, 
ENST00000350148, ENST00000379826, 
ENST00000483941, ENST00000399275, 
Fusion gene scores* DoF score1 X 1 X 1=12 X 2 X 2=8
# samples 12
** MAII scorelog2(1/1*10)=3.32192809488736log2(2/8*10)=1.32192809488736
Context

PubMed: RFXAP [Title/Abstract] AND SMAD9 [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

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
TCGARVDLBCTCGA-VB-A8QN-01ARFXAPchr13

37394094

+SMAD9chr13

37454012

-
* 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
5CDS-5UTRENST00000255476ENST00000350148RFXAPchr13

37394094

+SMAD9chr13

37454012

-
5CDS-5UTRENST00000255476ENST00000379826RFXAPchr13

37394094

+SMAD9chr13

37454012

-
5CDS-5UTRENST00000255476ENST00000483941RFXAPchr13

37394094

+SMAD9chr13

37454012

-
5CDS-intronENST00000255476ENST00000399275RFXAPchr13

37394094

+SMAD9chr13

37454012

-
intron-5UTRENST00000472888ENST00000350148RFXAPchr13

37394094

+SMAD9chr13

37454012

-
intron-5UTRENST00000472888ENST00000379826RFXAPchr13

37394094

+SMAD9chr13

37454012

-
intron-5UTRENST00000472888ENST00000483941RFXAPchr13

37394094

+SMAD9chr13

37454012

-
intron-intronENST00000472888ENST00000399275RFXAPchr13

37394094

+SMAD9chr13

37454012

-

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FusionProtFeatures for RFXAP_SMAD9


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

O00287

SMAD9

O15198

Part of the RFX complex that binds to the X-box of MHCII promoters. Transcriptional modulator activated by BMP (bonemorphogenetic proteins) type 1 receptor kinase. SMAD9 is areceptor-regulated SMAD (R-SMAD).

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 RFXAP_SMAD9


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 RFXAP_SMAD9


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
RFXAPRFX5, RFXANK, HDAC4, MLLT1, NCL, NHP2L1, EPS8, REV3L, ANKRA2SMAD9SMAD4, SMAD9, TOB1, HMGA2, KAT2A, KAT2B, NOTCH1, UBA6, MTMR11, EIF3F, PIR, KMT2D, KDM6A, ZEB2, MCM3AP, MAN1A2, SF3B1, DKK1, AP2A1, CSH1, CSH2, FTL, CYP11A1, PSAP, SNRNP70, RFX1, MGAT1, YWHAQ, ARNT, GRN, PHKA2, QARS, PSMD8, ZNF83, AFF1, METAP1, TERF1, EIF3E, ACTB, DSTN, LMO4, SPTBN1, FLI1, DST, PPARD, PAPPA, PABPC4, TRIM29, TRIP12, PLEC, SMAD2, PPP2R5E, CAMSAP1, RNF123, CEP135, E4F1, CTR9, TTC37, CXXC5, EVC2, CHPF, PELP1, VPS8, TMEM57, ZNF557, ZSCAN4, EXPH5, ARID1B, ZNF592, ZNF587B, ABTB1, PNPLA2, DNAJA3, OTUB1, VCPIP1, SVEP1, ERVV-1, ASB2, RANBP9, SECISBP2, EIF3C, DNAJC7, PKP2, ARHGAP9, TBCD, TINAGL1, CLPB, SIL1, UNC45A, C10orf2, RMND5A, HEYL, MAN1C1, BAZ1A, UBQLN4, DIAPH3, MTMR10, RRBP1, ASH2L, LRP5, NAGK, UBQLN1, LEMD3, HEY1, KDM1A, PRMT6, SMAD3, PSG9, DSG4, VSIG8, SMAD7, ZNF143, SMAP2, RBMS1


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 RFXAP_SMAD9


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 RFXAP_SMAD9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSMAD9C3888002PULMONARY HYPERTENSION, PRIMARY, 21UNIPROT