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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: 17935

FusionGeneSummary for ITPKA_RTF1

check button Fusion gene summary
Fusion gene informationFusion gene name: ITPKA_RTF1
Fusion gene ID: 17935
HgeneTgene
Gene symbol

ITPKA

RTF1

Gene ID

3706

23168

Gene nameinositol-trisphosphate 3-kinase ARTF1 homolog, Paf1/RNA polymerase II complex component
SynonymsIP3-3KA|IP3KAGTL7|KIAA0252
Cytomap

15q15.1

15q15.1

Type of geneprotein-codingprotein-coding
Descriptioninositol-trisphosphate 3-kinase AIP3 3-kinase AIP3K Ainositol 1,4,5-trisphosphate 3-kinase AinsP 3-kinase ARNA polymerase-associated protein RTF1 homologRtf1, Paf1/RNA polymerase II complex component, homologortholog of mouse gene trap locus 7
Modification date2018051920180523
UniProtAcc

P23677

Q92541

Ensembl transtripts involved in fusion geneENST00000260386, ENST00000389629, 
ENST00000462276, 
Fusion gene scores* DoF score3 X 2 X 3=187 X 8 X 3=168
# samples 39
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(9/168*10)=-0.900464326449086
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ITPKA [Title/Abstract] AND RTF1 [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
TgeneRTF1

GO:0019827

stem cell population maintenance

19345177

TgeneRTF1

GO:0032968

positive regulation of transcription elongation from RNA polymerase II promoter

20178742

TgeneRTF1

GO:0045944

positive regulation of transcription by RNA polymerase II

20178742


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
TCGARVLUSCTCGA-85-8071-01AITPKAchr15

41786614

+RTF1chr15

41745099

+
* 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
In-frameENST00000260386ENST00000389629ITPKAchr15

41786614

+RTF1chr15

41745099

+
5CDS-3UTRENST00000260386ENST00000462276ITPKAchr15

41786614

+RTF1chr15

41745099

+

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FusionProtFeatures for ITPKA_RTF1


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

P23677

RTF1

Q92541

Component of the PAF1 complex (PAF1C) which has multiplefunctions during transcription by RNA polymerase II and isimplicated in regulation of development and maintenance ofembryonic stem cell pluripotency. PAF1C associates with RNApolymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms andis involved in transcriptional elongation, acting bothindepentently and synergistically with TCEA1 and in cooperationwith the DSIF complex and HTATSF1. PAF1C is required fortranscription of Hox and Wnt target genes. PAF1C is involved inhematopoiesis and stimulates transcriptional activity ofKMT2A/MLL1; it promotes leukemogenesis through association withKMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histonemodifications such as ubiquitination of histone H2B andmethylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits theRNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzymeUBE2A or UBE2B to chromatin which mediate monoubiquitination of'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2Bubiquitination is proposed to be coupled to transcription. PAF1Cis involved in mRNA 3' end formation probably through associationwith cleavage and poly(A) factors. In case of infection byinfluenza A strain H3N2, PAF1C associates with viral NS1 protein,thereby regulating gene transcription. Binds single-stranded DNA.Required for maximal induction of heat-shock genes. Required forthe trimethylation of histone H3 'Lys-4' (H3K4me3) on genesinvolved in stem cell pluripotency; this function is synergisticwith CXXC1 indicative for an involvement of a SET1 complex (Bysimilarity). {ECO:0000250, ECO:0000269|PubMed:19345177,ECO:0000269|PubMed:20178742}.

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
TgeneRTF1chr15:41786614chr15:41745099ENST00000389629+118526_560103711Coiled coilOntology_term=ECO:0000255
TgeneRTF1chr15:41786614chr15:41745099ENST00000389629+118135_173103711Compositional biasNote=Ser-rich
TgeneRTF1chr15:41786614chr15:41745099ENST00000389629+118174_345103711Compositional biasNote=Glu-rich
TgeneRTF1chr15:41786614chr15:41745099ENST00000389629+118214_307103711Compositional biasNote=Lys-rich
TgeneRTF1chr15:41786614chr15:41745099ENST00000389629+118353_484103711DomainPlus3

- In-frame and not-retained protein feature among the 13 regional features.
>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneITPKAchr15:41786614chr15:41745099ENST00000260386+17249_251163462Nucleotide bindingATP
HgeneITPKAchr15:41786614chr15:41745099ENST00000260386+17287_295163462RegionCalmodulin-binding
HgeneITPKAchr15:41786614chr15:41745099ENST00000260386+17312_319163462RegionSubstrate binding
TgeneRTF1chr15:41786614chr15:41745099ENST00000389629+11810_18103711Compositional biasNote=Poly-Ala


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FusionGeneSequence for ITPKA_RTF1


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 ITPKA_RTF1


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
ITPKAITSN2, DBN1RTF1ARRB1, PAF1, CTR9, LEO1, TCEA1, CDC73, WDR61, NEDD4, HADHA, HADHB, PTPN11, APP, SUPT16H, CSNK2A1, SSRP1, TRPM8, CD81, DNMT3B, DNMT3A, SRPK2, ETF1, GSPT1, SNX6, YAP1, STAT1, DENND2D, CHD1, RPL37, BRD4, NUMA1, RPL35A, UBTF, ZC3H18, SRRM2, SUPT5H, NTRK1, PIP4K2A, ARRB2


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 ITPKA_RTF1


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 ITPKA_RTF1


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