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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: 32416

FusionGeneSummary for RUNX2_IFT88

check button Fusion gene summary
Fusion gene informationFusion gene name: RUNX2_IFT88
Fusion gene ID: 32416
HgeneTgene
Gene symbol

RUNX2

IFT88

Gene ID

860

8100

Gene namerunt related transcription factor 2intraflagellar transport 88
SynonymsAML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aAD13S1056E|DAF19|TG737|TTC10|hTg737
Cytomap

6p21.1

13q12.11

Type of geneprotein-codingprotein-coding
Descriptionrunt-related transcription factor 2PEA2-alpha APEBP2-alpha ASL3-3 enhancer factor 1 alpha A subunitSL3/AKV core-binding factor alpha A subunitacute myeloid leukemia 3 proteincore-binding factor, runt domain, alpha subunit 1oncogene AML-3osteoblastintraflagellar transport protein 88 homologTPR repeat protein 10intraflagellar transport 88 homologpolaris homologprobe hTg737 (polycystic kidney disease, autosomal recessive)recessive polycystic kidney disease protein Tg737 homologtesticular tissue
Modification date2018052320180523
UniProtAcc

Q13950

Q13099

Ensembl transtripts involved in fusion geneENST00000541979, ENST00000465038, 
ENST00000352853, ENST00000371438, 
ENST00000371436, ENST00000576263, 
ENST00000371432, ENST00000359524, 
ENST00000483243, 
ENST00000382778, 
ENST00000351808, ENST00000319980, 
ENST00000537103, ENST00000461115, 
Fusion gene scores* DoF score2 X 2 X 2=88 X 9 X 5=360
# samples 411
** MAII scorelog2(4/8*10)=2.32192809488736log2(11/360*10)=-1.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RUNX2 [Title/Abstract] AND IFT88 [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
HgeneRUNX2

GO:0045892

negative regulation of transcription, DNA-templated

11965546

HgeneRUNX2

GO:0045893

positive regulation of transcription, DNA-templated

11965546


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
TCGARVBRCATCGA-BH-A18V-06ARUNX2chr6

45459851

+IFT88chr13

21264844

+
TCGALDBRCATCGA-A7-A3J0-01ARUNX2chr6

45459851

+IFT88chr13

21265193

+
TCGALDBRCATCGA-BH-A18V-01ARUNX2chr6

45459851

+IFT88chr13

21264844

+
* 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-3UTRENST00000541979ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000541979ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000541979ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000541979ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000541979ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000465038ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000465038ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000465038ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000465038ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000465038ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000352853ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000352853ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000352853ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000352853ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000352853ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371438ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371438ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371438ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371438ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000371438ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371436ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371436ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371436ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371436ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000371436ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000576263ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000576263ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000576263ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000576263ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000576263ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371432ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371432ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371432ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000371432ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000371432ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000359524ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000359524ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000359524ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000359524ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-intronENST00000359524ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
intron-3UTRENST00000483243ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21264844

+
intron-3UTRENST00000483243ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21264844

+
intron-3UTRENST00000483243ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21264844

+
intron-3UTRENST00000483243ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21264844

+
intron-intronENST00000483243ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21264844

+
5CDS-3UTRENST00000541979ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000541979ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000541979ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000541979ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000541979ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000465038ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000465038ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000465038ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000465038ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000465038ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000352853ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000352853ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000352853ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000352853ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000352853ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371438ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371438ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371438ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371438ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000371438ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371436ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371436ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371436ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371436ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000371436ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000576263ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000576263ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000576263ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000576263ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000576263ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371432ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371432ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371432ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000371432ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000371432ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000359524ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000359524ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000359524ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-3UTRENST00000359524ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
5CDS-intronENST00000359524ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+
intron-3UTRENST00000483243ENST00000382778RUNX2chr6

45459851

+IFT88chr13

21265193

+
intron-3UTRENST00000483243ENST00000351808RUNX2chr6

45459851

+IFT88chr13

21265193

+
intron-3UTRENST00000483243ENST00000319980RUNX2chr6

45459851

+IFT88chr13

21265193

+
intron-3UTRENST00000483243ENST00000537103RUNX2chr6

45459851

+IFT88chr13

21265193

+
intron-intronENST00000483243ENST00000461115RUNX2chr6

45459851

+IFT88chr13

21265193

+

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FusionProtFeatures for RUNX2_IFT88


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RUNX2

Q13950

IFT88

Q13099

Transcription factor involved in osteoblasticdifferentiation and skeletal morphogenesis (PubMed:28505335,PubMed:28738062, PubMed:28703881). Essential for the maturation ofosteoblasts and both intramembranous and endochondralossification. CBF binds to the core site, 5'-PYGPYGGT-3', of anumber of enhancers and promoters, including murine leukemiavirus, polyomavirus enhancer, T-cell receptor enhancers,osteocalcin, osteopontin, bone sialoprotein, alpha 1(I) collagen,LCK, IL-3 and GM-CSF promoters. In osteoblasts, supportstranscription activation: synergizes with SPEN/MINT to enhanceFGFR2-mediated activation of the osteocalcin FGF-responsiveelement (OCFRE) (By similarity). Inhibits KAT6B-dependenttranscriptional activation. {ECO:0000250,ECO:0000269|PubMed:11965546, ECO:0000269|PubMed:28505335,ECO:0000269|PubMed:28703881, ECO:0000269|PubMed:28738062}. Involved in primary cilium biogenesis. Also involved inautophagy since it is required for trafficking of ATG16L and theexpansion of the autophagic compartment.{ECO:0000250|UniProtKB:Q61371}.

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 RUNX2_IFT88


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 RUNX2_IFT88


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
RUNX2HDAC3, KAT6B, HDAC6, ALYREF, SMAD1, SMAD3, YAP1, JUN, FOS, ETS1, SMAD2, SMAD5, MSX2, STUB1, TLE1, HDAC4, HDAC5, KAT2B, HDAC1, EP300, BMPR1A, HES1, XRCC6, XRCC5, CREBBP, HDAC7, NR0B2, SOX9, RBM14, STAT3, SUV39H1, UBTF, FHL2, HIVEP3, WWP1, SMURF2, SMURF1, HIF1A, PML, RB1, TP53, CBFB, STAT5A, FBXW7, SKP2IFT88PRRC2A, IFT81, IFT46, IFT57, CCDC151, IFT80, LCA5, CSNK2A2, ZWINT, CDKN2AIP, SMC6, UBXN10, VCP, TTC30A, TTC30B, FGF8, IFT172, IFT20, IFT74, IFT27, TRAF3IP1, CLUAP1, HSPB11, TTC26, IFT22, IFT52, ICK


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 RUNX2_IFT88


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 RUNX2_IFT88


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRUNX2C0008928Cleidocranial Dysplasia12CTD_human;ORPHANET;UNIPROT
HgeneRUNX2C0029463Osteosarcoma2CTD_human
HgeneRUNX2C0003872Arthritis, Psoriatic1CTD_human
HgeneRUNX2C0003873Rheumatoid Arthritis1CTD_human
HgeneRUNX2C0029408Degenerative polyarthritis1CTD_human
HgeneRUNX2C0040427Tooth Abnormalities1CTD_human
HgeneRUNX2C0041948Uremia1CTD_human
HgeneRUNX2C0243057Stomatognathic System Abnormalities1CTD_human
HgeneRUNX2C0376634Craniofacial Abnormalities1CTD_human
HgeneRUNX2C0949690Spondylarthritis1CTD_human
TgeneIFT88C0085548Autosomal Recessive Polycystic Kidney Disease2CTD_human
TgeneIFT88C0023903Liver neoplasms1CTD_human
TgeneIFT88C0032927Precancerous Conditions1CTD_human
TgeneIFT88C0152427Polydactyly1CTD_human