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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: 30474

FusionGeneSummary for RARA_PGAP3

check button Fusion gene summary
Fusion gene informationFusion gene name: RARA_PGAP3
Fusion gene ID: 30474
HgeneTgene
Gene symbol

RARA

PGAP3

Gene ID

5914

93210

Gene nameretinoic acid receptor alphapost-GPI attachment to proteins 3
SynonymsNR1B1|RARAGLA546|CAB2|PERLD1|PP1498|hCOS16
Cytomap

17q21.2

17q12

Type of geneprotein-codingprotein-coding
Descriptionretinoic acid receptor alphaRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid nuclear receptor alpha variant 1retinoic acid nuclear receptor alpha variant 2post-GPI attachment to proteins factor 3COS16 homologgene coamplified with ERBB2 proteinper1-like domain containing 1
Modification date2018052320180523
UniProtAcc

P10276

Q96FM1

Ensembl transtripts involved in fusion geneENST00000254066, ENST00000394089, 
ENST00000425707, ENST00000394086, 
ENST00000394081, ENST00000420042, 
ENST00000579146, ENST00000300658, 
ENST00000378011, ENST00000429199, 
Fusion gene scores* DoF score29 X 12 X 7=24362 X 2 X 1=4
# samples 422
** MAII scorelog2(42/2436*10)=-2.53605290024021
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/4*10)=2.32192809488736
Context

PubMed: RARA [Title/Abstract] AND PGAP3 [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
HgeneRARA

GO:0007165

signal transduction

2825025

HgeneRARA

GO:0030853

negative regulation of granulocyte differentiation

19917671

HgeneRARA

GO:0032689

negative regulation of interferon-gamma production

18416830

HgeneRARA

GO:0032720

negative regulation of tumor necrosis factor production

18416830

HgeneRARA

GO:0032736

positive regulation of interleukin-13 production

18416830

HgeneRARA

GO:0032753

positive regulation of interleukin-4 production

18416830

HgeneRARA

GO:0032754

positive regulation of interleukin-5 production

18416830

HgeneRARA

GO:0045630

positive regulation of T-helper 2 cell differentiation

18416830

HgeneRARA

GO:0045892

negative regulation of transcription, DNA-templated

20080953

HgeneRARA

GO:0045893

positive regulation of transcription, DNA-templated

18845237|19850744|20080953

HgeneRARA

GO:0045944

positive regulation of transcription by RNA polymerase II

19850744

HgeneRARA

GO:0071300

cellular response to retinoic acid

19917671

HgeneRARA

GO:0071391

cellular response to estrogen stimulus

20080953


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-A8-A08B-01ARARAchr17

38474700

+PGAP3chr17

37830932

-
TCGALDBRCATCGA-A8-A08B-01ARARAchr17

38474700

+PGAP3chr17

37842272

-
* 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
intron-intronENST00000254066ENST00000579146RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000254066ENST00000300658RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000254066ENST00000378011RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000254066ENST00000429199RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000394089ENST00000579146RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000394089ENST00000300658RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000394089ENST00000378011RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000394089ENST00000429199RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000425707ENST00000579146RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000425707ENST00000300658RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000425707ENST00000378011RARAchr17

38474700

+PGAP3chr17

37830932

-
5UTR-intronENST00000425707ENST00000429199RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394086ENST00000579146RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394086ENST00000300658RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394086ENST00000378011RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394086ENST00000429199RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394081ENST00000579146RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394081ENST00000300658RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394081ENST00000378011RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000394081ENST00000429199RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000420042ENST00000579146RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000420042ENST00000300658RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000420042ENST00000378011RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-intronENST00000420042ENST00000429199RARAchr17

38474700

+PGAP3chr17

37830932

-
intron-3CDSENST00000254066ENST00000579146RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000254066ENST00000300658RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000254066ENST00000378011RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000254066ENST00000429199RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000394089ENST00000579146RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000394089ENST00000300658RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000394089ENST00000378011RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000394089ENST00000429199RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000425707ENST00000579146RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000425707ENST00000300658RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000425707ENST00000378011RARAchr17

38474700

+PGAP3chr17

37842272

-
5UTR-3CDSENST00000425707ENST00000429199RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394086ENST00000579146RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394086ENST00000300658RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394086ENST00000378011RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394086ENST00000429199RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394081ENST00000579146RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394081ENST00000300658RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394081ENST00000378011RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000394081ENST00000429199RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000420042ENST00000579146RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000420042ENST00000300658RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000420042ENST00000378011RARAchr17

38474700

+PGAP3chr17

37842272

-
intron-3CDSENST00000420042ENST00000429199RARAchr17

38474700

+PGAP3chr17

37842272

-

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FusionProtFeatures for RARA_PGAP3


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

P10276

PGAP3

Q96FM1

Receptor for retinoic acid. Retinoic acid receptors bindas heterodimers to their target response elements in response totheir ligands, all-trans or 9-cis retinoic acid, and regulate geneexpression in various biological processes. The RXR/RARheterodimers bind to the retinoic acid response elements (RARE)composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In theabsence of ligand, the RXR-RAR heterodimers associate with amultiprotein complex containing transcription corepressors thatinduce histone acetylation, chromatin condensation andtranscriptional suppression. On ligand binding, the corepressorsdissociate from the receptors and associate with the coactivatorsleading to transcriptional activation. RARA plays an essentialrole in the regulation of retinoic acid-induced germ celldevelopment during spermatogenesis. Has a role in the survival ofearly spermatocytes at the beginning prophase of meiosis. InSertoli cells, may promote the survival and development of earlymeiotic prophase spermatocytes. In concert with RARG, required forskeletal growth, matrix homeostasis and growth plate function (Bysimilarity). {ECO:0000250|UniProtKB:P11416,ECO:0000269|PubMed:16417524, ECO:0000269|PubMed:19850744,ECO:0000269|PubMed:20215566}. Involved in the lipid remodeling steps of GPI-anchormaturation. Lipid remodeling steps consist in the generation of 2saturated fatty chains at the sn-2 position of GPI-anchorsproteins. Required for phospholipase A2 activity that removes anacyl-chain at the sn-2 position of GPI-anchors during theremodeling of GPI (Probable). {ECO:0000305|PubMed:17021251}.

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 RARA_PGAP3


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 RARA_PGAP3


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
RARANRBF2, ZBTB16, MECR, RXRG, RXRB, NCOA6, GADD45G, GADD45A, NRIP1, KAT2B, HDAC3, HDAC4, TDG, PML, TRIP4, KDM5A, RXRA, POU2F1, NCOR2, NR0B2, BAG1, TADA3, NCOR1, NKX2-1, TRIM24, IRX4, SP1, NPAS2, CLOCK, ARNTL, NR2E3, CCND3, NCOA2, SRC, AJUBA, LIMD1, WTIP, SKI, HR, PIN1, SUV39H1, PSMC5, EP300, PARP1, MED6, TOP2B, SAP130, HNRNPU, RFC4, NPM1, MRTO4, SNRNP40, MED1, NCOA1, HMGA1, RUVBL1, RUNX1, SIAH1, RARA, HDAC2, NCOA3, CREBBP, LRIF1, KLF5, SMARCD3, ARID1A, SPI1, PRDX6, NR1H2, ITGB1BP2, MED25, MAPK6, FOXO1, MAPK1, TRIM32, PHF8, TNIP1, HACE1, SQSTM1, UBQLN1, ARID5A, UBE3A, PRAM1, FAS, PRAME, TBL1XR1, SUZ12, EZH2, USP7, TMEM54, MMS19, AKT1, FN1, WWOX, E2F1, MBD3, MTA2, CBX5, CEBPA, HDAC1, NSD1, TEKT4, SNW1, SIRT1, ACTN4, SRF, MDM2, ZNF131, RARG, RARB, TRIM25PGAP3TBRG4, VKORC1L1


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 RARA_PGAP3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneRARAP10276DB00210AdapaleneRetinoic acid receptor alphasmall moleculeapproved
HgeneRARAP10276DB00459AcitretinRetinoic acid receptor alphasmall moleculeapproved
HgeneRARAP10276DB00982IsotretinoinRetinoic acid receptor alphasmall moleculeapproved
HgeneRARAP10276DB00523AlitretinoinRetinoic acid receptor alphasmall moleculeapproved|investigational
HgeneRARAP10276DB00799TazaroteneRetinoic acid receptor alphasmall moleculeapproved|investigational
HgeneRARAP10276DB00755TretinoinRetinoic acid receptor alphasmall moleculeapproved|investigational|nutraceutical

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RelatedDiseases for RARA_PGAP3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRARAC0023487Acute Promyelocytic Leukemia22CTD_human;HPO;ORPHANET
HgeneRARAC0036341Schizophrenia3PSYGENET
HgeneRARAC0005586Bipolar Disorder1PSYGENET
HgeneRARAC0010701Phyllodes Tumor1CTD_human
HgeneRARAC0085183Neoplasms, Second Primary1CTD_human
HgeneRARAC0149940Sciatic Neuropathy1CTD_human
HgeneRARAC0206650Fibroadenoma1CTD_human
HgeneRARAC0525045Mood Disorders1PSYGENET
HgeneRARAC1458155Mammary Neoplasms1CTD_human
HgeneRARAC2239176Liver carcinoma1CTD_human
TgenePGAP3C3810354HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 41UNIPROT