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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: 5576

FusionGeneSummary for CASC3_THRA

check button Fusion gene summary
Fusion gene informationFusion gene name: CASC3_THRA
Fusion gene ID: 5576
HgeneTgene
Gene symbol

CASC3

THRA

Gene ID

22794

7067

Gene nameCASC3, exon junction complex subunitthyroid hormone receptor alpha
SynonymsBTZ|MLN51AR7|CHNG6|EAR7|ERB-T-1|ERBA|ERBA1|NR1A1|THRA1|THRA2|c-ERBA-1
Cytomap

17q21.1

17q21.1

Type of geneprotein-codingprotein-coding
Descriptionprotein CASC3MLN 51barentszcancer susceptibility 3cancer susceptibility candidate 3cancer susceptibility candidate gene 3 proteinmetastatic lymph node 51metastatic lymph node gene 51 proteinprotein barentszthyroid hormone receptor alphaEAR-7ERBA-related 7V-erbA-related protein 7c-erbA-alphanuclear receptor subfamily 1 group A member 1thyroid hormone receptor alpha 1thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homo
Modification date2018052320180523
UniProtAcc

O15234

P10827

Ensembl transtripts involved in fusion geneENST00000264645, ENST00000394121, 
ENST00000264637, ENST00000584985, 
ENST00000450525, ENST00000546243, 
Fusion gene scores* DoF score15 X 7 X 8=8406 X 5 X 5=150
# samples 178
** MAII scorelog2(17/840*10)=-2.30485458152842
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/150*10)=-0.906890595608519
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CASC3 [Title/Abstract] AND THRA [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationOncogene involved fusion gene, in-frame and retained their domain.
Tumor suppressor gene involved fusion gene, in-frame but not retained their domain.
Tumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
Transcription factor involved fusion gene, inframe and retained DNA-binding domain.
* 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
TgeneTHRA

GO:0006357

regulation of transcription by RNA polymerase II

18052923

TgeneTHRA

GO:0006366

transcription by RNA polymerase II

8710870|9653119

TgeneTHRA

GO:0009755

hormone-mediated signaling pathway

18052923

TgeneTHRA

GO:0017055

negative regulation of RNA polymerase II transcriptional preinitiation complex assembly

8524305

TgeneTHRA

GO:0045892

negative regulation of transcription, DNA-templated

8710870

TgeneTHRA

GO:2000143

negative regulation of DNA-templated transcription, initiation

8524305


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
TCGARVCHOLTCGA-ZH-A8Y4-01ACASC3chr17

38324670

+THRAchr17

38249273

+
* 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-frameENST00000264645ENST00000394121CASC3chr17

38324670

+THRAchr17

38249273

+
Frame-shiftENST00000264645ENST00000264637CASC3chr17

38324670

+THRAchr17

38249273

+
5CDS-intronENST00000264645ENST00000584985CASC3chr17

38324670

+THRAchr17

38249273

+
5CDS-intronENST00000264645ENST00000450525CASC3chr17

38324670

+THRAchr17

38249273

+
5CDS-intronENST00000264645ENST00000546243CASC3chr17

38324670

+THRAchr17

38249273

+

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FusionProtFeatures for CASC3_THRA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CASC3

O15234

THRA

P10827

Core component of the splicing-dependent multiproteinexon junction complex (EJC) deposited at splice junctions onmRNAs. The EJC is a dynamic structure consisting of core proteinsand several peripheral nuclear and cytoplasmic associated factorsthat join the complex only transiently either during EJC assemblyor during subsequent mRNA metabolism. The EJC marks the positionof the exon-exon junction in the mature mRNA for the geneexpression machinery and the core components remain bound tospliced mRNAs throughout all stages of mRNA metabolism therebyinfluencing downstream processes including nuclear mRNA export,subcellular mRNA localization, translation efficiency andnonsense-mediated mRNA decay (NMD). Stimulates the ATPase and RNA-helicase activities of EIF4A3. Plays a role in the stress responseby participating in cytoplasmic stress granules assembly and byfavoring cell recovery following stress. Component of thedendritic ribonucleoprotein particles (RNPs) in hippocampalneurons. May play a role in mRNA transport. Binds spliced mRNA insequence-independent manner, 20-24 nucleotides upstream of mRNAexon-exon junctions. Binds poly(G) and poly(U) RNA homopolymer.{ECO:0000269|PubMed:17375189, ECO:0000269|PubMed:17652158}. Isoform Alpha-1: Nuclear hormone receptor that can actas a repressor or activator of transcription. High affinityreceptor for thyroid hormones, including triiodothyronine andthyroxine. {ECO:0000269|PubMed:12699376,ECO:0000269|PubMed:14673100, ECO:0000269|PubMed:18237438,ECO:0000269|PubMed:19926848}. Isoform Alpha-2: Does not bind thyroid hormone andfunctions as a weak dominant negative inhibitor of thyroid hormoneaction. {ECO:0000269|PubMed:8910441}.

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
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+111495_1316551130Coiled coilOntology_term=ECO:0000255
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114392_3956551130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+111441_466551130Compositional biasNote=Poly-Gly
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114425_4286551130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114643_6486551130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114204_2106551130MotifNuclear localization signal 1
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114254_2626551130MotifNuclear localization signal 2
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114462_4666551130MotifNote=Nuclear export signal
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114137_2836551130RegionNote=Sufficient to form the EJC
TgeneTHRAchr17:38324670chr17:38249273ENST00000450525+0953_127-164411DNA bindingNuclear receptor
TgeneTHRAchr17:38324670chr17:38249273ENST00000546243+0953_127-134411DNA bindingNuclear receptor
TgeneTHRAchr17:38324670chr17:38249273ENST00000584985+01053_127-194452DNA bindingNuclear receptor
TgeneTHRAchr17:38324670chr17:38249273ENST00000450525+09163_407-164411DomainNR LBD
TgeneTHRAchr17:38324670chr17:38249273ENST00000546243+09163_407-134411DomainNR LBD
TgeneTHRAchr17:38324670chr17:38249273ENST00000584985+010163_407-194452DomainNR LBD
TgeneTHRAchr17:38324670chr17:38249273ENST00000450525+091_52-164411RegionNote=Modulating
TgeneTHRAchr17:38324670chr17:38249273ENST00000546243+091_52-134411RegionNote=Modulating
TgeneTHRAchr17:38324670chr17:38249273ENST00000584985+0101_52-194452RegionNote=Modulating
TgeneTHRAchr17:38324670chr17:38249273ENST00000450525+0953_73-164411Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000450525+0991_115-164411Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000546243+0953_73-134411Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000546243+0991_115-134411Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000584985+01053_73-194452Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000584985+01091_115-194452Zinc fingerNR C4-type

- In-frame and not-retained protein feature among the 13 regional features.
>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114692_6956551130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38324670chr17:38249273ENST00000264645+1114377_7036551130RegionNote=Necessary for localization in cytoplasmic stress granules
TgeneTHRAchr17:38324670chr17:38249273ENST00000264637+81053_127370491DNA bindingNuclear receptor
TgeneTHRAchr17:38324670chr17:38249273ENST00000394121+81053_127370491DNA bindingNuclear receptor
TgeneTHRAchr17:38324670chr17:38249273ENST00000264637+810163_407370491DomainNR LBD
TgeneTHRAchr17:38324670chr17:38249273ENST00000394121+810163_407370491DomainNR LBD
TgeneTHRAchr17:38324670chr17:38249273ENST00000264637+8101_52370491RegionNote=Modulating
TgeneTHRAchr17:38324670chr17:38249273ENST00000394121+8101_52370491RegionNote=Modulating
TgeneTHRAchr17:38324670chr17:38249273ENST00000264637+81053_73370491Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000264637+81091_115370491Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000394121+81053_73370491Zinc fingerNR C4-type
TgeneTHRAchr17:38324670chr17:38249273ENST00000394121+81091_115370491Zinc fingerNR C4-type


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FusionGeneSequence for CASC3_THRA


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 CASC3_THRA


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
CASC3ELAVL1, CAND1, EIF4A3, MAGOH, CDK6, GRB2, NXF1, BMI1, VTI1B, TRA2A, PRR11, LUC7L, LUC7L2, SNIP1, UPF3B, AKT1, APC, CASP8, CDKN2A, ESR2, FGFR4, NBN, PHB, PTPN1, PTPRJ, EWSR1, XPO1, LLGL2, RBM8A, MED12, CHST15, KDM1B, UPF3A, WIBG, PNN, ELAVL2, GSPT2, U2AF2, CDX1, APOBEC3D, C11orf57, CLK2, PRDM5, CELF5, RBM3THRANCOA6, TDG, CCND1, MEF2A, EP300, YWHAQ, ITGB3BP, POU2F1, DAP3, NR0B2, NRIP1, HR, AKAP13, MED12, MED16, MED6, MED24, CDK8, MED21, TRIM24, COPS2, TRIP11, RXRA, MED1, FUS, HDAC3, NCOR1, ZBTB3, SUV39H1, PARP1, NCOA1, NCOA2, NCOA3, TAF11, TAF7, GRIP1, NCOR2, EMD, PRKDC, SMC1A, LIG3, XRCC5, XRCC6, HSPA4, TBL1XR1, GPS2, TBL1X, CUL1, RGN, SEPP1, CDK7, MED25, ARID5A, GTF2B, C1D, THRA, CLIC1, FOXJ1, BUB3, PTGES3, RANBP9, AMOTL2, L3MBTL3, ENO1, MOV10, NXF1, UBE2I, CEP76, TRIM63, A2ML1, HAL, CST6, MTNR1B


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 CASC3_THRA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneTHRAP10827DB00451LevothyroxineThyroid hormone receptor alphasmall moleculeapproved
TgeneTHRAP10827DB00509DextrothyroxineThyroid hormone receptor alphasmall moleculeapproved|investigational
TgeneTHRAP10827DB01118AmiodaroneThyroid hormone receptor alphasmall moleculeapproved|investigational
TgeneTHRAP10827DB00279LiothyronineThyroid hormone receptor alphasmall moleculeapproved|vet_approved

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RelatedDiseases for CASC3_THRA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneTHRAC3280817HYPOTHYROIDISM, CONGENITAL, NONGOITROUS, 62UNIPROT
TgeneTHRAC0014175Endometriosis1CTD_human
TgeneTHRAC0019284Diaphragmatic Hernia1CTD_human