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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:TIA1-BCL11A (FusionGDB2 ID:90180)

Fusion Gene Summary for TIA1-BCL11A

check button Fusion gene summary
Fusion gene informationFusion gene name: TIA1-BCL11A
Fusion gene ID: 90180
HgeneTgene
Gene symbol

TIA1

BCL11A

Gene ID

7072

53335

Gene nameTIA1 cytotoxic granule associated RNA binding proteinBAF chromatin remodeling complex subunit BCL11A
SynonymsTIA-1|WDMBCL11A-L|BCL11A-S|BCL11A-XL|BCL11a-M|CTIP1|DILOS|EVI9|HBFQTL5|ZNF856
Cytomap

2p13.3

2p16.1

Type of geneprotein-codingprotein-coding
Descriptionnucleolysin TIA-1 isoform p40nucleolysin TIA-1T-cell-restricted intracellular antigen-1p40-TIA-1 (containing p15-TIA-1)B-cell lymphoma/leukemia 11AB cell CLL/lymphoma 11AB-cell CLL/lymphoma 11A (zinc finger protein) isoform 2BCL11A B-cell CLL/lymphoma 11A (zinc finger protein) isoform 1BCL11A, BAF complex componentC2H2-type zinc finger proteinCOUP-TF-interacting pro
Modification date2020031320200313
UniProtAcc.

Q9H165

Ensembl transtripts involved in fusion geneENST00000433529, ENST00000415783, 
ENST00000282574, ENST00000445587, 
ENST00000482876, ENST00000416149, 
ENST00000356842, ENST00000359629, 
ENST00000538214, ENST00000537768, 
ENST00000335712, ENST00000477659, 
ENST00000358510, 
Fusion gene scores* DoF score11 X 9 X 8=79210 X 9 X 3=270
# samples 139
** MAII scorelog2(13/792*10)=-2.60698880705116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/270*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TIA1 [Title/Abstract] AND BCL11A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTIA1(70475537)-BCL11A(60743653), # samples:2
TIA1(70475537)-BCL11A(60695968), # samples:2
Anticipated loss of major functional domain due to fusion event.TIA1-BCL11A seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
TIA1-BCL11A seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
* 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
HgeneTIA1

GO:0048024

regulation of mRNA splicing, via spliceosome

11106748

TgeneBCL11A

GO:0000122

negative regulation of transcription by RNA polymerase II

19153051


check buttonFusion gene breakpoints across TIA1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across BCL11A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LUADTCGA-64-1676-01ATIA1chr2

70475537

-BCL11Achr2

60743653

-
ChimerDB4LUADTCGA-64-1676-01ATIA1chr2

70475537

-BCL11Achr2

60743653

-
ChimerDB4LUADTCGA-64-1676-01ATIA1chr2

70475537

-BCL11Achr2

60695968

-
ChimerDB4LUADTCGA-64-1676-01ATIA1chr2

70475537

-BCL11Achr2

60695968

-


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Fusion Gene ORF analysis for TIA1-BCL11A

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-intronENST00000433529ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000433529ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000433529ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000433529ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000433529ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000433529ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000433529ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000415783ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000415783ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000415783ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000415783ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000415783ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000415783ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000415783ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000282574ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000282574ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000282574ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000282574ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000282574ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000282574ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000282574ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000445587ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000445587ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000445587ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000445587ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000445587ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000445587ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000445587ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60743653

-
intron-intronENST00000482876ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60743653

-
intron-intronENST00000482876ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60743653

-
intron-intronENST00000482876ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60743653

-
intron-intronENST00000482876ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60743653

-
intron-intronENST00000482876ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60743653

-
intron-intronENST00000482876ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60743653

-
intron-intronENST00000482876ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000416149ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000416149ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000416149ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000416149ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000416149ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000416149ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60743653

-
5CDS-intronENST00000416149ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60743653

-
Frame-shiftENST00000433529ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000433529ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000433529ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000433529ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000433529ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000433529ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000433529ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000415783ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000415783ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000415783ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000415783ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000415783ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000415783ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000415783ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000282574ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000282574ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000282574ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000282574ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000282574ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000282574ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000282574ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000445587ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000445587ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000445587ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000445587ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000445587ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000445587ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000445587ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60695968

-
intron-3CDSENST00000482876ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60695968

-
intron-3CDSENST00000482876ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60695968

-
intron-intronENST00000482876ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60695968

-
intron-5UTRENST00000482876ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60695968

-
intron-5UTRENST00000482876ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60695968

-
intron-5UTRENST00000482876ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60695968

-
intron-intronENST00000482876ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000416149ENST00000356842TIA1chr2

70475537

-BCL11Achr2

60695968

-
Frame-shiftENST00000416149ENST00000359629TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000416149ENST00000538214TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000416149ENST00000537768TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000416149ENST00000335712TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-5UTRENST00000416149ENST00000477659TIA1chr2

70475537

-BCL11Achr2

60695968

-
5CDS-intronENST00000416149ENST00000358510TIA1chr2

70475537

-BCL11Achr2

60695968

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for TIA1-BCL11A


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for TIA1-BCL11A


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.BCL11A

Q9H165

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Transcription factor associated with the BAF SWI/SNF chromatin remodeling complex (By similarity). Repressor of fetal hemoglobin (HbF) level (PubMed:26375765). Involved in brain development (PubMed:27453576). May play a role in hematopoiesis. Essential factor in lymphopoiesis required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity). {ECO:0000250|UniProtKB:Q9QYE3, ECO:0000303|PubMed:26375765, ECO:0000303|PubMed:27453576}.

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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Fusion Gene Sequence for TIA1-BCL11A


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for TIA1-BCL11A


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


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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Related Drugs for TIA1-BCL11A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for TIA1-BCL11A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTIA1C0221054Welander Distal Myopathy3GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneTIA1C2931290Welander distal myopathy, Swedish type3CTD_human;ORPHANET
TgeneBCL11AC4310833INTELLECTUAL DEVELOPMENTAL DISORDER WITH PERSISTENCE OF FETAL HEMOGLOBIN2CTD_human;UNIPROT
TgeneBCL11AC0003635Apraxias1CTD_human
TgeneBCL11AC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneBCL11AC0023012Language Delay1CTD_human
TgeneBCL11AC0023014Language Development Disorders1CTD_human
TgeneBCL11AC0032460Polycystic Ovary Syndrome1CTD_human
TgeneBCL11AC0036095Salivary Gland Neoplasms1CTD_human
TgeneBCL11AC0036341Schizophrenia1PSYGENET
TgeneBCL11AC0220636Malignant neoplasm of salivary gland1CTD_human
TgeneBCL11AC0234526Ideational Apraxia1CTD_human
TgeneBCL11AC0234527Apraxia, Motor1CTD_human
TgeneBCL11AC0234529Dressing Apraxia1CTD_human
TgeneBCL11AC0241210Speech Delay1CTD_human
TgeneBCL11AC0264611Apraxia of Phonation1CTD_human
TgeneBCL11AC0349391Apraxia, Verbal1CTD_human
TgeneBCL11AC0422892Apraxia, Gestural1CTD_human
TgeneBCL11AC0454608Apraxia, Oral1CTD_human
TgeneBCL11AC0454655Semantic-Pragmatic Disorder1CTD_human
TgeneBCL11AC0750927Apraxia, Developmental Verbal1CTD_human
TgeneBCL11AC0750928Apraxia, Facial-Oral1CTD_human
TgeneBCL11AC0751257Auditory Processing Disorder, Central1CTD_human
TgeneBCL11AC1136382Sclerocystic Ovaries1CTD_human
TgeneBCL11AC3495144Apraxia, Articulatory1CTD_human
TgeneBCL11AC3714756Intellectual Disability1GENOMICS_ENGLAND