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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:CRIM1-AFF3 (FusionGDB2 ID:HG51232TG3899)

Fusion Gene Summary for CRIM1-AFF3

check button Fusion gene summary
Fusion gene informationFusion gene name: CRIM1-AFF3
Fusion gene ID: hg51232tg3899
HgeneTgene
Gene symbol

CRIM1

AFF3

Gene ID

51232

3899

Gene namecysteine rich transmembrane BMP regulator 1AF4/FMR2 family member 3
SynonymsCRIM-1|S52LAF4|MLLT2-like
Cytomap('CRIM1')('AFF3')

2p22.2

2q11.2

Type of geneprotein-codingprotein-coding
Descriptioncysteine-rich motor neuron 1 proteincysteine rich transmembrane BMP regulator 1 (chordin-like)cysteine-rich repeat-containing protein S52AF4/FMR2 family member 3MLLT2-related proteinlymphoid nuclear protein 4lymphoid nuclear protein related to AF4protein LAF-4
Modification date2020031320200313
UniProtAcc.

P51826

Ensembl transtripts involved in fusion geneENST00000280527, ENST00000473403, 
Fusion gene scores* DoF score15 X 11 X 8=132014 X 19 X 6=1596
# samples 1616
** MAII scorelog2(16/1320*10)=-3.04439411935845
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(16/1596*10)=-3.31831684133498
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CRIM1 [Title/Abstract] AND AFF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCRIM1(36669878)-AFF3(100368763), # samples:2
Anticipated loss of major functional domain due to fusion event.CRIM1-AFF3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CRIM1-AFF3 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CRIM1-AFF3 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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


check button Fusion gene information
* 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
ChimerDB4MESOTCGA-LK-A4O0-01ACRIM1chr2

36669878

-AFF3chr2

100368763

-
ChimerDB4MESOTCGA-LK-A4O0-01ACRIM1chr2

36669878

+AFF3chr2

100368763

-


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Fusion Gene ORF analysis for CRIM1-AFF3

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-intronENST00000280527ENST00000483600CRIM1chr2

36669878

+AFF3chr2

100368763

-
Frame-shiftENST00000280527ENST00000317233CRIM1chr2

36669878

+AFF3chr2

100368763

-
Frame-shiftENST00000280527ENST00000356421CRIM1chr2

36669878

+AFF3chr2

100368763

-
Frame-shiftENST00000280527ENST00000409236CRIM1chr2

36669878

+AFF3chr2

100368763

-
Frame-shiftENST00000280527ENST00000409579CRIM1chr2

36669878

+AFF3chr2

100368763

-
intron-3CDSENST00000473403ENST00000317233CRIM1chr2

36669878

+AFF3chr2

100368763

-
intron-3CDSENST00000473403ENST00000356421CRIM1chr2

36669878

+AFF3chr2

100368763

-
intron-3CDSENST00000473403ENST00000409236CRIM1chr2

36669878

+AFF3chr2

100368763

-
intron-3CDSENST00000473403ENST00000409579CRIM1chr2

36669878

+AFF3chr2

100368763

-
intron-intronENST00000473403ENST00000483600CRIM1chr2

36669878

+AFF3chr2

100368763

-

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 CRIM1-AFF3


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)


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Fusion Protein Features for CRIM1-AFF3


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:36669878/:100368763)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.AFF3

P51826

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Putative transcription activator that may function in lymphoid development and oncogenesis. Binds, in vitro, to double-stranded DNA.

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 CRIM1-AFF3


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 CRIM1-AFF3


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 CRIM1-AFF3


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 CRIM1-AFF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCRIM1C1865286MACROPHTHALMIA, COLOBOMATOUS, WITH MICROCORNEA2GENOMICS_ENGLAND;ORPHANET
TgeneC0003873Rheumatoid Arthritis2CTD_human
TgeneC0013146Drug abuse1CTD_human
TgeneC0013170Drug habituation1CTD_human
TgeneC0013222Drug Use Disorders1CTD_human
TgeneC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneC0036572Seizures1GENOMICS_ENGLAND
TgeneC0038580Substance Dependence1CTD_human
TgeneC0038586Substance Use Disorders1CTD_human
TgeneC0236969Substance-Related Disorders1CTD_human
TgeneC0740858Substance abuse problem1CTD_human
TgeneC1510472Drug Dependence1CTD_human
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4316881Prescription Drug Abuse1CTD_human