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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:SPECC1L-BCR (FusionGDB2 ID:85671)

Fusion Gene Summary for SPECC1L-BCR

check button Fusion gene summary
Fusion gene informationFusion gene name: SPECC1L-BCR
Fusion gene ID: 85671
HgeneTgene
Gene symbol

SPECC1L

BCR

Gene ID

23384

613

Gene namesperm antigen with calponin homology and coiled-coil domains 1 likeBCR activator of RhoGEF and GTPase
SynonymsCYTSA|GBBB2|OBLFC1|TBHSALL|BCR1|CML|D22S11|D22S662|PHL
Cytomap

22q11.23

22q11.23

Type of geneprotein-codingprotein-coding
Descriptioncytospin-ASPECC1-like proteincytokinesis and spindle organization Arenal carcinoma antigen NY-REN-22breakpoint cluster region proteinBCR, RhoGEF and GTPase activating proteinBCR/FGFR1 chimera proteinFGFR1/BCR chimera proteinbreakpoint cluster regionrenal carcinoma antigen NY-REN-26
Modification date2020031320200313
UniProtAcc.

P11274

Ensembl transtripts involved in fusion geneENST00000416735, ENST00000314328, 
ENST00000437398, ENST00000541492, 
ENST00000305877, ENST00000359540, 
ENST00000398512, ENST00000436990, 
Fusion gene scores* DoF score24 X 9 X 16=345615 X 58 X 7=6090
# samples 3761
** MAII scorelog2(37/3456*10)=-3.22350604164716
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(61/6090*10)=-3.31956108034345
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPECC1L [Title/Abstract] AND BCR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSPECC1L(24666951)-BCR(23651610), # samples:1
SPECC1L(24666951)-BCR(23651611), # samples:1
SPECC1L(24672771)-BCR(23651611), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneSPECC1L

GO:0007155

cell adhesion

21703590

TgeneBCR

GO:0090630

activation of GTPase activity

7479768


check buttonFusion gene breakpoints across SPECC1L (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 BCR (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
ChimerDB4OVTCGA-25-2392-01ASPECC1Lchr22

24666951

+BCRchr22

23651611

+
ChimerDB4OVTCGA-25-2392-01ASPECC1Lchr22

24672771

+BCRchr22

23651611

+
ChimerDB4OVTCGA-25-2392SPECC1Lchr22

24666951

+BCRchr22

23651610

+


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Fusion Gene ORF analysis for SPECC1L-BCR

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
3UTR-3CDSENST00000416735ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651611

+
3UTR-3CDSENST00000416735ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651610

+
3UTR-3CDSENST00000416735ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651611

+
3UTR-3CDSENST00000416735ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651610

+
3UTR-intronENST00000416735ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651611

+
3UTR-intronENST00000416735ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651610

+
3UTR-intronENST00000416735ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651611

+
3UTR-intronENST00000416735ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-3CDSENST00000314328ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-3CDSENST00000314328ENST00000305877SPECC1Lchr22

24672771

+BCRchr22

23651611

+
5UTR-3CDSENST00000314328ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-3CDSENST00000314328ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-3CDSENST00000314328ENST00000359540SPECC1Lchr22

24672771

+BCRchr22

23651611

+
5UTR-3CDSENST00000314328ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-3CDSENST00000437398ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-3CDSENST00000437398ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-3CDSENST00000437398ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-3CDSENST00000437398ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-3CDSENST00000541492ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-3CDSENST00000541492ENST00000305877SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-3CDSENST00000541492ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-3CDSENST00000541492ENST00000359540SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-intronENST00000314328ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-intronENST00000314328ENST00000398512SPECC1Lchr22

24672771

+BCRchr22

23651611

+
5UTR-intronENST00000314328ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-intronENST00000314328ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-intronENST00000314328ENST00000436990SPECC1Lchr22

24672771

+BCRchr22

23651611

+
5UTR-intronENST00000314328ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-intronENST00000437398ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-intronENST00000437398ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-intronENST00000437398ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-intronENST00000437398ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-intronENST00000541492ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-intronENST00000541492ENST00000398512SPECC1Lchr22

24666951

+BCRchr22

23651610

+
5UTR-intronENST00000541492ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651611

+
5UTR-intronENST00000541492ENST00000436990SPECC1Lchr22

24666951

+BCRchr22

23651610

+
intron-3CDSENST00000416735ENST00000305877SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-3CDSENST00000416735ENST00000359540SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-3CDSENST00000437398ENST00000305877SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-3CDSENST00000437398ENST00000359540SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-3CDSENST00000541492ENST00000305877SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-3CDSENST00000541492ENST00000359540SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-intronENST00000416735ENST00000398512SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-intronENST00000416735ENST00000436990SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-intronENST00000437398ENST00000398512SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-intronENST00000437398ENST00000436990SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-intronENST00000541492ENST00000398512SPECC1Lchr22

24672771

+BCRchr22

23651611

+
intron-intronENST00000541492ENST00000436990SPECC1Lchr22

24672771

+BCRchr22

23651611

+

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 SPECC1L-BCR


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)
SPECC1Lchr2224666951+BCRchr2223651610+9.62E-050.9999038
SPECC1Lchr2224666951+BCRchr2223651610+9.62E-050.9999038
SPECC1Lchr2224672771+BCRchr2223651610+2.64E-050.99997365
SPECC1Lchr2224666951+BCRchr2223651610+9.62E-050.9999038
SPECC1Lchr2224666951+BCRchr2223651610+9.62E-050.9999038
SPECC1Lchr2224672771+BCRchr2223651610+2.64E-050.99997365

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.
genomic feature of top 1%

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Fusion Protein Features for SPECC1L-BCR


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/:24666951/:23651610)
- 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
.BCR

P11274

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: Protein with a unique structure having two opposing regulatory activities toward small GTP-binding proteins. The C-terminus is a GTPase-activating protein (GAP) domain which stimulates GTP hydrolysis by RAC1, RAC2 and CDC42. Accelerates the intrinsic rate of GTP hydrolysis of RAC1 or CDC42, leading to down-regulation of the active GTP-bound form (PubMed:7479768, PubMed:1903516, PubMed:17116687). The central Dbl homology (DH) domain functions as guanine nucleotide exchange factor (GEF) that modulates the GTPases CDC42, RHOA and RAC1. Promotes the conversion of CDC42, RHOA and RAC1 from the GDP-bound to the GTP-bound form (PubMed:7479768, PubMed:23940119). The amino terminus contains an intrinsic kinase activity (PubMed:1657398). Functions as an important negative regulator of neuronal RAC1 activity (By similarity). Regulates macrophage functions such as CSF1-directed motility and phagocytosis through the modulation of RAC1 activity (PubMed:17116687). Plays a major role as a RHOA GEF in keratinocytes being involved in focal adhesion formation and keratinocyte differentiation (PubMed:23940119). {ECO:0000250|UniProtKB:Q6PAJ1, ECO:0000269|PubMed:1657398, ECO:0000269|PubMed:17116687, ECO:0000269|PubMed:1903516, ECO:0000269|PubMed:23940119, ECO:0000269|PubMed:7479768}.

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 SPECC1L-BCR


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 SPECC1L-BCR


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 SPECC1L-BCR


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 SPECC1L-BCR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource