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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:HSPA12B-BRE (FusionGDB2 ID:37840)

Fusion Gene Summary for HSPA12B-BRE

check button Fusion gene summary
Fusion gene informationFusion gene name: HSPA12B-BRE
Fusion gene ID: 37840
HgeneTgene
Gene symbol

HSPA12B

BRE

Gene ID

116835

9577

Gene nameheat shock protein family A (Hsp70) member 12BBRISC and BRCA1 A complex member 2
SynonymsC20orf60BRCC4|BRCC45|BRE
Cytomap

20p13

2p23.2

Type of geneprotein-codingprotein-coding
Descriptionheat shock 70 kDa protein 12BBRISC and BRCA1-A complex member 2BRCA1-A complex subunit BREBRCA1/BRCA2-containing complex subunit 45BRCA1/BRCA2-containing complex, subunit 4brain and reproductive organ-expressed (TNFRSF1A modulator)brain and reproductive organ-expressed protein
Modification date2020031320200313
UniProtAcc

Q96MM6

.
Ensembl transtripts involved in fusion geneENST00000254963, ENST00000542646, 
ENST00000342045, ENST00000361704, 
ENST00000379624, ENST00000379632, 
ENST00000603461, ENST00000344773, 
Fusion gene scores* DoF score1 X 1 X 1=120 X 20 X 12=4800
# samples 130
** MAII scorelog2(1/1*10)=3.32192809488736log2(30/4800*10)=-4
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HSPA12B [Title/Abstract] AND BRE [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHSPA12B(3731554)-BRE(28550141), # 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
TgeneBRE

GO:0043066

negative regulation of apoptotic process

15465831


check buttonFusion gene breakpoints across HSPA12B (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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

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
ChimerDB4UCSTCGA-N5-A4RA-01AHSPA12Bchr20

3731554

-BREchr2

28550141

+


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Fusion Gene ORF analysis for HSPA12B-BRE

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-intronENST00000254963ENST00000342045HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000254963ENST00000361704HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000254963ENST00000379624HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000254963ENST00000379632HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000254963ENST00000603461HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000542646ENST00000342045HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000542646ENST00000361704HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000542646ENST00000379624HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000542646ENST00000379632HSPA12Bchr20

3731554

-BREchr2

28550141

+
5CDS-intronENST00000542646ENST00000603461HSPA12Bchr20

3731554

-BREchr2

28550141

+
In-frameENST00000254963ENST00000344773HSPA12Bchr20

3731554

-BREchr2

28550141

+
In-frameENST00000542646ENST00000344773HSPA12Bchr20

3731554

-BREchr2

28550141

+

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)
ENST00000254963HSPA12Bchr203731554-ENST00000344773BREchr228550141+21761550401803587
ENST00000542646HSPA12Bchr203731554-ENST00000344773BREchr228550141+196613403731593406

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
ENST00000254963ENST00000344773HSPA12Bchr203731554-BREchr228550141+0.104669770.89533025
ENST00000542646ENST00000344773HSPA12Bchr203731554-BREchr228550141+0.183994860.8160052

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Fusion Genomic Features for HSPA12B-BRE


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.
genomic feature

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 HSPA12B-BRE


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/chr20:3731554/chr2:28550141)
- 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
HSPA12B

Q96MM6

.
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}.

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
TgeneBREchr20:3731554chr2:28550141ENST00000342045013275_3640384.0RegionNote=UEV-like 2
TgeneBREchr20:3731554chr2:28550141ENST0000034204501330_1470384.0RegionNote=UEV-like 1
TgeneBREchr20:3731554chr2:28550141ENST00000361704013275_3640511.0RegionNote=UEV-like 2
TgeneBREchr20:3731554chr2:28550141ENST0000036170401330_1470511.0RegionNote=UEV-like 1
TgeneBREchr20:3731554chr2:28550141ENST00000379624012275_3640384.0RegionNote=UEV-like 2
TgeneBREchr20:3731554chr2:28550141ENST0000037962401230_1470384.0RegionNote=UEV-like 1
TgeneBREchr20:3731554chr2:28550141ENST00000379632014275_3640511.0RegionNote=UEV-like 2
TgeneBREchr20:3731554chr2:28550141ENST0000037963201430_1470511.0RegionNote=UEV-like 1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneBREchr20:3731554chr2:28550141ENST000003447731013275_364362528.6666666666666RegionNote=UEV-like 2
TgeneBREchr20:3731554chr2:28550141ENST00000344773101330_147362528.6666666666666RegionNote=UEV-like 1


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Fusion Gene Sequence for HSPA12B-BRE


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.
>37840_37840_1_HSPA12B-BRE_HSPA12B_chr20_3731554_ENST00000254963_BRE_chr2_28550141_ENST00000344773_length(transcript)=2176nt_BP=1550nt
GAGGAGGCGGGAGGCCTCAGGGCCGGGCGCACGTCGAGGGCTGCGGCCGCCGCAGCGGGCACGGCCAACGAGCTGCGGGCCCGGGATCGC
GGCGGCTGGACGGGGCTGGAGCTGTCGGGAGGGCGGAGCTACAGGGCCTGCAAGGATGTTGGCTGTCCCGGAGATGGGCCTGCAGGGGCT
GTACATCGGCTCCAGCCCGGAGCGGTCCCCAGTGCCTAGCCCACCCGGCTCCCCGAGGACCCAGGAAAGCTGCGGCATTGCCCCCCTCAC
ACCCTCGCAGTCTCCAAAACCCGAGGTCCGAGCCCCCCAGCAGGCCTCCTTCTCTGTGGTGGTGGCCATTGACTTCGGCACCACGTCTAG
TGGCTATGCTTTCAGCTTTGCCAGTGACCCTGAGGCCATCCACATGATGAGGAAATGGGAGGGCGGAGACCCGGGCGTGGCCCACCAGAA
GACCCCGACCTGCCTGCTGCTGACTCCGGAGGGCGCCTTCCACAGCTTTGGCTACACCGCCCGCGATTACTACCATGACCTGGACCCCGA
AGAGGCGCGGGACTGGCTCTACTTCGAGAAGTTCAAGATGAAGATCCACAGCGCCACGGATCTCACCTTGAAGACCCAGCTAGAGGCAGT
AAATGGAAAGACGATGCCCGCCCTGGAGGTGTTCGCCCATGCCCTGCGCTTCTTCAGGGAGCACGCCCTTCAGGAGCTGAGGGAGCAGAG
CCCATCGCTGCCAGAGAAGGACACTGTGCGCTGGGTGTTGACGGTGCCTGCCATCTGGAAACAGCCAGCCAAGCAGTTCATGCGGGAGGC
TGCCTACCTGGCTGGACTAGTGTCCCGAGAGAATGCAGAGCAGCTACTCATCGCCCTGGAGCCCGAGGCCGCCTCGGTATACTGCCGCAA
GCTGCGCCTGCACCAGCTCCTGGACCTGAGTGGCCGGGCCCCAGGTGGTGGGCGCCTGGGTGAGCGCCGCTCCATCGACTCCAGCTTCCG
TCAGGCTCGGGAGCAGCTGCGAAGGTCCCGCCACAGCCGCACGTTCCTGGTGGAGTCAGGCGTAGGAGAGCTGTGGGCAGAGATGCAAGC
AGGAGACCGCTACGTGGTGGCCGACTGCGGCGGAGGCACCGTGGACCTGACGGTGCACCAGCTGGAGCAGCCCCATGGCACCCTCAAGGA
GCTCTACAAGGCATCTGGGGGCCCTTATGGCGCGGTGGGCGTGGACCTGGCCTTCGAGCAGCTGCTGTGCCGCATCTTCGGCGAGGACTT
CATCGCCACCTTCAAAAGGCAACGGCCGGCAGCCTGGGTAGATCTGACCATCGCCTTCGAGGCTCGCAAGCGCACTGCTGGCCCACACCG
TGCAGGGGCGCTCAACATCTCGCTGCCCTTCTCCTTCATTGACTTCTACCGCAAGCAGCGGGGCCACAACGTGGAGACCGCTCTGCGCAG
GAGCAGCGTGAACTTCGTGAAGTGGTCCTCACAGGGGATGCTCCGAATGTCTTGTGAAGCCATGAACGAGCTCTTTCAGCCCACCGTCAG
CGGGATCATCCAGCACATAGGGGATGCCAAGGGAGCAGAGATGCCTGCAGCCCGTGGGAGCAAGTCCTGGCCTTTGCAGTTGCAAAAACT
GGCTGCAAGCTGCTCCAGCCCCAGAGGAACTGGCCAAGCTCCAGAGGGCCTCCTTGGAGGGCCTCAGAGGGAGAGAGAACTGCTCAGTAA
TTTTGATCACTTTGGGCTTATTTCAAAACCTTTGTCCCTCAGTTCCAGGAGGCAGCATTTGCCAATGGAAAGCTCTAGGAAACACCAGTC
TTGAGAGGTGGCCAGCCAGACTGCCTGTCCACATGCGTGTCAGCACATACAGCCGCTTCCTGGAAGCCGCCTGGAATGTCTTCACGGCAG
CGTTTTGCTCACACAGCAGCTTTTGCACGCCCCAGGCAGCCCCGACTGCTGAAATCCAACTTGAGCTGGCTGGTGGTCCCTGGATCCTAG
AGCCCTTCACTTCGGGTTACTCCCTCTTTCTTGCCTCTATTTCTTAGTTGGAAGAAATAAACTCACAAATTATGGTGCAGTAATTTTCCG
GGGAAAGTAAAGCCTCAGGAATGCCCACGCCTTTCTTCCAAAGCCTTTGTCTCTGAGACCTCTTAAGTTCTAAGATTAAATGCCCCTCGC

>37840_37840_1_HSPA12B-BRE_HSPA12B_chr20_3731554_ENST00000254963_BRE_chr2_28550141_ENST00000344773_length(amino acids)=587AA_BP=503
MRPPQRARPTSCGPGIAAAGRGWSCREGGATGPARMLAVPEMGLQGLYIGSSPERSPVPSPPGSPRTQESCGIAPLTPSQSPKPEVRAPQ
QASFSVVVAIDFGTTSSGYAFSFASDPEAIHMMRKWEGGDPGVAHQKTPTCLLLTPEGAFHSFGYTARDYYHDLDPEEARDWLYFEKFKM
KIHSATDLTLKTQLEAVNGKTMPALEVFAHALRFFREHALQELREQSPSLPEKDTVRWVLTVPAIWKQPAKQFMREAAYLAGLVSRENAE
QLLIALEPEAASVYCRKLRLHQLLDLSGRAPGGGRLGERRSIDSSFRQAREQLRRSRHSRTFLVESGVGELWAEMQAGDRYVVADCGGGT
VDLTVHQLEQPHGTLKELYKASGGPYGAVGVDLAFEQLLCRIFGEDFIATFKRQRPAAWVDLTIAFEARKRTAGPHRAGALNISLPFSFI
DFYRKQRGHNVETALRRSSVNFVKWSSQGMLRMSCEAMNELFQPTVSGIIQHIGDAKGAEMPAARGSKSWPLQLQKLAASCSSPRGTGQA

--------------------------------------------------------------
>37840_37840_2_HSPA12B-BRE_HSPA12B_chr20_3731554_ENST00000542646_BRE_chr2_28550141_ENST00000344773_length(transcript)=1966nt_BP=1340nt
GGAGGCCTCAGGGCCGGGCGCACGTCGAGGGCTGCGGCCGCCGCAGCGGGCACGGCCAACGAGCTGCGGGCCCGGGATCGCGGCGGCTGG
ACGGGGCTGGAGCTGTCGGGAGGGCGGAGCTACAGGGCCTGCAAGGATGTTGGCTGTCCCGGAGATGGGCCTGCAGGGGCTGTACATCGG
AAATGGGAGGGCGGAGACCCGGGCGTGGCCCACCAGAAGACCCCGACCTGCCTGCTGCTGACTCCGGAGGGCGCCTTCCACAGCTTTGGC
TACACCGCCCGCGATTACTACCATGACCTGGACCCCGAAGAGGCGCGGGACTGGCTCTACTTCGAGAAGTTCAAGATGAAGATCCACAGC
GCCACGAGCCGCCCTGTGTCCCTGCCAGGATCTCACCTTGAAGACCCAGCTAGAGGCAGTAAATGGAAAGACGATGCCCGCCCTGGAGGT
GTTCGCCCATGCCCTGCGCTTCTTCAGGGAGCACGCCCTTCAGGAGCTGAGGGAGCAGAGCCCATCGCTGCCAGAGAAGGACACTGTGCG
CTGGGTGTTGACGGTGCCTGCCATCTGGAAACAGCCAGCCAAGCAGTTCATGCGGGAGGCTGCCTACCTGGCTGGACTAGTGTCCCGAGA
GAATGCAGAGCAGCTACTCATCGCCCTGGAGCCCGAGGCCGCCTCGGTATACTGCCGCAAGCTGCGCCTGCACCAGCTCCTGGACCTGAG
TGGCCGGGCCCCAGGTGGTGGGCGCCTGGGTGAGCGCCGCTCCATCGACTCCAGCTTCCGTCAGGCTCGGGAGCAGCTGCGAAGGTCCCG
CCACAGCCGCACGTTCCTGGTGGAGTCAGGCGTAGGAGAGCTGTGGGCAGAGATGCAAGCAGGAGACCGCTACGTGGTGGCCGACTGCGG
CGGAGGCACCGTGGACCTGACGGTGCACCAGCTGGAGCAGCCCCATGGCACCCTCAAGGAGCTCTACAAGGCATCTGGGGGCCCTTATGG
CGCGGTGGGCGTGGACCTGGCCTTCGAGCAGCTGCTGTGCCGCATCTTCGGCGAGGACTTCATCGCCACCTTCAAAAGGCAACGGCCGGC
AGCCTGGGTAGATCTGACCATCGCCTTCGAGGCTCGCAAGCGCACTGCTGGCCCACACCGTGCAGGGGCGCTCAACATCTCGCTGCCCTT
CTCCTTCATTGACTTCTACCGCAAGCAGCGGGGCCACAACGTGGAGACCGCTCTGCGCAGGAGCAGCGTGAACTTCGTGAAGTGGTCCTC
ACAGGGGATGCTCCGAATGTCTTGTGAAGCCATGAACGAGCTCTTTCAGCCCACCGTCAGCGGGATCATCCAGCACATAGGGGATGCCAA
GGGAGCAGAGATGCCTGCAGCCCGTGGGAGCAAGTCCTGGCCTTTGCAGTTGCAAAAACTGGCTGCAAGCTGCTCCAGCCCCAGAGGAAC
TGGCCAAGCTCCAGAGGGCCTCCTTGGAGGGCCTCAGAGGGAGAGAGAACTGCTCAGTAATTTTGATCACTTTGGGCTTATTTCAAAACC
TTTGTCCCTCAGTTCCAGGAGGCAGCATTTGCCAATGGAAAGCTCTAGGAAACACCAGTCTTGAGAGGTGGCCAGCCAGACTGCCTGTCC
ACATGCGTGTCAGCACATACAGCCGCTTCCTGGAAGCCGCCTGGAATGTCTTCACGGCAGCGTTTTGCTCACACAGCAGCTTTTGCACGC
CCCAGGCAGCCCCGACTGCTGAAATCCAACTTGAGCTGGCTGGTGGTCCCTGGATCCTAGAGCCCTTCACTTCGGGTTACTCCCTCTTTC
TTGCCTCTATTTCTTAGTTGGAAGAAATAAACTCACAAATTATGGTGCAGTAATTTTCCGGGGAAAGTAAAGCCTCAGGAATGCCCACGC

>37840_37840_2_HSPA12B-BRE_HSPA12B_chr20_3731554_ENST00000542646_BRE_chr2_28550141_ENST00000344773_length(amino acids)=406AA_BP=322
MCPCQDLTLKTQLEAVNGKTMPALEVFAHALRFFREHALQELREQSPSLPEKDTVRWVLTVPAIWKQPAKQFMREAAYLAGLVSRENAEQ
LLIALEPEAASVYCRKLRLHQLLDLSGRAPGGGRLGERRSIDSSFRQAREQLRRSRHSRTFLVESGVGELWAEMQAGDRYVVADCGGGTV
DLTVHQLEQPHGTLKELYKASGGPYGAVGVDLAFEQLLCRIFGEDFIATFKRQRPAAWVDLTIAFEARKRTAGPHRAGALNISLPFSFID
FYRKQRGHNVETALRRSSVNFVKWSSQGMLRMSCEAMNELFQPTVSGIIQHIGDAKGAEMPAARGSKSWPLQLQKLAASCSSPRGTGQAP

--------------------------------------------------------------

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Fusion Gene PPI Analysis for HSPA12B-BRE


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 HSPA12B-BRE


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 HSPA12B-BRE


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