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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:LDHB-RARB

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LDHB-RARB
FusionPDB ID: 44346
FusionGDB2.0 ID: 44346
HgeneTgene
Gene symbol

LDHB

RARB

Gene ID

3945

5915

Gene namelactate dehydrogenase Bretinoic acid receptor beta
SynonymsHEL-S-281|LDH-B|LDH-H|LDHBD|TRG-5HAP|MCOPS12|NR1B2|RARbeta1|RRB2
Cytomap

12p12.1

3p24.2

Type of geneprotein-codingprotein-coding
DescriptionL-lactate dehydrogenase B chainLDH heart subunitepididymis secretory protein Li 281lactate dehydrogenase H chainrenal carcinoma antigen NY-REN-46testicular secretory protein Li 25retinoic acid receptor betaHBV-activated proteinRAR-betaRAR-epsilonhepatitis B virus activated proteinnuclear receptor subfamily 1 group B member 2retinoic acid receptor, beta polypeptide
Modification date2020032620200328
UniProtAcc

P07195

.
Ensembl transtripts involved in fusion geneENST idsENST00000350669, ENST00000396076, 
ENST00000535112, 
ENST00000458646, 
ENST00000462272, ENST00000330688, 
ENST00000404969, ENST00000437042, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 8 X 6=4804 X 4 X 2=32
# samples 104
** MAII scorelog2(10/480*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: LDHB [Title/Abstract] AND RARB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LDHB(21790005)-RARB(25637911), # samples:1
Anticipated loss of major functional domain due to fusion event.LDHB-RARB seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
LDHB-RARB seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
LDHB-RARB seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
LDHB-RARB seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
LDHB-RARB seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
LDHB-RARB seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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 buttonFusion gene breakpoints across LDHB (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 RARB (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-A4R8-01ALDHBchr12

21790005

-RARBchr3

25637911

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000396076LDHBchr1221790005-ENST00000404969RARBchr325637911+136711701711184337

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
ENST00000396076ENST00000404969LDHBchr1221790005-RARBchr325637911+0.0037607090.9962393

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>44346_44346_1_LDHB-RARB_LDHB_chr12_21790005_ENST00000396076_RARB_chr3_25637911_ENST00000404969_length(amino acids)=337AA_BP=
MSIRPRALTLPLSLGRRGGRALAEEQKAEGSSCGSAERLVAFAAKTRPYLSLCKMATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMAC
AISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIV
KYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELN

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

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Fusion Protein Functional Features


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/chr12:21790005/chr3:25637911)
- 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
LDHB

P07195

.
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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLDHBchr12:21790005chr3:25637911ENST00000350669-7831_53279.0335.0Nucleotide bindingNAD
HgeneLDHBchr12:21790005chr3:25637911ENST00000396076-7831_53279.0335.0Nucleotide bindingNAD

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneRARBchr12:21790005chr3:25637911ENST000003306886888_153383.3333333333333449.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST000004049696888_153390.3333333333333456.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST000004370426888_153271.3333333333333337.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST000004586466888_153271.3333333333333337.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST0000033068868183_417383.3333333333333449.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000040496968183_417390.3333333333333456.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000043704268183_417271.3333333333333337.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000045864668183_417271.3333333333333337.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000033068868154_182383.3333333333333449.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000330688681_87383.3333333333333449.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000040496968154_182390.3333333333333456.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000404969681_87390.3333333333333456.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000043704268154_182271.3333333333333337.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000437042681_87271.3333333333333337.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000045864668154_182271.3333333333333337.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000458646681_87271.3333333333333337.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000033068868124_148383.3333333333333449.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000003306886888_108383.3333333333333449.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST0000040496968124_148390.3333333333333456.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000004049696888_108390.3333333333333456.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST0000043704268124_148271.3333333333333337.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000004370426888_108271.3333333333333337.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST0000045864668124_148271.3333333333333337.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000004586466888_108271.3333333333333337.0Zinc fingerNR C4-type


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
LDHB
RARB


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to LDHB-RARB


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to LDHB-RARB


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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