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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:ARID5B-ABLIM1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARID5B-ABLIM1
FusionPDB ID: 6496
FusionGDB2.0 ID: 6496
HgeneTgene
Gene symbol

ARID5B

ABLIM1

Gene ID

84159

3983

Gene nameAT-rich interaction domain 5Bactin binding LIM protein 1
SynonymsDESRT|MRF-2|MRF2ABLIM|LIMAB1|LIMATIN|abLIM-1
Cytomap

10q21.2

10q25.3

Type of geneprotein-codingprotein-coding
DescriptionAT-rich interactive domain-containing protein 5BARID domain-containing protein 5BAT-rich interactive domain 5B (MRF1-like)MRF1-like proteinmodulator recognition factor 2 (MRF2)actin-binding LIM protein 1actin-binding LIM protein family member 1actin-binding double-zinc-finger protein
Modification date2020031320200313
UniProtAcc

Q14865

O14639

Ensembl transtripts involved in fusion geneENST idsENST00000279873, ENST00000309334, 
ENST00000477638, ENST00000277895, 
ENST00000369252, ENST00000369253, 
ENST00000369266, ENST00000392952, 
ENST00000533213, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 15 X 7=189013 X 14 X 4=728
# samples 1814
** MAII scorelog2(18/1890*10)=-3.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/728*10)=-2.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ARID5B [Title/Abstract] AND ABLIM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARID5B(63700167)-ABLIM1(116201545), # samples:4
Anticipated loss of major functional domain due to fusion event.ARID5B-ABLIM1 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.
ARID5B-ABLIM1 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.
ARID5B-ABLIM1 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.
ARID5B-ABLIM1 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.
* 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
HgeneARID5B

GO:0000122

negative regulation of transcription by RNA polymerase II

8649988

HgeneARID5B

GO:0051091

positive regulation of DNA-binding transcription factor activity

21532585


check buttonFusion gene breakpoints across ARID5B (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 ABLIM1 (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
ChimerDB4BRCATCGA-AO-A12G-01AARID5Bchr10

63700167

-ABLIM1chr10

116201545

-
ChimerDB4BRCATCGA-AO-A12G-01AARID5Bchr10

63700167

+ABLIM1chr10

116201545

-
ChimerDB4BRCATCGA-AO-A12GARID5Bchr10

63700167

+ABLIM1chr10

116201545

-


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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)
ENST00000279873ARID5Bchr1063700167+ENST00000369252ABLIM1chr10116201545-64639124101315301
ENST00000279873ARID5Bchr1063700167+ENST00000533213ABLIM1chr10116201545-64639124101315301
ENST00000279873ARID5Bchr1063700167+ENST00000277895ABLIM1chr10116201545-15389124101315301
ENST00000279873ARID5Bchr1063700167+ENST00000369266ABLIM1chr10116201545-64639124101315301
ENST00000279873ARID5Bchr1063700167+ENST00000392952ABLIM1chr10116201545-64639124101315301
ENST00000279873ARID5Bchr1063700167+ENST00000369253ABLIM1chr10116201545-21359124101315301

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
ENST00000279873ENST00000369252ARID5Bchr1063700167+ABLIM1chr10116201545-0.001067390.99893266
ENST00000279873ENST00000533213ARID5Bchr1063700167+ABLIM1chr10116201545-0.001099050.9989009
ENST00000279873ENST00000277895ARID5Bchr1063700167+ABLIM1chr10116201545-0.0054035420.99459654
ENST00000279873ENST00000369266ARID5Bchr1063700167+ABLIM1chr10116201545-0.001099050.9989009
ENST00000279873ENST00000392952ARID5Bchr1063700167+ABLIM1chr10116201545-0.001067390.99893266
ENST00000279873ENST00000369253ARID5Bchr1063700167+ABLIM1chr10116201545-0.0044442170.9955558

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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

>6496_6496_1_ARID5B-ABLIM1_ARID5B_chr10_63700167_ENST00000279873_ABLIM1_chr10_116201545_ENST00000277895_length(amino acids)=301AA_BP=167
MEPNSLQWVGSPCGLHGPYIFYKAFQFHLEGKPRILSLGDFFFVRCTPKDPICIAELQLLWEERTSRQLLSSSKLYFLPEDTPQGRNSDH
GEDEVIAVSEKVIVKLEDLVKWVHSDFSKWRCGFHAGPVKTEALGRNGQKEALLKYRQSTLNSGLNFKDVLKEKADLASHIPSSKTASLP
GYGRNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEMLMVTNRGRNKILREVDRTRLERHLAPE

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

>6496_6496_2_ARID5B-ABLIM1_ARID5B_chr10_63700167_ENST00000279873_ABLIM1_chr10_116201545_ENST00000369252_length(amino acids)=301AA_BP=167
MEPNSLQWVGSPCGLHGPYIFYKAFQFHLEGKPRILSLGDFFFVRCTPKDPICIAELQLLWEERTSRQLLSSSKLYFLPEDTPQGRNSDH
GEDEVIAVSEKVIVKLEDLVKWVHSDFSKWRCGFHAGPVKTEALGRNGQKEALLKYRQSTLNSGLNFKDVLKEKADLASHIPSSKTASLP
GYGRNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEMLMVTNRGRNKILREVDRTRLERHLAPE

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

>6496_6496_3_ARID5B-ABLIM1_ARID5B_chr10_63700167_ENST00000279873_ABLIM1_chr10_116201545_ENST00000369253_length(amino acids)=301AA_BP=167
MEPNSLQWVGSPCGLHGPYIFYKAFQFHLEGKPRILSLGDFFFVRCTPKDPICIAELQLLWEERTSRQLLSSSKLYFLPEDTPQGRNSDH
GEDEVIAVSEKVIVKLEDLVKWVHSDFSKWRCGFHAGPVKTEALGRNGQKEALLKYRQSTLNSGLNFKDVLKEKADLASHIPSSKTASLP
GYGRNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEMLMVTNRGRNKILREVDRTRLERHLAPE

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

>6496_6496_4_ARID5B-ABLIM1_ARID5B_chr10_63700167_ENST00000279873_ABLIM1_chr10_116201545_ENST00000369266_length(amino acids)=301AA_BP=167
MEPNSLQWVGSPCGLHGPYIFYKAFQFHLEGKPRILSLGDFFFVRCTPKDPICIAELQLLWEERTSRQLLSSSKLYFLPEDTPQGRNSDH
GEDEVIAVSEKVIVKLEDLVKWVHSDFSKWRCGFHAGPVKTEALGRNGQKEALLKYRQSTLNSGLNFKDVLKEKADLASHIPSSKTASLP
GYGRNGLHRPVSTDFAQYNSYGDVSGGVRDFQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEMLMVTNRGRNKILREVDRTRLERHLAPE

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

>6496_6496_5_ARID5B-ABLIM1_ARID5B_chr10_63700167_ENST00000279873_ABLIM1_chr10_116201545_ENST00000392952_length(amino acids)=301AA_BP=167
MEPNSLQWVGSPCGLHGPYIFYKAFQFHLEGKPRILSLGDFFFVRCTPKDPICIAELQLLWEERTSRQLLSSSKLYFLPEDTPQGRNSDH
GEDEVIAVSEKVIVKLEDLVKWVHSDFSKWRCGFHAGPVKTEALGRNGQKEALLKYRQSTLNSGLNFKDVLKEKADLASHIPSSKTASLP
GYGRNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEMLMVTNRGRNKILREVDRTRLERHLAPE

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

>6496_6496_6_ARID5B-ABLIM1_ARID5B_chr10_63700167_ENST00000279873_ABLIM1_chr10_116201545_ENST00000533213_length(amino acids)=301AA_BP=167
MEPNSLQWVGSPCGLHGPYIFYKAFQFHLEGKPRILSLGDFFFVRCTPKDPICIAELQLLWEERTSRQLLSSSKLYFLPEDTPQGRNSDH
GEDEVIAVSEKVIVKLEDLVKWVHSDFSKWRCGFHAGPVKTEALGRNGQKEALLKYRQSTLNSGLNFKDVLKEKADLASHIPSSKTASLP
GYGRNGLHRPVSTDFAQYNSYGDVSGGVRDFQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEMLMVTNRGRNKILREVDRTRLERHLAPE

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

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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/chr10:63700167/chr10:116201545)
- 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
ARID5B

Q14865

ABLIM1

O14639

FUNCTION: Transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer. {ECO:0000269|PubMed:21532585}.FUNCTION: May act as scaffold protein (By similarity). May play a role in the development of the retina. Has been suggested to play a role in axon guidance. {ECO:0000250, ECO:0000269|PubMed:9245787}.

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
TgeneABLIM1chr10:63700167chr10:116201545ENST000003692521623590_614584.3333333333334719.0Coiled coilOntology_term=ECO:0000255
TgeneABLIM1chr10:63700167chr10:116201545ENST00000369253916590_614267.3333333333333402.0Coiled coilOntology_term=ECO:0000255
TgeneABLIM1chr10:63700167chr10:116201545ENST000003929521118590_614321.3333333333333456.0Coiled coilOntology_term=ECO:0000255
TgeneABLIM1chr10:63700167chr10:116201545ENST000002778951623710_778644.3333333333334779.0DomainHP
TgeneABLIM1chr10:63700167chr10:116201545ENST000003692521623710_778584.3333333333334719.0DomainHP
TgeneABLIM1chr10:63700167chr10:116201545ENST00000369253916283_343267.3333333333333402.0DomainLIM zinc-binding 4
TgeneABLIM1chr10:63700167chr10:116201545ENST00000369253916710_778267.3333333333333402.0DomainHP
TgeneABLIM1chr10:63700167chr10:116201545ENST000003929521118710_778321.3333333333333456.0DomainHP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneARID5Bchr10:63700167chr10:116201545ENST00000279873+310318_410167.333333333333341189.0DomainARID
HgeneARID5Bchr10:63700167chr10:116201545ENST00000309334+17318_4100946.0DomainARID
TgeneABLIM1chr10:63700167chr10:116201545ENST000002778951623590_614644.3333333333334779.0Coiled coilOntology_term=ECO:0000255
TgeneABLIM1chr10:63700167chr10:116201545ENST000002778951623156_216644.3333333333334779.0DomainLIM zinc-binding 2
TgeneABLIM1chr10:63700167chr10:116201545ENST000002778951623224_283644.3333333333334779.0DomainLIM zinc-binding 3
TgeneABLIM1chr10:63700167chr10:116201545ENST000002778951623283_343644.3333333333334779.0DomainLIM zinc-binding 4
TgeneABLIM1chr10:63700167chr10:116201545ENST00000277895162397_156644.3333333333334779.0DomainLIM zinc-binding 1
TgeneABLIM1chr10:63700167chr10:116201545ENST000003692521623156_216584.3333333333334719.0DomainLIM zinc-binding 2
TgeneABLIM1chr10:63700167chr10:116201545ENST000003692521623224_283584.3333333333334719.0DomainLIM zinc-binding 3
TgeneABLIM1chr10:63700167chr10:116201545ENST000003692521623283_343584.3333333333334719.0DomainLIM zinc-binding 4
TgeneABLIM1chr10:63700167chr10:116201545ENST00000369252162397_156584.3333333333334719.0DomainLIM zinc-binding 1
TgeneABLIM1chr10:63700167chr10:116201545ENST00000369253916156_216267.3333333333333402.0DomainLIM zinc-binding 2
TgeneABLIM1chr10:63700167chr10:116201545ENST00000369253916224_283267.3333333333333402.0DomainLIM zinc-binding 3
TgeneABLIM1chr10:63700167chr10:116201545ENST0000036925391697_156267.3333333333333402.0DomainLIM zinc-binding 1
TgeneABLIM1chr10:63700167chr10:116201545ENST000003929521118156_216321.3333333333333456.0DomainLIM zinc-binding 2
TgeneABLIM1chr10:63700167chr10:116201545ENST000003929521118224_283321.3333333333333456.0DomainLIM zinc-binding 3
TgeneABLIM1chr10:63700167chr10:116201545ENST000003929521118283_343321.3333333333333456.0DomainLIM zinc-binding 4
TgeneABLIM1chr10:63700167chr10:116201545ENST00000392952111897_156321.3333333333333456.0DomainLIM zinc-binding 1


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>541_ARID5B_63700167_ABLIM1_116201545_ranked_0.pdbARID5B6370016763700167ENST00000369253ABLIM1chr10116201545-
MEPNSLQWVGSPCGLHGPYIFYKAFQFHLEGKPRILSLGDFFFVRCTPKDPICIAELQLLWEERTSRQLLSSSKLYFLPEDTPQGRNSDH
GEDEVIAVSEKVIVKLEDLVKWVHSDFSKWRCGFHAGPVKTEALGRNGQKEALLKYRQSTLNSGLNFKDVLKEKADLASHIPSSKTASLP
GYGRNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEMLMVTNRGRNKILREVDRTRLERHLAPE
301


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
ARID5B_pLDDT.png
all structure
all structure
ABLIM1_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
ARID5B
ABLIM1


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 ARID5B-ABLIM1


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 ARID5B-ABLIM1


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