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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:MLLT3-AKAP2 (FusionGDB2 ID:54284)

Fusion Gene Summary for MLLT3-AKAP2

check button Fusion gene summary
Fusion gene informationFusion gene name: MLLT3-AKAP2
Fusion gene ID: 54284
HgeneTgene
Gene symbol

MLLT3

AKAP2

Gene ID

4300

445815

Gene nameMLLT3 super elongation complex subunitPALM2 and AKAP2 fusion
SynonymsAF9|YEATS3AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PALM2-AKAP2|PRKA2
Cytomap

9p21.3

9q31.3

Type of geneprotein-codingprotein-coding
Descriptionprotein AF-9ALL1-fused gene from chromosome 9 proteinKMT2A/MLLT3 fusionKMT2A/MLLT3 fusion proteinYEATS domain-containing protein 3myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog); translocated to, 3myeloid/lymphoid or mixed-lineage leuA-kinase anchor protein 2PALM2-AKAP2 proteinparalemmin-2A kinase (PRKA) anchor protein 2A-kinase anchoring protein 2PALM2-AKAP2 fusionPALM2-AKAP2 readthroughparalemmin 2protein kinase A anchoring protein 2protein kinase A2
Modification date2020032720200313
UniProtAcc

P42568

Q9Y2D5

Ensembl transtripts involved in fusion geneENST00000380338, ENST00000429426, 
ENST00000355930, ENST00000475957, 
ENST00000380321, 		ENST00000259318, 
ENST00000374525, ENST00000434623, 
ENST00000482335, ENST00000510514, 
ENST00000555236, 
Fusion gene scores* DoF score18 X 14 X 11=27724 X 5 X 4=80
# samples 254
** MAII scorelog2(25/2772*10)=-3.47092725747513
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/80*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MLLT3 [Title/Abstract] AND AKAP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMLLT3(20620653)-AKAP2(112629771), # samples:1
Anticipated loss of major functional domain due to fusion event.MLLT3-AKAP2 seems lost the major protein functional domain in Hgene partner, which is a CGC 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
HgeneMLLT3

GO:0045893

positive regulation of transcription, DNA-templated

25417107|27105114

HgeneMLLT3

GO:0090090

negative regulation of canonical Wnt signaling pathway

19591803


check buttonFusion gene breakpoints across MLLT3 (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 AKAP2 (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
ChimerDB4LGGTCGA-FG-A87NMLLT3chr9

20620653

-AKAP2chr9

112629771

+


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Fusion Gene ORF analysis for MLLT3-AKAP2

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-intronENST00000380338ENST00000259318MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5CDS-intronENST00000380338ENST00000374525MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5CDS-intronENST00000380338ENST00000434623MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5CDS-intronENST00000380338ENST00000482335MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5CDS-intronENST00000429426ENST00000259318MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5CDS-intronENST00000429426ENST00000374525MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5CDS-intronENST00000429426ENST00000434623MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5CDS-intronENST00000429426ENST00000482335MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-3CDSENST00000355930ENST00000510514MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-3CDSENST00000355930ENST00000555236MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-3CDSENST00000475957ENST00000510514MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-3CDSENST00000475957ENST00000555236MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000355930ENST00000259318MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000355930ENST00000374525MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000355930ENST00000434623MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000355930ENST00000482335MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000475957ENST00000259318MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000475957ENST00000374525MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000475957ENST00000434623MLLT3chr9

20620653

-AKAP2chr9

112629771

+
5UTR-intronENST00000475957ENST00000482335MLLT3chr9

20620653

-AKAP2chr9

112629771

+
Frame-shiftENST00000380338ENST00000510514MLLT3chr9

20620653

-AKAP2chr9

112629771

+
Frame-shiftENST00000380338ENST00000555236MLLT3chr9

20620653

-AKAP2chr9

112629771

+
Frame-shiftENST00000429426ENST00000510514MLLT3chr9

20620653

-AKAP2chr9

112629771

+
Frame-shiftENST00000429426ENST00000555236MLLT3chr9

20620653

-AKAP2chr9

112629771

+
intron-3CDSENST00000380321ENST00000510514MLLT3chr9

20620653

-AKAP2chr9

112629771

+
intron-3CDSENST00000380321ENST00000555236MLLT3chr9

20620653

-AKAP2chr9

112629771

+
intron-intronENST00000380321ENST00000259318MLLT3chr9

20620653

-AKAP2chr9

112629771

+
intron-intronENST00000380321ENST00000374525MLLT3chr9

20620653

-AKAP2chr9

112629771

+
intron-intronENST00000380321ENST00000434623MLLT3chr9

20620653

-AKAP2chr9

112629771

+
intron-intronENST00000380321ENST00000482335MLLT3chr9

20620653

-AKAP2chr9

112629771

+

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 MLLT3-AKAP2


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.

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 MLLT3-AKAP2


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/:20620653/:112629771)
- 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
MLLT3

P42568

AKAP2

Q9Y2D5

FUNCTION: Chromatin reader component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA (PubMed:20159561, PubMed:20471948, PubMed:25417107, PubMed:27105114, PubMed:27545619). Specifically recognizes and binds acylated histone H3, with a preference for histone H3 that is crotonylated (PubMed:25417107, PubMed:27105114, PubMed:27545619, PubMed:30374167, PubMed:30385749). Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors (PubMed:25417107, PubMed:27105114, PubMed:27545619). Recognizes and binds histone H3 crotonylated at 'Lys-9' (H3K9cr), and with slightly lower affinity histone H3 crotonylated at 'Lys-18' (H3K18cr) (PubMed:27105114). Also recognizes and binds histone H3 acetylated and butyrylated at 'Lys-9' (H3K9ac and H3K9bu, respectively), but with lower affinity than crotonylated histone H3 (PubMed:25417107, PubMed:27105114, PubMed:30385749). In the SEC complex, MLLT3 is required to recruit the complex to crotonylated histones (PubMed:27105114, PubMed:27545619). Recruitment of the SEC complex to crotonylated histones promotes recruitment of DOT1L on active chromatin to deposit histone H3 'Lys-79' methylation (H3K79me) (PubMed:25417107). Plays a key role in hematopoietic stem cell (HSC) maintenance by preserving, rather than confering, HSC stemness (PubMed:31776511). Acts by binding to the transcription start site of active genes in HSCs and sustaining level of H3K79me2, probably by recruiting DOT1L (PubMed:31776511). {ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948, ECO:0000269|PubMed:25417107, ECO:0000269|PubMed:27105114, ECO:0000269|PubMed:27545619, ECO:0000269|PubMed:30374167, ECO:0000269|PubMed:30385749, ECO:0000269|PubMed:31776511}.FUNCTION: Binds to regulatory subunit (RII) of protein kinase A. May be involved in establishing polarity in signaling systems or in integrating PKA-RII isoforms with downstream effectors to capture, amplify and focus diffuse, trans-cellular signals carried by cAMP (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

- 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 MLLT3-AKAP2


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 MLLT3-AKAP2


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 MLLT3-AKAP2


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 MLLT3-AKAP2


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