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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:AFF1-PABPC1L (FusionGDB2 ID:2776)

Fusion Gene Summary for AFF1-PABPC1L

check button Fusion gene summary
Fusion gene informationFusion gene name: AFF1-PABPC1L
Fusion gene ID: 2776
HgeneTgene
Gene symbol

AFF1

PABPC1L

Gene ID

4299

80336

Gene nameAF4/FMR2 family member 1poly(A) binding protein cytoplasmic 1 like
SynonymsAF4|MLLT2|PBM1C20orf119|EPAB|PABPC1L1|dJ1069P2.3
Cytomap

4q21.3-q22.1

20q13.12

Type of geneprotein-codingprotein-coding
DescriptionAF4/FMR2 family member 1ALL1-fused gene from chromosome 4 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2pre-B-cell monocytic leukemia partner 1proto-oncogene AF4polyadenylate-binding protein 1-likeembryonic poly(A) binding protein
Modification date2020031320200313
UniProtAcc

P51825

.
Ensembl transtripts involved in fusion geneENST00000395146, ENST00000307808, 
ENST00000544085, ENST00000511996, 
ENST00000217074, ENST00000255136, 
ENST00000537323, ENST00000217073, 
ENST00000490798, ENST00000372824, 
ENST00000372819, ENST00000217075, 
Fusion gene scores* DoF score27 X 51 X 13=179016 X 5 X 5=150
# samples 686
** MAII scorelog2(68/17901*10)=-4.71836162613835
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/150*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFF1 [Title/Abstract] AND PABPC1L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAFF1(87869723)-PABPC1L(43559159), # samples:1
Anticipated loss of major functional domain due to fusion event.AFF1-PABPC1L seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
AFF1-PABPC1L seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AFF1-PABPC1L seems lost the major protein functional domain in Tgene partner, which is a essential gene 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 AFF1 (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 PABPC1L (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
ChimerDB4Non-CancerERR315373AFF1chr4

87869723

+PABPC1Lchr20

43559159

+


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Fusion Gene ORF analysis for AFF1-PABPC1L

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
Frame-shiftENST00000395146ENST00000217074AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
Frame-shiftENST00000395146ENST00000255136AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
Frame-shiftENST00000395146ENST00000537323AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
Frame-shiftENST00000395146ENST00000217073AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
5CDS-3UTRENST00000395146ENST00000490798AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
5CDS-intronENST00000395146ENST00000372824AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
5CDS-intronENST00000395146ENST00000372819AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
5CDS-intronENST00000395146ENST00000217075AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000307808ENST00000217074AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000307808ENST00000255136AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000307808ENST00000537323AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000307808ENST00000217073AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3UTRENST00000307808ENST00000490798AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-intronENST00000307808ENST00000372824AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-intronENST00000307808ENST00000372819AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-intronENST00000307808ENST00000217075AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000544085ENST00000217074AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000544085ENST00000255136AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000544085ENST00000537323AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3CDSENST00000544085ENST00000217073AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-3UTRENST00000544085ENST00000490798AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-intronENST00000544085ENST00000372824AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-intronENST00000544085ENST00000372819AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
intron-intronENST00000544085ENST00000217075AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-3CDSENST00000511996ENST00000217074AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-3CDSENST00000511996ENST00000255136AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-3CDSENST00000511996ENST00000537323AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-3CDSENST00000511996ENST00000217073AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-3UTRENST00000511996ENST00000490798AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-intronENST00000511996ENST00000372824AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-intronENST00000511996ENST00000372819AFF1chr4

87869723

+PABPC1Lchr20

43559159

+
3UTR-intronENST00000511996ENST00000217075AFF1chr4

87869723

+PABPC1Lchr20

43559159

+

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 AFF1-PABPC1L


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)
AFF1chr487869723+PABPC1Lchr2043559158+1.66E-171
AFF1chr487869723+PABPC1Lchr2043559158+1.66E-171

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.

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Fusion Protein Features for AFF1-PABPC1L


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
AFF1

P51825

.
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.
- 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 AFF1-PABPC1L


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 AFF1-PABPC1L


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 AFF1-PABPC1L


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 AFF1-PABPC1L


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