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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:HNRNPA3-ITSN1 (FusionGDB2 ID:37108)

Fusion Gene Summary for HNRNPA3-ITSN1

check button Fusion gene summary
Fusion gene informationFusion gene name: HNRNPA3-ITSN1
Fusion gene ID: 37108
HgeneTgene
Gene symbol

HNRNPA3

ITSN1

Gene ID

220988

6453

Gene nameheterogeneous nuclear ribonucleoprotein A3intersectin 1
Synonyms2610510D13Rik|D10S102|FBRNP|HNRPA3ITSN|SH3D1A|SH3P17
Cytomap

2q31.2

21q22.11

Type of geneprotein-codingprotein-coding
Descriptionheterogeneous nuclear ribonucleoprotein A3epididymis secretory sperm binding proteinintersectin-1SH3 domain-containing protein 1ASrc homology 3 domain-containing proteinhuman intersectin-SH3 domain-containing protein SH3P17intersectin 1 (SH3 domain protein)intersectin 1 short form variant 3intersectin 1 short form variant, 11inter
Modification date2020031320200313
UniProtAcc

P51991

Q15811

Ensembl transtripts involved in fusion geneENST00000411529, ENST00000392524, 
ENST00000435711, 		ENST00000379960, 
ENST00000381285, ENST00000381291, 
ENST00000381318, ENST00000399326, 
ENST00000399338, ENST00000399349, 
ENST00000399352, ENST00000399353, 
ENST00000399355, ENST00000399367, 
ENST00000437442, ENST00000488166, 
Fusion gene scores* DoF score13 X 11 X 3=42919 X 21 X 7=2793
# samples 1422
** MAII scorelog2(14/429*10)=-1.61555082055458
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2793*10)=-3.66624014475529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HNRNPA3 [Title/Abstract] AND ITSN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHNRNPA3(178084855)-ITSN1(35097462), # samples:1
ITSN1(35097462)-HNRNPA3(178084855), # 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

check buttonFusion gene breakpoints across HNRNPA3 (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 ITSN1 (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
ChiTaRS5.0N/ACB049973HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-


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Fusion Gene ORF analysis for HNRNPA3-ITSN1

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
3UTR-intronENST00000411529ENST00000379960HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000381285HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000381291HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000381318HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000399326HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000399338HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000399349HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000399352HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000399353HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000399355HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000399367HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000437442HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
3UTR-intronENST00000411529ENST00000488166HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000379960HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000381285HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000381291HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000381318HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000399326HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000399338HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000399349HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000399352HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000399353HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000399355HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000399367HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000437442HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000392524ENST00000488166HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000379960HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000381285HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000381291HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000381318HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000399326HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000399338HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000399349HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000399352HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000399353HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000399355HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000399367HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000437442HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-
intron-intronENST00000435711ENST00000488166HNRNPA3chr2

178084855

+ITSN1chr21

35097462

-

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 HNRNPA3-ITSN1


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.

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Fusion Protein Features for HNRNPA3-ITSN1


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/:178084855/:35097462)
- 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
HNRNPA3

P51991

ITSN1

Q15811

FUNCTION: Plays a role in cytoplasmic trafficking of RNA. Binds to the cis-acting response element, A2RE. May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:11886857}.FUNCTION: Adapter protein that provides a link between the endocytic membrane traffic and the actin assembly machinery (PubMed:11584276, PubMed:29887380). Acts as guanine nucleotide exchange factor (GEF) for CDC42, and thereby stimulates actin nucleation mediated by WASL and the ARP2/3 complex (PubMed:11584276). Plays a role in the assembly and maturation of clathrin-coated vesicles (By similarity). Recruits FCHSD2 to clathrin-coated pits (PubMed:29887380). Involved in endocytosis of activated EGFR, and probably also other growth factor receptors (By similarity). Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR may involve association with DAB2 (PubMed:22648170). Promotes ubiquitination and subsequent degradation of EGFR, and thereby contributes to the down-regulation of EGFR-dependent signaling pathways. In chromaffin cells, required for normal exocytosis of catecholamines. Required for rapid replenishment of release-ready synaptic vesicles at presynaptic active zones (By similarity). Inhibits ARHGAP31 activity toward RAC1 (PubMed:11744688). {ECO:0000250|UniProtKB:Q9WVE9, ECO:0000250|UniProtKB:Q9Z0R4, ECO:0000269|PubMed:11584276, ECO:0000269|PubMed:11744688, ECO:0000269|PubMed:22648170, ECO:0000269|PubMed:29887380}.; FUNCTION: [Isoform 1]: Plays a role in synaptic vesicle endocytosis in brain neurons. {ECO:0000250|UniProtKB:Q9Z0R4}.

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 HNRNPA3-ITSN1


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 HNRNPA3-ITSN1


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 HNRNPA3-ITSN1


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 HNRNPA3-ITSN1


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