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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 16520

FusionGeneSummary for HNRNPA1_BEST3

check button Fusion gene summary
Fusion gene informationFusion gene name: HNRNPA1_BEST3
Fusion gene ID: 16520
HgeneTgene
Gene symbol

HNRNPA1

BEST3

Gene ID

3178

144453

Gene nameheterogeneous nuclear ribonucleoprotein A1bestrophin 3
SynonymsALS19|ALS20|HNRPA1|HNRPA1L3|IBMPFD3|UP 1|hnRNP A1|hnRNP-A1VMD2L3
Cytomap

12q13.13

12q15

Type of geneprotein-codingprotein-coding
Descriptionheterogeneous nuclear ribonucleoprotein A1helix-destabilizing proteinheterogeneous nuclear ribonucleoprotein A1B proteinheterogeneous nuclear ribonucleoprotein B2 proteinheterogeneous nuclear ribonucleoprotein core protein A1hnRNP core protein A1-likbestrophin-3vitelliform macular dystrophy 2-like 3vitelliform macular dystrophy 2-like protein 3
Modification date2018052320180523
UniProtAcc

P09651

Q8N1M1

Ensembl transtripts involved in fusion geneENST00000546500, ENST00000340913, 
ENST00000330752, ENST00000547276, 
ENST00000551803, 		ENST00000331471, 
ENST00000488961, ENST00000330891, 
ENST00000553096, ENST00000476098, 
ENST00000266661, ENST00000551160, 
ENST00000393365, ENST00000533674, 
Fusion gene scores* DoF score2 X 2 X 2=810 X 6 X 5=300
# samples 210
** MAII scorelog2(2/8*10)=1.32192809488736log2(10/300*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HNRNPA1 [Title/Abstract] AND BEST3 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneHNRNPA1

GO:0032212

positive regulation of telomere maintenance via telomerase

23935072

HgeneHNRNPA1

GO:0051168

nuclear export

8521471

HgeneHNRNPA1

GO:0051170

import into nucleus

8521471

HgeneHNRNPA1

GO:1903936

cellular response to sodium arsenite

27694260


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1CR748314HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
intron-intronENST00000546500ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-

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FusionProtFeatures for HNRNPA1_BEST3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
HNRNPA1

P09651

BEST3

Q8N1M1

Involved in the packaging of pre-mRNA into hnRNPparticles, transport of poly(A) mRNA from the nucleus to thecytoplasm and may modulate splice site selection(PubMed:17371836). May bind to specific miRNA hairpins(PubMed:28431233). {ECO:0000269|PubMed:17371836,ECO:0000269|PubMed:28431233}. (Microbial infection) May play a role in HCV RNAreplication. {ECO:0000269|PubMed:17229681}. Forms calcium-sensitive chloride channels. Permeable tobicarbonate. {ECO:0000269|PubMed:12907679}.

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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FusionGeneSequence for HNRNPA1_BEST3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for HNRNPA1_BEST3


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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RelatedDrugs for HNRNPA1_BEST3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for HNRNPA1_BEST3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHNRNPA1C3715156AMYOTROPHIC LATERAL SCLEROSIS 202UNIPROT
HgeneHNRNPA1C3809469INCLUSION BODY MYOPATHY WITH EARLY-ONSET PAGET DISEASE WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA 32UNIPROT
HgeneHNRNPA1C0024667Animal Mammary Neoplasms1CTD_human
HgeneHNRNPA1C0024668Mammary Neoplasms, Experimental1CTD_human