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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:HNRNPR-SRRM1 (FusionGDB2 ID:37138)

Fusion Gene Summary for HNRNPR-SRRM1

check button Fusion gene summary
Fusion gene informationFusion gene name: HNRNPR-SRRM1
Fusion gene ID: 37138
HgeneTgene
Gene symbol

HNRNPR

SRRM1

Gene ID

10236

10250

Gene nameheterogeneous nuclear ribonucleoprotein Rserine and arginine repetitive matrix 1
SynonymsHNRPR|hnRNP-R160-KD|POP101|SRM160
Cytomap

1p36.12

1p36.11

Type of geneprotein-codingprotein-coding
Descriptionheterogeneous nuclear ribonucleoprotein Rserine/arginine repetitive matrix protein 1SR-related nuclear matrix protein of 160 kDaSer/Arg-related nuclear matrix protein
Modification date2020031520200313
UniProtAcc

O43390

.
Ensembl transtripts involved in fusion geneENST00000478691, ENST00000374616, 
ENST00000476660, ENST00000374612, 
ENST00000302271, ENST00000427764, 
ENST00000606561, ENST00000426846, 
ENST00000323848, ENST00000447431, 
ENST00000374389, ENST00000479034, 
ENST00000537199, 
Fusion gene scores* DoF score6 X 5 X 4=1207 X 11 X 4=308
# samples 711
** MAII scorelog2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/308*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HNRNPR [Title/Abstract] AND SRRM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHNRNPR(23660011)-SRRM1(24973158), # samples:1
Anticipated loss of major functional domain due to fusion event.HNRNPR-SRRM1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
HNRNPR-SRRM1 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 HNRNPR (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 SRRM1 (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
ChimerDB4STADTCGA-BR-A4IY-01AHNRNPRchr1

23660011

-SRRM1chr1

24973158

+


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Fusion Gene ORF analysis for HNRNPR-SRRM1

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-shiftENST00000478691ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000478691ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000478691ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-3UTRENST00000478691ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-intronENST00000478691ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000374616ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000374616ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000374616ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-3UTRENST00000374616ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-intronENST00000374616ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000476660ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000476660ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000476660ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3UTRENST00000476660ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-intronENST00000476660ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000374612ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000374612ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000374612ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-3UTRENST00000374612ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-intronENST00000374612ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000302271ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000302271ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000302271ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-3UTRENST00000302271ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-intronENST00000302271ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000427764ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000427764ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000427764ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3UTRENST00000427764ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-intronENST00000427764ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000606561ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000606561ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3CDSENST00000606561ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-3UTRENST00000606561ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
intron-intronENST00000606561ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000426846ENST00000323848HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000426846ENST00000447431HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
Frame-shiftENST00000426846ENST00000374389HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-3UTRENST00000426846ENST00000479034HNRNPRchr1

23660011

-SRRM1chr1

24973158

+
5CDS-intronENST00000426846ENST00000537199HNRNPRchr1

23660011

-SRRM1chr1

24973158

+

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 HNRNPR-SRRM1


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)
HNRNPRchr123660010-SRRM1chr124973157+0.0006142540.9993857
HNRNPRchr123660010-SRRM1chr124973157+0.0006142540.9993857

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 HNRNPR-SRRM1


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
HNRNPR

O43390

.
FUNCTION: Component of ribonucleosomes, which are complexes of at least 20 other different heterogeneous nuclear ribonucleoproteins (hnRNP). hnRNP play an important role in processing of precursor mRNA in the nucleus.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 HNRNPR-SRRM1


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 HNRNPR-SRRM1


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 HNRNPR-SRRM1


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 HNRNPR-SRRM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHNRNPRC0006142Malignant neoplasm of breast1CTD_human
HgeneHNRNPRC0036572Seizures1GENOMICS_ENGLAND
HgeneHNRNPRC0557874Global developmental delay1GENOMICS_ENGLAND
HgeneHNRNPRC0678222Breast Carcinoma1CTD_human
HgeneHNRNPRC1257931Mammary Neoplasms, Human1CTD_human
HgeneHNRNPRC1458155Mammary Neoplasms1CTD_human
HgeneHNRNPRC1847514Postnatal microcephaly1GENOMICS_ENGLAND
HgeneHNRNPRC3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneHNRNPRC4023124Short digit1GENOMICS_ENGLAND
HgeneHNRNPRC4225275MENTAL RETARDATION, AUTOSOMAL DOMINANT 401GENOMICS_ENGLAND
HgeneHNRNPRC4704874Mammary Carcinoma, Human1CTD_human