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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:RPL5-HMGN1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RPL5-HMGN1
FusionPDB ID: 76919
FusionGDB2.0 ID: 76919
HgeneTgene
Gene symbol

RPL5

HMGN1

Gene ID

6125

3150

Gene nameribosomal protein L5high mobility group nucleosome binding domain 1
SynonymsL5|MSTP030|PPP1R135|uL18HMG14
Cytomap

1p22.1

21q22.2

Type of geneprotein-codingprotein-coding
Description60S ribosomal protein L5large ribosomal subunit protein uL18protein phosphatase 1, regulatory subunit 135non-histone chromosomal protein HMG-14high mobility group nucleosome-binding domain-containing protein 1high-mobility group (nonhistone chromosomal) protein 14high-mobility group nucleosome binding 1nonhistone chromosomal protein HMG-14
Modification date2020031320200320
UniProtAcc.

P05114

Ensembl transtripts involved in fusion geneENST idsENST00000370321, ENST00000380747, 
ENST00000489072, ENST00000361263, 
ENST00000380748, ENST00000380749, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 7 X 9=10715 X 4 X 5=100
# samples 205
** MAII scorelog2(20/1071*10)=-2.42088657497553
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: RPL5 [Title/Abstract] AND HMGN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RPL5(93297674)-HMGN1(40717200), # samples:1
Anticipated loss of major functional domain due to fusion event.RPL5-HMGN1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
RPL5-HMGN1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
RPL5-HMGN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
RPL5-HMGN1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
RPL5-HMGN1 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor 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
HgeneRPL5

GO:0010628

positive regulation of gene expression

18560357

HgeneRPL5

GO:0045727

positive regulation of translation

16213212

HgeneRPL5

GO:1904667

negative regulation of ubiquitin protein ligase activity

18560357

HgeneRPL5

GO:2000059

negative regulation of ubiquitin-dependent protein catabolic process

18560357

HgeneRPL5

GO:2000435

negative regulation of protein neddylation

18560357


check buttonFusion gene breakpoints across RPL5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across HMGN1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-CancerERR315358RPL5chr1

93297674

+HMGN1chr21

40717200

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000370321RPL5chr193297674+ENST00000380749HMGN1chr2140717200-106793190582130
ENST00000370321RPL5chr193297674+ENST00000380748HMGN1chr2140717200-69093190582130

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
ENST00000370321ENST00000380749RPL5chr193297674+HMGN1chr2140717200-0.866450970.13354905
ENST00000370321ENST00000380748RPL5chr193297674+HMGN1chr2140717200-0.79816020.20183973

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>76919_76919_1_RPL5-HMGN1_RPL5_chr1_93297674_ENST00000370321_HMGN1_chr21_40717200_ENST00000380748_length(amino acids)=130AA_BP=
MRKTGKRRLRRVQPLMKQERKKPSLINNHIPCLISGPCLPSCTIQRNIFINYFVNASFLVALETFLRRRESHLIPFFKCKCFFLRGEIIC

--------------------------------------------------------------

>76919_76919_2_RPL5-HMGN1_RPL5_chr1_93297674_ENST00000370321_HMGN1_chr21_40717200_ENST00000380749_length(amino acids)=130AA_BP=
MRKTGKRRLRRVQPLMKQERKKPSLINNHIPCLISGPCLPSCTIQRNIFINYFVNASFLVALETFLRRRESHLIPFFKCKCFFLRGEIIC

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr1:93297674/chr21:40717200)
- 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
.HMGN1

P05114

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.FUNCTION: Binds to the inner side of the nucleosomal DNA thus altering the interaction between the DNA and the histone octamer. May be involved in the process which maintains transcribable genes in a unique chromatin conformation. Inhibits the phosphorylation of nucleosomal histones H3 and H2A by RPS6KA5/MSK1 and RPS6KA3/RSK2 (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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RPL5
HMGN1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to RPL5-HMGN1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to RPL5-HMGN1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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