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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:SRSF7-HNRNPLL

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SRSF7-HNRNPLL
FusionPDB ID: 86647
FusionGDB2.0 ID: 86647
HgeneTgene
Gene symbol

SRSF7

HNRNPLL

Gene ID

6432

92906

Gene nameserine and arginine rich splicing factor 7heterogeneous nuclear ribonucleoprotein L like
Synonyms9G8|AAG3|SFRS7HNRPLL|SRRF
Cytomap

2p22.1

2p22.1

Type of geneprotein-codingprotein-coding
Descriptionserine/arginine-rich splicing factor 7SR splicing factor 7aging-associated protein 3splicing factor 9G8splicing factor, arginine/serine-rich 7, 35kDaheterogeneous nuclear ribonucleoprotein L-likestromal RNA regulating factor
Modification date2020031320200327
UniProtAcc.

Q8WVV9

Ensembl transtripts involved in fusion geneENST idsENST00000313117, ENST00000409276, 
ENST00000446327, 
ENST00000498516, 
ENST00000358367, ENST00000378915, 
ENST00000409328, ENST00000449105, 
ENST00000608859, ENST00000409636, 
ENST00000410076, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 4 X 2=326 X 7 X 4=168
# samples 46
** MAII scorelog2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(6/168*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SRSF7 [Title/Abstract] AND HNRNPLL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SRSF7(38973286)-HNRNPLL(38829742), # samples:2
Anticipated loss of major functional domain due to fusion event.SRSF7-HNRNPLL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SRSF7-HNRNPLL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SRSF7-HNRNPLL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
SRSF7-HNRNPLL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
SRSF7-HNRNPLL seems lost the major protein functional domain in Hgene 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
HgeneSRSF7

GO:0008380

RNA splicing

8013463

HgeneSRSF7

GO:0048025

negative regulation of mRNA splicing, via spliceosome

15009664

TgeneHNRNPLL

GO:0033120

positive regulation of RNA splicing

18669861


check buttonFusion gene breakpoints across SRSF7 (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 HNRNPLL (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
ChimerDB4CESCTCGA-DS-A1O9-01ASRSF7chr2

38973286

-HNRNPLLchr2

38829742

-
ChimerDB4CESCTCGA-DS-A1O9SRSF7chr2

38973286

-HNRNPLLchr2

38829742

-


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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)
ENST00000313117SRSF7chr238973286-ENST00000409636HNRNPLLchr238829742-4707900522502816
ENST00000313117SRSF7chr238973286-ENST00000410076HNRNPLLchr238829742-2514900521716554
ENST00000409276SRSF7chr238973286-ENST00000409636HNRNPLLchr238829742-4562755152357780
ENST00000409276SRSF7chr238973286-ENST00000410076HNRNPLLchr238829742-2369755151571518

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
ENST00000313117ENST00000409636SRSF7chr238973286-HNRNPLLchr238829742-0.0002985630.99970144
ENST00000313117ENST00000410076SRSF7chr238973286-HNRNPLLchr238829742-0.0027929760.997207
ENST00000409276ENST00000409636SRSF7chr238973286-HNRNPLLchr238829742-0.0002767990.99972314
ENST00000409276ENST00000410076SRSF7chr238973286-HNRNPLLchr238829742-0.0034117040.99658835

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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

>86647_86647_1_SRSF7-HNRNPLL_SRSF7_chr2_38973286_ENST00000313117_HNRNPLL_chr2_38829742_ENST00000409636_length(amino acids)=816AA_BP=1
MCRAEQRDDACAKRSGRIYKREPGLFLVVPPGLLAGEGVCQLLRHSSPGRCLLKSRARGSVIMSRYGRYGGETKVYVGNLGTGAGKGELE
RAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYD
CHRYSRRRRSRSRSRSHSRSRGRRYSRSRSRSRGRRSRSASPRRSRSISLRRSRSASLRRSRSGSIKGSRYFQSPSRSRSRSRSISRPRS
SRSKSRSPSPKRRETYEEDREYESQAKRLKTEEGEIDYSAEEGENRREATPRGGGDGGGGGRSFSQPEAGGSHHKVSVSPVVHVRGLCES
VVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRITRPGNTDDPSGGNKVLLLSIQNP
LYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYLGR
RDRGKGRQRQAILGEHPSSFRHDGYGSHGPLLPLPSRYRMGSRDTPELVAYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLF
CLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMSKNNRFTSAGQASK
NIIQPPSCVLHYYNVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKPSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYTLKLCF

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

>86647_86647_2_SRSF7-HNRNPLL_SRSF7_chr2_38973286_ENST00000313117_HNRNPLL_chr2_38829742_ENST00000410076_length(amino acids)=554AA_BP=1
MCRAEQRDDACAKRSGRIYKREPGLFLVVPPGLLAGEGVCQLLRHSSPGRCLLKSRARGSVIMSRYGRYGGETKVYVGNLGTGAGKGELE
RAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYD
CHRYSRRRRSRSRSRSHSRSRGRRYSRSRSRSRGRRSRSASPRRSRSISLRRSRSASLRRSRSGSIKGSRYFQSPSRSRSRSRSISRPRS
SRSKSRSPSPKRRETYEEDREYESQAKRLKTEEGEIDYSAEEGENRREATPRGGGDGGGGGRSFSQPEAGGSHHKVSVSPVVHVRGLCES
VVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRITRPGNTDDPSGGNKVLLLSIQNP
LYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYLGR

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

>86647_86647_3_SRSF7-HNRNPLL_SRSF7_chr2_38973286_ENST00000409276_HNRNPLL_chr2_38829742_ENST00000409636_length(amino acids)=780AA_BP=149
MAGEGVCQLLRHSSPGRCLLKSRARGSVIMSRYGRYGGETKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAE
DAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRGRRYSRSRSRSR
GRRSRSASPRRSRSISLRRSRSASLRRSRSGSIKGSRSPSRSRSRSRSISRPRSSRSKSRSPSPKRRETYEEDREYESQAKRLKTEEGEI
DYSAEEGENRREATPRGGGDGGGGGRSFSQPEAGGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENID
SAKECVTFAADEPVYIAGQQAFFNYSTSKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEF
ESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYLGRRDRGKGRQRQAILGEHPSSFRHDGYGSHGPLLPLPS
RYRMGSRDTPELVAYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHL
NNVKLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMSKNNRFTSAGQASKNIIQPPSCVLHYYNVPLCVTEETFTKLCNDHEVLTF

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

>86647_86647_4_SRSF7-HNRNPLL_SRSF7_chr2_38973286_ENST00000409276_HNRNPLL_chr2_38829742_ENST00000410076_length(amino acids)=518AA_BP=149
MAGEGVCQLLRHSSPGRCLLKSRARGSVIMSRYGRYGGETKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAE
DAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRGRRYSRSRSRSR
GRRSRSASPRRSRSISLRRSRSASLRRSRSGSIKGSRSPSRSRSRSRSISRPRSSRSKSRSPSPKRRETYEEDREYESQAKRLKTEEGEI
DYSAEEGENRREATPRGGGDGGGGGRSFSQPEAGGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENID
SAKECVTFAADEPVYIAGQQAFFNYSTSKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEF

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

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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/chr2:38973286/chr2:38829742)
- 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
.HNRNPLL

Q8WVV9

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: RNA-binding protein that functions as regulator of alternative splicing for multiple target mRNAs, including PTPRC/CD45 and STAT5A. Required for alternative splicing of PTPRC. {ECO:0000269|PubMed:18669861}.

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
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-7811_84220.66666666666666239.0DomainRRM
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78153_160220.66666666666666239.0RepeatNote=1
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78161_168220.66666666666666239.0RepeatNote=2
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78169_176220.66666666666666239.0RepeatNote=3
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78177_184220.66666666666666239.0RepeatNote=4
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78211_218220.66666666666666239.0RepeatNote=5%3B approximate
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78104_120220.66666666666666239.0Zinc fingerCCHC-type
TgeneHNRNPLLchr2:38973286chr2:38829742ENST000004096360142_73.6666666666666665538.0Compositional biasNote=Poly-Ser
TgeneHNRNPLLchr2:38973286chr2:38829742ENST0000040963601449_573.6666666666666665538.0Compositional biasNote=Poly-Gly
TgeneHNRNPLLchr2:38973286chr2:38829742ENST00000410076072_73.6666666666666665276.0Compositional biasNote=Poly-Ser
TgeneHNRNPLLchr2:38973286chr2:38829742ENST000004100760749_573.6666666666666665276.0Compositional biasNote=Poly-Gly
TgeneHNRNPLLchr2:38973286chr2:38829742ENST00000409636014166_2443.6666666666666665538.0DomainRRM 2
TgeneHNRNPLLchr2:38973286chr2:38829742ENST00000409636014335_4093.6666666666666665538.0DomainRRM 3
TgeneHNRNPLLchr2:38973286chr2:38829742ENST0000040963601476_1503.6666666666666665538.0DomainRRM 1
TgeneHNRNPLLchr2:38973286chr2:38829742ENST0000041007607166_2443.6666666666666665276.0DomainRRM 2
TgeneHNRNPLLchr2:38973286chr2:38829742ENST0000041007607335_4093.6666666666666665276.0DomainRRM 3
TgeneHNRNPLLchr2:38973286chr2:38829742ENST000004100760776_1503.6666666666666665276.0DomainRRM 1

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78121_238220.66666666666666239.0Compositional biasNote=Arg/Ser-rich (RS domain)
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17121_2380227.0Compositional biasNote=Arg/Ser-rich (RS domain)
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-1711_840227.0DomainRRM
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78153_226220.66666666666666239.0RegionNote=6 X 8 AA repeats of R-R-S-R-S-X-S-X
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17153_2260227.0RegionNote=6 X 8 AA repeats of R-R-S-R-S-X-S-X
HgeneSRSF7chr2:38973286chr2:38829742ENST00000313117-78219_226220.66666666666666239.0RepeatNote=6%3B approximate
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17153_1600227.0RepeatNote=1
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17161_1680227.0RepeatNote=2
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17169_1760227.0RepeatNote=3
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17177_1840227.0RepeatNote=4
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17211_2180227.0RepeatNote=5%3B approximate
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17219_2260227.0RepeatNote=6%3B approximate
HgeneSRSF7chr2:38973286chr2:38829742ENST00000446327-17104_1200227.0Zinc fingerCCHC-type


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1594_SRSF7_38973286_HNRNPLL_38829742_ranked_0.pdbSRSF73897328638973286ENST00000410076HNRNPLLchr238829742-
MCRAEQRDDACAKRSGRIYKREPGLFLVVPPGLLAGEGVCQLLRHSSPGRCLLKSRARGSVIMSRYGRYGGETKVYVGNLGTGAGKGELE
RAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYD
CHRYSRRRRSRSRSRSHSRSRGRRYSRSRSRSRGRRSRSASPRRSRSISLRRSRSASLRRSRSGSIKGSRYFQSPSRSRSRSRSISRPRS
SRSKSRSPSPKRRETYEEDREYESQAKRLKTEEGEIDYSAEEGENRREATPRGGGDGGGGGRSFSQPEAGGSHHKVSVSPVVHVRGLCES
VVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRITRPGNTDDPSGGNKVLLLSIQNP
LYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYLGR
RDRGKGRQRQAILGEHPSSFRHDGYGSHGPLLPLPSRYRMGSRDTPELVAYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLF
CLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMSKNNRFTSAGQASK
NIIQPPSCVLHYYNVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKPSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYTLKLCF
816


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
SRSF7_pLDDT.png
all structure
all structure
HNRNPLL_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
SRSF7
HNRNPLL


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 SRSF7-HNRNPLL


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 SRSF7-HNRNPLL


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