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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:HELLS-CXCL12 (FusionGDB2 ID:36075)

Fusion Gene Summary for HELLS-CXCL12

check button Fusion gene summary
Fusion gene informationFusion gene name: HELLS-CXCL12
Fusion gene ID: 36075
HgeneTgene
Gene symbol

HELLS

CXCL12

Gene ID

3070

6387

Gene namehelicase, lymphoid specificC-X-C motif chemokine ligand 12
SynonymsICF4|LSH|Nbla10143|PASG|SMARCA6IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1
Cytomap

10q23.33

10q11.21

Type of geneprotein-codingprotein-coding
Descriptionlymphoid-specific helicaseSWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6proliferation-associated SNF2-like proteinstromal cell-derived factor 1chemokine (C-X-C motif) ligand 12intercrine reduced in hepatomaspre-B cell growth-stimulating factor
Modification date2020032220200313
UniProtAcc

Q9NRZ9

P48061

Ensembl transtripts involved in fusion geneENST00000239026, ENST00000348459, 
ENST00000371332, ENST00000394036, 
ENST00000394044, ENST00000394045, 
ENST00000462057, 		ENST00000343575, 
ENST00000374426, ENST00000374429, 
ENST00000395793, ENST00000395794, 
ENST00000395795, ENST00000496375, 
Fusion gene scores* DoF score7 X 8 X 4=2246 X 4 X 4=96
# samples 76
** MAII scorelog2(7/224*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HELLS [Title/Abstract] AND CXCL12 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHELLS(96324678)-CXCL12(44794448), # 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
TgeneCXCL12

GO:0033622

integrin activation

29301984

TgeneCXCL12

GO:0045785

positive regulation of cell adhesion

23620790

TgeneCXCL12

GO:0060326

cell chemotaxis

18308860

TgeneCXCL12

GO:0070098

chemokine-mediated signaling pathway

20388803

TgeneCXCL12

GO:0090026

positive regulation of monocyte chemotaxis

18802065

TgeneCXCL12

GO:1902230

negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage

20388803

TgeneCXCL12

GO:1903237

negative regulation of leukocyte tethering or rolling

18308860

TgeneCXCL12

GO:2000406

positive regulation of T cell migration

23620790

TgeneCXCL12

GO:2000669

negative regulation of dendritic cell apoptotic process

15059845


check buttonFusion gene breakpoints across HELLS (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 CXCL12 (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/AAV700167HELLSchr10

96324678

+CXCL12chr10

44794448

+


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Fusion Gene ORF analysis for HELLS-CXCL12

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-intronENST00000239026ENST00000343575HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000239026ENST00000374426HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000239026ENST00000374429HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000239026ENST00000395793HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000239026ENST00000395794HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000239026ENST00000395795HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000239026ENST00000496375HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000348459ENST00000343575HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000348459ENST00000374426HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000348459ENST00000374429HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000348459ENST00000395793HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000348459ENST00000395794HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000348459ENST00000395795HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000348459ENST00000496375HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000371332ENST00000343575HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000371332ENST00000374426HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000371332ENST00000374429HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000371332ENST00000395793HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000371332ENST00000395794HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000371332ENST00000395795HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000371332ENST00000496375HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394036ENST00000343575HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394036ENST00000374426HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394036ENST00000374429HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394036ENST00000395793HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394036ENST00000395794HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394036ENST00000395795HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394036ENST00000496375HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394044ENST00000343575HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394044ENST00000374426HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394044ENST00000374429HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394044ENST00000395793HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394044ENST00000395794HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394044ENST00000395795HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394044ENST00000496375HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394045ENST00000343575HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394045ENST00000374426HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394045ENST00000374429HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394045ENST00000395793HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394045ENST00000395794HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394045ENST00000395795HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000394045ENST00000496375HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000462057ENST00000343575HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000462057ENST00000374426HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000462057ENST00000374429HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000462057ENST00000395793HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000462057ENST00000395794HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000462057ENST00000395795HELLSchr10

96324678

+CXCL12chr10

44794448

+
intron-intronENST00000462057ENST00000496375HELLSchr10

96324678

+CXCL12chr10

44794448

+

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 HELLS-CXCL12


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 HELLS-CXCL12


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/:96324678/:44794448)
- 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
HELLS

Q9NRZ9

CXCL12

P48061

FUNCTION: Plays an essential role in normal development and survival. Involved in regulation of the expansion or survival of lymphoid cells. Required for de novo or maintenance DNA methylation. May control silencing of the imprinted CDKN1C gene through DNA methylation. May play a role in formation and organization of heterochromatin, implying a functional role in the regulation of transcription and mitosis (By similarity). {ECO:0000250|UniProtKB:Q60848}.FUNCTION: Chemoattractant active on T-lymphocytes and monocytes but not neutrophils. Activates the C-X-C chemokine receptor CXCR4 to induce a rapid and transient rise in the level of intracellular calcium ions and chemotaxis. SDF-1-beta(3-72) and SDF-1-alpha(3-67) show a reduced chemotactic activity. Binding to cell surface proteoglycans seems to inhibit formation of SDF-1-alpha(3-67) and thus to preserve activity on local sites. Also binds to atypical chemokine receptor ACKR3, which activates the beta-arrestin pathway and acts as a scavenger receptor for SDF-1. Binds to the allosteric site (site 2) of integrins and activates integrins ITGAV:ITGB3, ITGA4:ITGB1 and ITGA5:ITGB1 in a CXCR4-independent manner (PubMed:29301984). Acts as a positive regulator of monocyte migration and a negative regulator of monocyte adhesion via the LYN kinase. Stimulates migration of monocytes and T-lymphocytes through its receptors, CXCR4 and ACKR3, and decreases monocyte adherence to surfaces coated with ICAM-1, a ligand for beta-2 integrins. SDF1A/CXCR4 signaling axis inhibits beta-2 integrin LFA-1 mediated adhesion of monocytes to ICAM-1 through LYN kinase. Inhibits CXCR4-mediated infection by T-cell line-adapted HIV-1. Plays a protective role after myocardial infarction. Induces down-regulation and internalization of ACKR3 expressed in various cells. Has several critical functions during embryonic development; required for B-cell lymphopoiesis, myelopoiesis in bone marrow and heart ventricular septum formation. Stimulates the proliferation of bone marrow-derived B-cell progenitors in the presence of IL7 as well as growth of stromal cell-dependent pre-B-cells (By similarity). {ECO:0000250|UniProtKB:P40224, ECO:0000269|PubMed:11069075, ECO:0000269|PubMed:11859124, ECO:0000269|PubMed:16107333, ECO:0000269|PubMed:18802065, ECO:0000269|PubMed:19255243, ECO:0000269|PubMed:29301984, ECO:0000269|PubMed:8752281}.

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 HELLS-CXCL12


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 HELLS-CXCL12


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 HELLS-CXCL12


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 HELLS-CXCL12


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