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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:OLFM2-HLA-DPA1 (FusionGDB2 ID:61474)

Fusion Gene Summary for OLFM2-HLA-DPA1

Fusion gene summary

Fusion gene information	Fusion gene name: OLFM2-HLA-DPA1
	Fusion gene ID: 61474
		Hgene	Tgene
	Gene symbol	OLFM2	HLA-DPA1
	Gene ID	93145	3113
	Gene name	olfactomedin 2	major histocompatibility complex, class II, DP alpha 1
	Synonyms	NOE2\|NOELIN2\|NOELIN2_V1\|OlfC	DP(W3)\|DP(W4)\|DPA1\|HLA-DP1A\|HLA-DPB1\|HLADP\|HLASB\|PLT1
	Cytomap	19p13.2	6p21.32
	Type of gene	protein-coding	protein-coding
	Description	noelin-2neuronal olfactomedin related ER localized protein 2	HLA class II histocompatibility antigen, DP alpha 1 chainHLA DPA1HLA-DPA101:03:01:NewHLA-DPA102:01:01:NEWHLA-SB alpha chainMHC class II DP alpha chainMHC class II DP3-alphaMHC class II HLA-DPA1 antigen
	Modification date	20200313	20200313
	UniProtAcc	.	P20036
	Ensembl transtripts involved in fusion gene	ENST00000264833, ENST00000590841,	ENST00000419277, ENST00000374808, ENST00000383224, ENST00000415247, ENST00000422504, ENST00000428995, ENST00000443117, ENST00000454805, ENST00000463066, ENST00000474244, ENST00000475500, ENST00000480521, ENST00000484255, ENST00000488565, ENST00000494775, ENST00000502285, ENST00000515317, ENST00000549300, ENST00000550456, ENST00000550806, ENST00000551196, ENST00000551933, ENST00000552158,
Fusion gene scores	* DoF score	12 X 3 X 8=288	6 X 9 X 1=54
	# samples	15	9
	** MAII score	log2(15/288*10)=-0.941106310946431 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/54*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: OLFM2 [Title/Abstract] AND HLA-DPA1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	OLFM2(9973926)-HLA-DPA1(33041426), # 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	OLFM2	GO:0009306	protein secretion	21228389
Tgene	HLA-DPA1	GO:0071346	cellular response to interferon-gamma	8568247

Fusion gene breakpoints across OLFM2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across HLA-DPA1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChiTaRS5.0	N/A	DT219158	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-

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Fusion Gene ORF analysis for OLFM2-HLA-DPA1

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
intron-5UTR	ENST00000264833	ENST00000419277	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-5UTR	ENST00000590841	ENST00000419277	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000374808	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000383224	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000415247	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000422504	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000428995	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000443117	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000454805	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000463066	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000474244	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000475500	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000480521	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000484255	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000488565	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000494775	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000502285	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000515317	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000549300	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000550456	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000550806	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000551196	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000551933	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000264833	ENST00000552158	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000374808	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000383224	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000415247	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000422504	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000428995	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000443117	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000454805	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000463066	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000474244	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000475500	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000480521	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000484255	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000488565	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000494775	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000502285	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000515317	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000549300	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000550456	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000550806	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000551196	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000551933	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-
intron-intron	ENST00000590841	ENST00000552158	OLFM2	chr19	9973926	-	HLA-DPA1	chr6	33041426	-

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for OLFM2-HLA-DPA1

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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 OLFM2-HLA-DPA1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:9973926/:33041426)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	HLA-DPA1 P20036
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.	FUNCTION: Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and efficient peptide loading.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for OLFM2-HLA-DPA1

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 OLFM2-HLA-DPA1

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for OLFM2-HLA-DPA1

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for OLFM2-HLA-DPA1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source