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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:PTBP1-SCGB1C1 (FusionGDB2 ID:69836)

Fusion Gene Summary for PTBP1-SCGB1C1

Fusion gene summary

Fusion gene information	Fusion gene name: PTBP1-SCGB1C1
	Fusion gene ID: 69836
		Hgene	Tgene
	Gene symbol	PTBP1	SCGB1C1
	Gene ID	5725	653486
	Gene name	polypyrimidine tract binding protein 1	secretoglobin family 1C member 2
	Synonyms	HNRNP-I\|HNRNPI\|HNRPI\|PTB\|PTB-1\|PTB-T\|PTB2\|PTB3\|PTB4\|pPTB	SCGB1C1
	Cytomap	19p13.3	17p13.3
	Type of gene	protein-coding	protein-coding
	Description	polypyrimidine tract-binding protein 157 kDa RNA-binding protein PPTB-1RNA-binding proteinheterogeneous nuclear ribonucleoprotein Iheterogeneous nuclear ribonucleoprotein polypeptide IhnRNP Ipolypyrimidine tract binding protein (heterogeneous nuclea	secretoglobin family 1C member 2Secretoglobin RYD5Secretoglobin family 1C member 1secretoglobin, family 1C, member 1-like
	Modification date	20200313	20200313
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000349038, ENST00000350092, ENST00000356948, ENST00000394601,	ENST00000342878,
Fusion gene scores	* DoF score	16 X 17 X 9=2448	2 X 2 X 2=8
	# samples	17	2
	** MAII score	log2(17/2448*10)=-3.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(2/8*10)=1.32192809488736
Context	PubMed: PTBP1 [Title/Abstract] AND SCGB1C1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	PTBP1(799443)-SCGB1C1(193712), # samples:1 PTBP1(799443)-SCGB1C1(194418), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTBP1-SCGB1C1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. PTBP1-SCGB1C1 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)

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	PTBP1	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	16260624\|21518792
Hgene	PTBP1	GO:0033119	negative regulation of RNA splicing	18335065
Hgene	PTBP1	GO:0048025	negative regulation of mRNA splicing, via spliceosome	15009664
Hgene	PTBP1	GO:0051148	negative regulation of muscle cell differentiation	21518792

Fusion gene breakpoints across PTBP1 (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 SCGB1C1 (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
ChimerDB4	MESO	TCGA-TS-A7P6-01A	PTBP1	chr19	799443	+	SCGB1C1	chr11	193712	+
ChimerDB4	MESO	TCGA-TS-A7P6-01A	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+

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Fusion Gene ORF analysis for PTBP1-SCGB1C1

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
Frame-shift	ENST00000349038	ENST00000342878	PTBP1	chr19	799443	+	SCGB1C1	chr11	193712	+
Frame-shift	ENST00000350092	ENST00000342878	PTBP1	chr19	799443	+	SCGB1C1	chr11	193712	+
Frame-shift	ENST00000356948	ENST00000342878	PTBP1	chr19	799443	+	SCGB1C1	chr11	193712	+
Frame-shift	ENST00000394601	ENST00000342878	PTBP1	chr19	799443	+	SCGB1C1	chr11	193712	+
In-frame	ENST00000349038	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+
In-frame	ENST00000350092	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+
In-frame	ENST00000356948	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+
In-frame	ENST00000394601	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+

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)
ENST00000356948	PTBP1	chr19	799443	-	ENST00000342878	SCGB1C1	chr11	194418	+	618	462	459	130	109
ENST00000350092	PTBP1	chr19	799443	-	ENST00000342878	SCGB1C1	chr11	194418	+	301	145	43	177	44
ENST00000349038	PTBP1	chr19	799443	-	ENST00000342878	SCGB1C1	chr11	194418	+	268	112	10	144	44
ENST00000394601	PTBP1	chr19	799443	-	ENST00000342878	SCGB1C1	chr11	194418	+	241	85	132	1	44

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
ENST00000356948	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+	0.7869479	0.21305215
ENST00000350092	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+	0.504072	0.495928
ENST00000349038	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+	0.4281408	0.57185924
ENST00000394601	ENST00000342878	PTBP1	chr19	799443	-	SCGB1C1	chr11	194418	+	0.3389298	0.6610702

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Fusion Genomic Features for PTBP1-SCGB1C1

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)
PTBP1	chr19	799443	+	SCGB1C1	chr11	193711	+	2.84E-06	0.99999714
PTBP1	chr19	799443	+	SCGB1C1	chr11	193711	+	2.84E-06	0.99999714

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 PTBP1-SCGB1C1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:799443/chr11:193712)
- 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
.	.
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: 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}.

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

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000349038

316_323

532.0

Compositional bias

Note=Poly-Ala

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000356948

316_323

558.0

Compositional bias

Note=Poly-Ala

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000394601

316_323

551.0

Compositional bias

Note=Poly-Ala

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000349038

184_260

532.0

Domain

RRM 2

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000349038

337_411

532.0

Domain

RRM 3

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000349038

454_529

532.0

Domain

RRM 4

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000349038

59_143

532.0

Domain

RRM 1

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000356948

184_260

558.0

Domain

RRM 2

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000356948

337_411

558.0

Domain

RRM 3

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000356948

454_529

558.0

Domain

RRM 4

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000356948

59_143

558.0

Domain

RRM 1

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000394601

184_260

551.0

Domain

RRM 2

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000394601

337_411

551.0

Domain

RRM 3

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000394601

454_529

551.0

Domain

RRM 4

Hgene

PTBP1

chr19:799443

chr11:194418

ENST00000394601

59_143

551.0

Domain

RRM 1

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Fusion Gene Sequence for PTBP1-SCGB1C1

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.

>69836_69836_1_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000349038_SCGB1C1_chr11_194418_ENST00000342878_length(transcript)=268nt_BP=112nt
CTCGGAGCCGTTGGGTCGGTTCCTGCTATTCCGGCGCCTCCACTCCGTCCCCCGCGGGTCTGCTCTGTGTGCCATGGACGGCATTGTCCC
AGATATAGCCGTTGGTACAAAGGTGCAAGTGCTGGGCAGTCAGGACGGTGCCTAAGTGGACCTCAGACATGGCTCAGCCATAGGACCTGC

>69836_69836_1_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000349038_SCGB1C1_chr11_194418_ENST00000342878_length(amino acids)=44AA_BP=

--------------------------------------------------------------
>69836_69836_2_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000350092_SCGB1C1_chr11_194418_ENST00000342878_length(transcript)=301nt_BP=145nt
TGCGGGCGTCTCCGCCATTTTGTGAGTCTATAACTCGGAGCCGTTGGGTCGGTTCCTGCTATTCCGGCGCCTCCACTCCGTCCCCCGCGG
GTCTGCTCTGTGTGCCATGGACGGCATTGTCCCAGATATAGCCGTTGGTACAAAGGTGCAAGTGCTGGGCAGTCAGGACGGTGCCTAAGT
GGACCTCAGACATGGCTCAGCCATAGGACCTGCCACACAAGCAGCCGTGGACACAACGCCCACTACCACCTCCCACATGGAAATGTATCC

>69836_69836_2_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000350092_SCGB1C1_chr11_194418_ENST00000342878_length(amino acids)=44AA_BP=

--------------------------------------------------------------
>69836_69836_3_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000356948_SCGB1C1_chr11_194418_ENST00000342878_length(transcript)=618nt_BP=462nt
GGGCAAAGCACGCTTCCCGCCGCCTGACTCGCCACGTACCCACTCTCAAGATGGCGTCTCCCGCAAAGCCACGCGCCAGCTGACTGGCTC
AGACGCCGTCACGTGATCCCATTTTCTCCCCCTCCCCCGACTACACAAGCCGTTTCCGCCTTCGGCCTTGAGGAATAACCGCCTCCCCCA
ATAGGCGCCTGCGATTTCTCTGGGTCCCGCCCCCGGGCGGCCTTCTGGCCAGTGGGAGGTGCTGGCGGGGGCCCGCGGGGCTCTCCCCGC
CCCCTGGCTGCAGCGGGAGCCAATGGGCAGCGCGCGCGGGGGACGTGTGCGGGCGTCTCCGCCATTTTGTGAGTCTATAACTCGGAGCCG
TTGGGTCGGTTCCTGCTATTCCGGCGCCTCCACTCCGTCCCCCGCGGGTCTGCTCTGTGTGCCATGGACGGCATTGTCCCAGATATAGCC
GTTGGTACAAAGGTGCAAGTGCTGGGCAGTCAGGACGGTGCCTAAGTGGACCTCAGACATGGCTCAGCCATAGGACCTGCCACACAAGCA

>69836_69836_3_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000356948_SCGB1C1_chr11_194418_ENST00000342878_length(amino acids)=109AA_BP=
MYQRLYLGQCRPWHTEQTRGGRSGGAGIAGTDPTAPSYRLTKWRRRPHTSPARAAHWLPLQPGGGESPAGPRQHLPLARRPPGGGTQRNR

--------------------------------------------------------------
>69836_69836_4_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000394601_SCGB1C1_chr11_194418_ENST00000342878_length(transcript)=241nt_BP=85nt
ATTCCGGCGCCTCCACTCCGTCCCCCGCGGGTCTGCTCTGTGTGCCATGGACGGCATTGTCCCAGATATAGCCGTTGGTACAAAGGTGCA
AGTGCTGGGCAGTCAGGACGGTGCCTAAGTGGACCTCAGACATGGCTCAGCCATAGGACCTGCCACACAAGCAGCCGTGGACACAACGCC

>69836_69836_4_PTBP1-SCGB1C1_PTBP1_chr19_799443_ENST00000394601_SCGB1C1_chr11_194418_ENST00000342878_length(amino acids)=44AA_BP=0

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

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Fusion Gene PPI Analysis for PTBP1-SCGB1C1

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 PTBP1-SCGB1C1

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 PTBP1-SCGB1C1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source