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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:PABPC1-GRSF1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PABPC1-GRSF1
	FusionPDB ID: 62187
	FusionGDB2.0 ID: 62187
		Hgene	Tgene
	Gene symbol	PABPC1	GRSF1
	Gene ID	26986	2926
	Gene name	poly(A) binding protein cytoplasmic 1	G-rich RNA sequence binding factor 1
	Synonyms	PAB1\|PABP\|PABP1\|PABPC2\|PABPL1	-
	Cytomap	8q22.3	4q13.3
	Type of gene	protein-coding	protein-coding
	Description	polyadenylate-binding protein 1poly(A) binding protein, cytoplasmic 2	G-rich sequence factor 1
	Modification date	20200313	20200313
	UniProtAcc	.	Q12849
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000318607, ENST00000519004, ENST00000522387, ENST00000519596,	ENST00000508091, ENST00000254799, ENST00000439371, ENST00000502323, ENST00000545193,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	31 X 28 X 11=9548	11 X 10 X 4=440
	# samples	37	11
	** MAII score	log2(37/9548*10)=-4.68960139056546 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(11/440*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PABPC1 [Title/Abstract] AND GRSF1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PABPC1(101730000)-GRSF1(71691148), # samples:1
Anticipated loss of major functional domain due to fusion event.	PABPC1-GRSF1 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. PABPC1-GRSF1 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. PABPC1-GRSF1 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. PABPC1-GRSF1 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.

* 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	PABPC1	GO:2000623	negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	18447585
Tgene	GRSF1	GO:0000962	positive regulation of mitochondrial RNA catabolic process	29967381

Fusion gene breakpoints across PABPC1 (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 GRSF1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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	STAD	TCGA-SW-A7EA	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)
ENST00000318607	PABPC1	chr8	101730000	-	ENST00000254799	GRSF1	chr4	71691148	-	6923	1632	1129	1794	221
ENST00000318607	PABPC1	chr8	101730000	-	ENST00000439371	GRSF1	chr4	71691148	-	6918	1632	1129	1794	221
ENST00000318607	PABPC1	chr8	101730000	-	ENST00000502323	GRSF1	chr4	71691148	-	2393	1632	1129	1794	221
ENST00000318607	PABPC1	chr8	101730000	-	ENST00000545193	GRSF1	chr4	71691148	-	2330	1632	1129	1794	221
ENST00000519004	PABPC1	chr8	101730000	-	ENST00000254799	GRSF1	chr4	71691148	-	6022	731	363	893	176
ENST00000519004	PABPC1	chr8	101730000	-	ENST00000439371	GRSF1	chr4	71691148	-	6017	731	363	893	176
ENST00000519004	PABPC1	chr8	101730000	-	ENST00000502323	GRSF1	chr4	71691148	-	1492	731	363	893	176
ENST00000519004	PABPC1	chr8	101730000	-	ENST00000545193	GRSF1	chr4	71691148	-	1429	731	363	893	176
ENST00000522387	PABPC1	chr8	101730000	-	ENST00000254799	GRSF1	chr4	71691148	-	6014	723	316	885	189
ENST00000522387	PABPC1	chr8	101730000	-	ENST00000439371	GRSF1	chr4	71691148	-	6009	723	316	885	189
ENST00000522387	PABPC1	chr8	101730000	-	ENST00000502323	GRSF1	chr4	71691148	-	1484	723	316	885	189
ENST00000522387	PABPC1	chr8	101730000	-	ENST00000545193	GRSF1	chr4	71691148	-	1421	723	316	885	189

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
ENST00000318607	ENST00000254799	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.000470586	0.9995295
ENST00000318607	ENST00000439371	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.000456025	0.99954396
ENST00000318607	ENST00000502323	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.002395175	0.99760485
ENST00000318607	ENST00000545193	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.002723405	0.9972766
ENST00000519004	ENST00000254799	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.004750941	0.99524903
ENST00000519004	ENST00000439371	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.004517912	0.9954821
ENST00000519004	ENST00000502323	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.007146679	0.99285334
ENST00000519004	ENST00000545193	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.007937769	0.9920622
ENST00000522387	ENST00000254799	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.000636421	0.9993636
ENST00000522387	ENST00000439371	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.000605067	0.9993949
ENST00000522387	ENST00000502323	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.001798164	0.99820185
ENST00000522387	ENST00000545193	PABPC1	chr8	101730000	-	GRSF1	chr4	71691148	-	0.002385687	0.9976144

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Fusion Amino Acid Sequences

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

>62187_62187_1_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000318607_GRSF1_chr4_71691148_ENST00000254799_length(amino acids)=221AA_BP=168
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPW

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

>62187_62187_2_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000318607_GRSF1_chr4_71691148_ENST00000439371_length(amino acids)=221AA_BP=168
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPW

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

>62187_62187_3_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000318607_GRSF1_chr4_71691148_ENST00000502323_length(amino acids)=221AA_BP=168
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPW

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

>62187_62187_4_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000318607_GRSF1_chr4_71691148_ENST00000545193_length(amino acids)=221AA_BP=168
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPW

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

>62187_62187_5_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000519004_GRSF1_chr4_71691148_ENST00000254799_length(amino acids)=176AA_BP=123
MITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN

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

>62187_62187_6_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000519004_GRSF1_chr4_71691148_ENST00000439371_length(amino acids)=176AA_BP=123
MITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN

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

>62187_62187_7_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000519004_GRSF1_chr4_71691148_ENST00000502323_length(amino acids)=176AA_BP=123
MITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN

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

>62187_62187_8_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000519004_GRSF1_chr4_71691148_ENST00000545193_length(amino acids)=176AA_BP=123
MITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN

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

>62187_62187_9_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000522387_GRSF1_chr4_71691148_ENST00000254799_length(amino acids)=189AA_BP=136
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPWNTAPVGRPLEKLMCTLRPMRMLLQRCSRIGPT

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

>62187_62187_10_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000522387_GRSF1_chr4_71691148_ENST00000439371_length(amino acids)=189AA_BP=136
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPWNTAPVGRPLEKLMCTLRPMRMLLQRCSRIGPT

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

>62187_62187_11_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000522387_GRSF1_chr4_71691148_ENST00000502323_length(amino acids)=189AA_BP=136
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPWNTAPVGRPLEKLMCTLRPMRMLLQRCSRIGPT

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

>62187_62187_12_PABPC1-GRSF1_PABPC1_chr8_101730000_ENST00000522387_GRSF1_chr4_71691148_ENST00000545193_length(amino acids)=189AA_BP=136
MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD
PSLRKSGVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFLLHSSLLESPWNTAPVGRPLEKLMCTLRPMRMLLQRCSRIGPT

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:101730000/chr4:71691148)
- 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
.	GRSF1 Q12849
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: Regulator of post-transcriptional mitochondrial gene expression, required for assembly of the mitochondrial ribosome and for recruitment of mRNA and lncRNA. Binds RNAs containing the 14 base G-rich element. Preferentially binds RNAs transcribed from three contiguous genes on the light strand of mtDNA, the ND6 mRNA, and the long non-coding RNAs for MT-CYB and MT-ND5, each of which contains multiple consensus binding sequences (PubMed:23473033, PubMed:23473034, PubMed:29967381). Involved in the degradosome-mediated decay of non-coding mitochondrial transcripts (MT-ncRNA) and tRNA-like molecules (PubMed:29967381). Acts by unwinding G-quadruplex RNA structures in MT-ncRNA, thus facilitating their degradation by the degradosome (PubMed:29967381). G-quadruplexes (G4) are non-canonical 4 stranded structures formed by transcripts from the light strand of mtDNA (PubMed:29967381). {ECO:0000269\|PubMed:23473033, ECO:0000269\|PubMed:23473034, ECO:0000269\|PubMed:29967381}.

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.

- 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

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

11_89

167.66666666666666

311.0

Domain

RRM 1

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000439371

401_480

257.0

1891.3333333333333

Domain

RRM 3

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000502323

401_480

257.0

430.6666666666667

Domain

RRM 3

- 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

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

495_501

167.66666666666666

311.0

Compositional bias

Note=Poly-Ala

Hgene

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

191_268

167.66666666666666

311.0

Domain

RRM 3

Hgene

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

294_370

167.66666666666666

311.0

Domain

RRM 4

Hgene

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

542_619

167.66666666666666

311.0

Domain

PABC

Hgene

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

99_175

167.66666666666666

311.0

Domain

RRM 2

Hgene

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

166_289

167.66666666666666

311.0

Region

Note=CSDE1-binding

Hgene

PABPC1

chr8:101730000

chr4:71691148

ENST00000318607

541_636

167.66666666666666

311.0

Region

(Microbial infection) Binding to HRSV M2-1 protein

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000254799

55_111

419.0

1988.6666666666667

Compositional bias

Note=Ala-rich

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000439371

55_111

257.0

1891.3333333333333

Compositional bias

Note=Ala-rich

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000502323

55_111

257.0

430.6666666666667

Compositional bias

Note=Ala-rich

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000254799

122_246

419.0

1988.6666666666667

Domain

RRM 1

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000254799

250_326

419.0

1988.6666666666667

Domain

RRM 2

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000254799

401_480

419.0

1988.6666666666667

Domain

RRM 3

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000439371

122_246

257.0

1891.3333333333333

Domain

RRM 1

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000439371

250_326

257.0

1891.3333333333333

Domain

RRM 2

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000502323

122_246

257.0

430.6666666666667

Domain

RRM 1

Tgene

GRSF1

chr8:101730000

chr4:71691148

ENST00000502323

250_326

257.0

430.6666666666667

Domain

RRM 2

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Fusion Protein-Protein Interaction

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 from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
PABPC1
GRSF1

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to PABPC1-GRSF1

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to PABPC1-GRSF1

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source