UTHEALTH HOME ABOUT SBMI A-Z WEBMAIL INSIDE THE UNIVERSITY

Home

Download

Statistics

Examples

Help

Contact

level2

	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:PCID2-SNRPA

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PCID2-SNRPA
	FusionPDB ID: 63314
	FusionGDB2.0 ID: 63314
		Hgene	Tgene
	Gene symbol	PCID2	SNRPA
	Gene ID	55795	6626
	Gene name	PCI domain containing 2	small nuclear ribonucleoprotein polypeptide A
	Synonyms	F10	Mud1\|U1-A\|U1A
	Cytomap	13q34	19q13.2
	Type of gene	protein-coding	protein-coding
	Description	PCI domain-containing protein 2CSN12-like protein	U1 small nuclear ribonucleoprotein AU1 small nuclear RNP-specific AU1 snRNP AU1 snRNP-specific protein A
	Modification date	20200313	20200327
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000246505, ENST00000337344, ENST00000375477, ENST00000375479, ENST00000375457, ENST00000375459, ENST00000493650,	ENST00000599570, ENST00000243563,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 7 X 4=196	3 X 4 X 2=24
	# samples	6	4
	** MAII score	log2(6/196*10)=-1.70781924850669 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/24*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PCID2 [Title/Abstract] AND SNRPA [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PCID2(113862913)-SNRPA(41265336), # samples:3
Anticipated loss of major functional domain due to fusion event.	PCID2-SNRPA 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. PCID2-SNRPA 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. PCID2-SNRPA 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. PCID2-SNRPA 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

Fusion gene breakpoints across PCID2 (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 SNRPA (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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	LGG	TCGA-E1-A7Z2-01A	PCID2	chr13	113862913	-	SNRPA	chr19	41265336	+
ChimerDB4	LGG	TCGA-E1-A7Z2	PCID2	chr13	113862912	-	SNRPA	chr19	41265335	+
ChimerDB4	LGG	TCGA-E1-A7Z2	PCID2	chr13	113862913	-	SNRPA	chr19	41265336	+

Top

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)
ENST00000337344	PCID2	chr13	113862913	-	ENST00000243563	SNRPA	chr19	41265336	+	938	113	874	137	245
ENST00000375477	PCID2	chr13	113862913	-	ENST00000243563	SNRPA	chr19	41265336	+	893	68	829	92	245
ENST00000375479	PCID2	chr13	113862913	-	ENST00000243563	SNRPA	chr19	41265336	+	942	117	878	141	245
ENST00000246505	PCID2	chr13	113862913	-	ENST00000243563	SNRPA	chr19	41265336	+	896	71	832	95	245
ENST00000337344	PCID2	chr13	113862912	-	ENST00000243563	SNRPA	chr19	41265335	+	938	113	874	137	245
ENST00000375477	PCID2	chr13	113862912	-	ENST00000243563	SNRPA	chr19	41265335	+	893	68	829	92	245
ENST00000375479	PCID2	chr13	113862912	-	ENST00000243563	SNRPA	chr19	41265335	+	942	117	878	141	245
ENST00000246505	PCID2	chr13	113862912	-	ENST00000243563	SNRPA	chr19	41265335	+	896	71	832	95	245

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
ENST00000337344	ENST00000243563	PCID2	chr13	113862913	-	SNRPA	chr19	41265336	+	0.002752372	0.99724764
ENST00000375477	ENST00000243563	PCID2	chr13	113862913	-	SNRPA	chr19	41265336	+	0.002341439	0.9976585
ENST00000375479	ENST00000243563	PCID2	chr13	113862913	-	SNRPA	chr19	41265336	+	0.002790515	0.9972095
ENST00000246505	ENST00000243563	PCID2	chr13	113862913	-	SNRPA	chr19	41265336	+	0.002064665	0.9979354
ENST00000337344	ENST00000243563	PCID2	chr13	113862912	-	SNRPA	chr19	41265335	+	0.002752372	0.99724764
ENST00000375477	ENST00000243563	PCID2	chr13	113862912	-	SNRPA	chr19	41265335	+	0.002341439	0.9976585
ENST00000375479	ENST00000243563	PCID2	chr13	113862912	-	SNRPA	chr19	41265335	+	0.002790515	0.9972095
ENST00000246505	ENST00000243563	PCID2	chr13	113862912	-	SNRPA	chr19	41265335	+	0.002064665	0.9979354

Top

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

>63314_63314_1_PCID2-SNRPA_PCID2_chr13_113862912_ENST00000246505_SNRPA_chr19_41265335_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

>63314_63314_2_PCID2-SNRPA_PCID2_chr13_113862912_ENST00000337344_SNRPA_chr19_41265335_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

>63314_63314_3_PCID2-SNRPA_PCID2_chr13_113862912_ENST00000375477_SNRPA_chr19_41265335_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

>63314_63314_4_PCID2-SNRPA_PCID2_chr13_113862912_ENST00000375479_SNRPA_chr19_41265335_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

>63314_63314_5_PCID2-SNRPA_PCID2_chr13_113862913_ENST00000246505_SNRPA_chr19_41265336_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

>63314_63314_6_PCID2-SNRPA_PCID2_chr13_113862913_ENST00000337344_SNRPA_chr19_41265336_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

>63314_63314_7_PCID2-SNRPA_PCID2_chr13_113862913_ENST00000375477_SNRPA_chr19_41265336_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

>63314_63314_8_PCID2-SNRPA_PCID2_chr13_113862913_ENST00000375479_SNRPA_chr19_41265336_ENST00000243563_length(amino acids)=245AA_BP=
MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG
DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH

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

Top

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/chr13:113862913/chr19:41265336)
- 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: 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: 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.

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

Tgene

SNRPA

chr13:113862912

chr19:41265335

ENST00000243563

140_206

82.0

283.0

Compositional bias

Note=Pro-rich

Tgene

SNRPA

chr13:113862913

chr19:41265336

ENST00000243563

140_206

82.0

283.0

Compositional bias

Note=Pro-rich

Tgene

SNRPA

chr13:113862912

chr19:41265335

ENST00000243563

208_282

82.0

283.0

Domain

RRM 2

Tgene

SNRPA

chr13:113862913

chr19:41265336

ENST00000243563

208_282

82.0

283.0

Domain

RRM 2

- 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

PCID2

chr13:113862912

chr19:41265335

ENST00000246505

210_391

12.0

560.0

Domain

PCI

Hgene

PCID2

chr13:113862912

chr19:41265335

ENST00000337344

210_391

12.0

400.0

Domain

PCI

Hgene

PCID2

chr13:113862912

chr19:41265335

ENST00000375457

210_391

398.0

Domain

PCI

Hgene

PCID2

chr13:113862912

chr19:41265335

ENST00000375459

210_391

510.6666666666667

Domain

PCI

Hgene

PCID2

chr13:113862912

chr19:41265335

ENST00000375477

210_391

12.0

518.0

Domain

PCI

Hgene

PCID2

chr13:113862912

chr19:41265335

ENST00000375479

210_391

12.0

491.0

Domain

PCI

Hgene

PCID2

chr13:113862913

chr19:41265336

ENST00000246505

210_391

12.0

560.0

Domain

PCI

Hgene

PCID2

chr13:113862913

chr19:41265336

ENST00000337344

210_391

12.0

400.0

Domain

PCI

Hgene

PCID2

chr13:113862913

chr19:41265336

ENST00000375457

210_391

398.0

Domain

PCI

Hgene

PCID2

chr13:113862913

chr19:41265336

ENST00000375459

210_391

510.6666666666667

Domain

PCI

Hgene

PCID2

chr13:113862913

chr19:41265336

ENST00000375477

210_391

12.0

518.0

Domain

PCI

Hgene

PCID2

chr13:113862913

chr19:41265336

ENST00000375479

210_391

12.0

491.0

Domain

PCI

Tgene

SNRPA

chr13:113862912

chr19:41265335

ENST00000243563

10_89

82.0

283.0

Domain

RRM 1

Tgene

SNRPA

chr13:113862913

chr19:41265336

ENST00000243563

10_89

82.0

283.0

Domain

RRM 1

Top

Fusion Protein Structures

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)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>399_PCID2_113862913_SNRPA_41265336_ranked_0.pdb	PCID2	113862912	113862913	ENST00000243563	SNRPA	chr19	41265336	+	MGTDSGYNAVWRPLTHTRLQEGPQGGTYLQGAEPRGKGVAPEQGKGQAWGEKVLLLGKGDLHGVVLRDLKALQGIASCPCLYLIVKLHEG DVMPPGYQTDLLEARELIEKHGQHELVGLLWQVGEEQDVIRWILRKRLGRGHLSWHKLLRGHGPWWDLARCKAWRGDHTRGRHVGRLARH	245

Top

pLDDT score distribution

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.

PCID2_pLDDT.png

SNRPA_pLDDT.png

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

Top

Ramachandran Plot of Fusion Protein Structure

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

Top

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
PCID2
SNRPA

- 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

Top

Related Drugs to PCID2-SNRPA

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to PCID2-SNRPA

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