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	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:PAPD7-RAF1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PAPD7-RAF1
	FusionPDB ID: 62587
	FusionGDB2.0 ID: 62587
		Hgene	Tgene
	Gene symbol	PAPD7	RAF1
	Gene ID	11044	6037
	Gene name	terminal nucleotidyltransferase 4A	ribonuclease A family member 3
	Synonyms	LAK-1\|LAK1\|PAPD7\|POLK\|POLS\|TRF4\|TRF4-1\|TRF41\|TUTASE5	ECP\|RAF1\|RNS3
	Cytomap	5p15.31	14q11.2
	Type of gene	protein-coding	protein-coding
	Description	terminal nucleotidyltransferase 4ADNA polymerase kappaDNA polymerase sigmaPAP-associated domain-containing protein 7TRAMP-like complex polyadenylate polymerasenon-canonical poly(A) RNA polymerase PAPD7poly(A) RNA polymerase D7, non-canonicalpolymer	eosinophil cationic proteinRNase 3cytotoxic ribonucleaseribonuclease 3ribonuclease, RNase A family, 3
	Modification date	20200313	20200313
	UniProtAcc	.	P04049
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000230859,	ENST00000251849, ENST00000442415, ENST00000534997, ENST00000542177,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 9 X 7=504	19 X 16 X 7=2128
	# samples	10	18
	** MAII score	log2(10/504*10)=-2.33342373372519 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(18/2128*10)=-3.56342933917152 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PAPD7 [Title/Abstract] AND RAF1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PAPD7(6751310)-RAF1(12641307), # samples:3
Anticipated loss of major functional domain due to fusion event.	PAPD7-RAF1 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. PAPD7-RAF1 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. PAPD7-RAF1 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. PAPD7-RAF1 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	PAPD7	GO:0042493	response to drug	10066793
Tgene	RAF1	GO:0002227	innate immune response in mucosa	12860195
Tgene	RAF1	GO:0019731	antibacterial humoral response	12860195
Tgene	RAF1	GO:0043152	induction of bacterial agglutination	23992292
Tgene	RAF1	GO:0045087	innate immune response	23992292
Tgene	RAF1	GO:0050829	defense response to Gram-negative bacterium	23992292
Tgene	RAF1	GO:0050830	defense response to Gram-positive bacterium	12860195\|23992292
Tgene	RAF1	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	12860195

Fusion gene breakpoints across PAPD7 (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 RAF1 (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	PRAD	TCGA-HC-8256-01A	PAPD7	chr5	6751310	-	RAF1	chr3	12641307	-
ChimerDB4	PRAD	TCGA-HC-8256-01A	PAPD7	chr5	6751310	+	RAF1	chr3	12641307	-
ChimerDB4	PRAD	TCGA-HC-8256	PAPD7	chr5	6751310	+	RAF1	chr3	12641307	-

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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)
ENST00000230859	PAPD7	chr5	6751310	+	ENST00000251849	RAF1	chr3	12641307	-	3268	1398	129	2354	741
ENST00000230859	PAPD7	chr5	6751310	+	ENST00000442415	RAF1	chr3	12641307	-	3071	1398	129	2354	741
ENST00000230859	PAPD7	chr5	6751310	+	ENST00000534997	RAF1	chr3	12641307	-	2602	1398	129	2354	741
ENST00000230859	PAPD7	chr5	6751310	+	ENST00000542177	RAF1	chr3	12641307	-	2536	1398	129	2354	741

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
ENST00000230859	ENST00000251849	PAPD7	chr5	6751310	+	RAF1	chr3	12641307	-	0.004169403	0.9958306
ENST00000230859	ENST00000442415	PAPD7	chr5	6751310	+	RAF1	chr3	12641307	-	0.006545413	0.9934546
ENST00000230859	ENST00000534997	PAPD7	chr5	6751310	+	RAF1	chr3	12641307	-	0.006169954	0.99383
ENST00000230859	ENST00000542177	PAPD7	chr5	6751310	+	RAF1	chr3	12641307	-	0.006235265	0.99376476

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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

>62587_62587_1_PAPD7-RAF1_PAPD7_chr5_6751310_ENST00000230859_RAF1_chr3_12641307_ENST00000251849_length(amino acids)=741AA_BP=422
MSPCPEEAAMRREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPII
KLTDQETEVKVDISFNMETGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQLHPRIDARRADENLG
MLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPSMLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLAR
SYPNRDAESTLGRIIKVTQEVIDYRRWIKEKWGSKAHPSPGMDSRIKIKERIATCNGEQTQNREPESPYGQRLTLSLSSPQLLSSGSSAS
SVSSLSGSDVDSDTPPCTTPSVYQFSLQAPAPLMAGLPTALPMPSGKPQPTTSRTLIMTTNNQRPRGQRDSSYYWEIEASEVMLSTRIGS
GSFGTVYKGKWHGDVAVKILKVVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLID
IARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMAPEVIRMQDNNPFSFQSDVYSYGIV
LYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHR

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

>62587_62587_2_PAPD7-RAF1_PAPD7_chr5_6751310_ENST00000230859_RAF1_chr3_12641307_ENST00000442415_length(amino acids)=741AA_BP=422
MSPCPEEAAMRREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPII
KLTDQETEVKVDISFNMETGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQLHPRIDARRADENLG
MLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPSMLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLAR
SYPNRDAESTLGRIIKVTQEVIDYRRWIKEKWGSKAHPSPGMDSRIKIKERIATCNGEQTQNREPESPYGQRLTLSLSSPQLLSSGSSAS
SVSSLSGSDVDSDTPPCTTPSVYQFSLQAPAPLMAGLPTALPMPSGKPQPTTSRTLIMTTNNQRPRGQRDSSYYWEIEASEVMLSTRIGS
GSFGTVYKGKWHGDVAVKILKVVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLID
IARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMAPEVIRMQDNNPFSFQSDVYSYGIV
LYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHR

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

>62587_62587_3_PAPD7-RAF1_PAPD7_chr5_6751310_ENST00000230859_RAF1_chr3_12641307_ENST00000534997_length(amino acids)=741AA_BP=422
MSPCPEEAAMRREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPII
KLTDQETEVKVDISFNMETGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQLHPRIDARRADENLG
MLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPSMLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLAR
SYPNRDAESTLGRIIKVTQEVIDYRRWIKEKWGSKAHPSPGMDSRIKIKERIATCNGEQTQNREPESPYGQRLTLSLSSPQLLSSGSSAS
SVSSLSGSDVDSDTPPCTTPSVYQFSLQAPAPLMAGLPTALPMPSGKPQPTTSRTLIMTTNNQRPRGQRDSSYYWEIEASEVMLSTRIGS
GSFGTVYKGKWHGDVAVKILKVVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLID
IARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMAPEVIRMQDNNPFSFQSDVYSYGIV
LYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHR

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

>62587_62587_4_PAPD7-RAF1_PAPD7_chr5_6751310_ENST00000230859_RAF1_chr3_12641307_ENST00000542177_length(amino acids)=741AA_BP=422
MSPCPEEAAMRREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPII
KLTDQETEVKVDISFNMETGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQLHPRIDARRADENLG
MLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPSMLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLAR
SYPNRDAESTLGRIIKVTQEVIDYRRWIKEKWGSKAHPSPGMDSRIKIKERIATCNGEQTQNREPESPYGQRLTLSLSSPQLLSSGSSAS
SVSSLSGSDVDSDTPPCTTPSVYQFSLQAPAPLMAGLPTALPMPSGKPQPTTSRTLIMTTNNQRPRGQRDSSYYWEIEASEVMLSTRIGS
GSFGTVYKGKWHGDVAVKILKVVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLID
IARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMAPEVIRMQDNNPFSFQSDVYSYGIV
LYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHR

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

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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/chr5:6751310/chr3:12641307)
- 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
.	RAF1 P04049
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: Serine/threonine-protein kinase that acts as a regulatory link between the membrane-associated Ras GTPases and the MAPK/ERK cascade, and this critical regulatory link functions as a switch determining cell fate decisions including proliferation, differentiation, apoptosis, survival and oncogenic transformation. RAF1 activation initiates a mitogen-activated protein kinase (MAPK) cascade that comprises a sequential phosphorylation of the dual-specific MAPK kinases (MAP2K1/MEK1 and MAP2K2/MEK2) and the extracellular signal-regulated kinases (MAPK3/ERK1 and MAPK1/ERK2). The phosphorylated form of RAF1 (on residues Ser-338 and Ser-339, by PAK1) phosphorylates BAD/Bcl2-antagonist of cell death at 'Ser-75'. Phosphorylates adenylyl cyclases: ADCY2, ADCY5 and ADCY6, resulting in their activation. Phosphorylates PPP1R12A resulting in inhibition of the phosphatase activity. Phosphorylates TNNT2/cardiac muscle troponin T. Can promote NF-kB activation and inhibit signal transducers involved in motility (ROCK2), apoptosis (MAP3K5/ASK1 and STK3/MST2), proliferation and angiogenesis (RB1). Can protect cells from apoptosis also by translocating to the mitochondria where it binds BCL2 and displaces BAD/Bcl2-antagonist of cell death. Regulates Rho signaling and migration, and is required for normal wound healing. Plays a role in the oncogenic transformation of epithelial cells via repression of the TJ protein, occludin (OCLN) by inducing the up-regulation of a transcriptional repressor SNAI2/SLUG, which induces down-regulation of OCLN. Restricts caspase activation in response to selected stimuli, notably Fas stimulation, pathogen-mediated macrophage apoptosis, and erythroid differentiation. {ECO:0000269\|PubMed:11427728, ECO:0000269\|PubMed:11719507, ECO:0000269\|PubMed:15385642, ECO:0000269\|PubMed:15618521, ECO:0000269\|PubMed:15849194, ECO:0000269\|PubMed:16892053, ECO:0000269\|PubMed:16924233, ECO:0000269\|PubMed:9360956}.

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

PAPD7

chr5:6751310

chr3:12641307

ENST00000230859

27_79

423.0

543.0

Compositional bias

Note=Ala-rich

Hgene

PAPD7

chr5:6751310

chr3:12641307

ENST00000230859

85_117

423.0

543.0

Compositional bias

Note=Ser-rich

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000251849

349_609

330.0

649.0

Domain

Protein kinase

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000442415

349_609

350.0

669.0

Domain

Protein kinase

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000251849

355_363

330.0

649.0

Nucleotide binding

ATP

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000442415

355_363

350.0

669.0

Nucleotide binding

ATP

- 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

PAPD7

chr5:6751310

chr3:12641307

ENST00000230859

576_602

423.0

543.0

Compositional bias

Note=Ser-rich

Hgene

PAPD7

chr5:6751310

chr3:12641307

ENST00000230859

408_468

423.0

543.0

Domain

Note=PAP-associated

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000251849

56_131

330.0

649.0

Domain

RBD

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000442415

56_131

350.0

669.0

Domain

RBD

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000251849

138_184

330.0

649.0

Zinc finger

Phorbol-ester/DAG-type

Tgene

RAF1

chr5:6751310

chr3:12641307

ENST00000442415

138_184

350.0

669.0

Zinc finger

Phorbol-ester/DAG-type

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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)

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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.

RAF1_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.

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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

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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

RAF1

YWHAQ, YWHAG, YWHAZ, Hras, SFN, HRAS, VDAC1, PEBP4, CNKSR1, RASD2, CNKSR2, ERAS, SPRY4, SPRY2, YWHAB, OIP5, PHKA2, CCT3, MYC, AR, MRAS, KRAS, LRPAP1, RRAS2, SHOC2, TSC22D3, STK26, MAPK1, MAPK3, PRKCE, BCL2, BCL2L1, PEBP1, MAP2K1, GRB10, NRAS, MAPK8IP3, AKT1, HSP90AA1, GNG4, GNB2, VAV1, RHEB, RAP1A, SRC, FYN, RB1, RBL2, PRKG1, JAK2, YWHAH, CFLAR, CDC25A, BRAF, MAP3K1, PDGFRB, MAP3K5, MAPK7, PHB, BAG1, PAK1, PRKCZ, RRAS, PRPF6, UBE2D2, YWHAE, NR3C1, LCK, LTK, JAK1, XIAP, BIRC2, BIRC3, STUB1, Arrb2, EEF1A1, HSP82, HSPA8, HSPA5, CALM1, SGK1, NEDD4, SCNN1B, NEDD4L, STK3, BRAP, WDR83, KSR1, LATS1, MAP2K2, Rfxank, RFXANK, PPP1CC, VCP, HSPD1, BAD, BCL6, BIRC7, PIN1, MMS19, PPP2R1A, PPP2R2B, PPP2CA, HSPA4, RAF1, PPP2CB, MAPK8, RBBP8, YY1, PKM, CDK20, HIPK4, TBXA2R, SH3KBP1, ILK, GPRASP2, CDC37, IRS4, FAM96B, HUWE1, Prkab1, RANBP9, TMEM70, PACSIN3, NPLOC4, PRKAR1A, DCAF8, PURA, FYCO1, MYBPC1, COPS7A, MOV10, NXF1, EGFR, CALU, CCT8, DNAJA1, EMD, TIMM50, LOX, ARRB2, AGTR1, CASZ1, MRC2, PDLIM2, HERC2, XPO1, ACOX1, PCDH7, MAD2L1, SYNPO, TMEM63B, EEF1E1, COPS5, SS18L2, Smn1, Cep152, Aldh4a1, Ksr1, NUP133, RPGRIP1L, NCAPG2, NUP107, MSH2, LAS1L, AMER1, NUP160, EIF3D, SPATA7, NPHP4, DYNLL2, DYNLL1, IQCB1, RMDN3, TRIM25, Mapkbp1, EGLN3, RIPK4, MAPK6, CSNK1A1, HERC1, LZTR1, QKI, COPS3, TRIM28, MAEA, NANOG, ITCH, IRF7, PSMB9, MAP2K5, CDK4, CDK6, CDKN2B, FGFR4, MAP2K3, NF2, PDGFRA, TEAD2, RASSF1, ABCB5, BECN1, CBLC, GLIS2, GRM1, HGF, MAP2K6, ARNT, CCND2, CD44, CDKN2A, CDKN2C, EPHA2, ERBB2, KEAP1, LATS2, MET, NF1, TERT, DUSP2, MBP, PAK2, PLEKHA4, CRBN, ARAF, SLC25A3, TUBB4B, TUBB, HSPA6, HSP90AB3P, HSP90AB1, HSPA1A, HSPB1, BAG2, CCT7, DSG1, CCT2, CCT4, CCT6A, TCP1, AKAP8L, ATAD3A, ABCD3, SLC25A22, TMEM33, TUBA4A, HPX, MGST1, TUBB4A, TMEM161A, HSP90AB2P, CCAR2, SLC25A10, FANCD2, TUBB6, HSD17B12, SLC25A11, SLC25A1, ARL1, DNAJA2, DPM1, CCT5, AIFM1, SQSTM1, TUBG2, TUBG1, STK39, GCN1L1, ABCF2, POLD1, NUBP2, TM9SF3, NCLN, SEC61A2, SEC61A1, ALDH1A3, TUBB3, POLR2B, IARS2, TMED1, CIT, AURKB, KIF20A, BRD1, TRIM66, HAX1, CUL4A, ACTR1A, AKAP1, FLOT1, LAMTOR1, LMAN1, RAB2A, RAB4A, STX7, NPAS1, OPALIN, METTL21B, SSSCA1, FAM174A, CRKL, DDB1, DICER1, LDHB, PIK3R1, NONO, DVL2,

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
PAPD7
RAF1

- 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
Tgene	RAF1	chr5:6751310	chr3:12641307	ENST00000442415		9	18	331_349	350.0	669.0	PEBP1/RKIP

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Related Drugs to PAPD7-RAF1

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 PAPD7-RAF1

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
Tgene	RAF1	C0028326	Noonan Syndrome	10	CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
Tgene	RAF1	C0175704	LEOPARD Syndrome	7	CLINGEN;CTD_human;GENOMICS_ENGLAND
Tgene	RAF1	C1969057	Noonan Syndrome 5	4	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	RAF1	C1969056	LEOPARD SYNDROME 2	3	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	RAF1	C0007194	Hypertrophic Cardiomyopathy	2	CTD_human
Tgene	RAF1	C0041409	Turner Syndrome, Male	2	CTD_human
Tgene	RAF1	C1519086	Pilomyxoid astrocytoma	2	ORPHANET
Tgene	RAF1	C1527404	Female Pseudo-Turner Syndrome	2	CTD_human
Tgene	RAF1	C4551472	Hypertrophic obstructive cardiomyopathy	2	CTD_human
Tgene	RAF1	C4551602	Noonan Syndrome 1	2	CTD_human
Tgene	RAF1	C0006142	Malignant neoplasm of breast	1	CTD_human
Tgene	RAF1	C0007131	Non-Small Cell Lung Carcinoma	1	CTD_human
Tgene	RAF1	C0007193	Cardiomyopathy, Dilated	1	CTD_human
Tgene	RAF1	C0017638	Glioma	1	CTD_human
Tgene	RAF1	C0020429	Hyperalgesia	1	CTD_human
Tgene	RAF1	C0022665	Kidney Neoplasm	1	CTD_human
Tgene	RAF1	C0023903	Liver neoplasms	1	CTD_human
Tgene	RAF1	C0024121	Lung Neoplasms	1	CTD_human
Tgene	RAF1	C0242379	Malignant neoplasm of lung	1	CTD_human
Tgene	RAF1	C0259783	mixed gliomas	1	CTD_human
Tgene	RAF1	C0340427	Familial dilated cardiomyopathy	1	ORPHANET
Tgene	RAF1	C0345904	Malignant neoplasm of liver	1	CTD_human
Tgene	RAF1	C0345967	Malignant mesothelioma	1	CTD_human
Tgene	RAF1	C0458247	Allodynia	1	CTD_human
Tgene	RAF1	C0555198	Malignant Glioma	1	CTD_human
Tgene	RAF1	C0587248	Costello syndrome (disorder)	1	CLINGEN
Tgene	RAF1	C0678222	Breast Carcinoma	1	CTD_human
Tgene	RAF1	C0740457	Malignant neoplasm of kidney	1	CTD_human
Tgene	RAF1	C0751211	Hyperalgesia, Primary	1	CTD_human
Tgene	RAF1	C0751212	Hyperalgesia, Secondary	1	CTD_human
Tgene	RAF1	C0751213	Tactile Allodynia	1	CTD_human
Tgene	RAF1	C0751214	Hyperalgesia, Thermal	1	CTD_human
Tgene	RAF1	C1257931	Mammary Neoplasms, Human	1	CTD_human
Tgene	RAF1	C1275081	Cardio-facio-cutaneous syndrome	1	CLINGEN
Tgene	RAF1	C1449563	Cardiomyopathy, Familial Idiopathic	1	CTD_human
Tgene	RAF1	C1458155	Mammary Neoplasms	1	CTD_human
Tgene	RAF1	C2936719	Mechanical Allodynia	1	CTD_human
Tgene	RAF1	C4014656	CARDIOMYOPATHY, DILATED, 1NN	1	CTD_human;UNIPROT
Tgene	RAF1	C4551484	Leopard Syndrome 1	1	CTD_human;GENOMICS_ENGLAND
Tgene	RAF1	C4704874	Mammary Carcinoma, Human	1	CTD_human
Tgene	RAF1	C4721610	Carcinoma, Ovarian Epithelial	1	CTD_human