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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:PDE4D-KHDRBS3

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PDE4D-KHDRBS3
	FusionPDB ID: 63743
	FusionGDB2.0 ID: 63743
		Hgene	Tgene
	Gene symbol	PDE4D	KHDRBS3
	Gene ID	5144	10656
	Gene name	phosphodiesterase 4D	KH RNA binding domain containing, signal transduction associated 3
	Synonyms	ACRDYS2\|DPDE3\|HSPDE4D\|PDE43\|PDE4DN2\|STRK1	Etle\|SALP\|SLM-2\|SLM2\|T-STAR\|TSTAR\|etoile
	Cytomap	5q11.2-q12.1	8q24.23
	Type of gene	protein-coding	protein-coding
	Description	cAMP-specific 3',5'-cyclic phosphodiesterase 4DcAMP-specific phosphodiesterase PDE4D6phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila)testicular tissue protein Li 136	KH domain-containing, RNA-binding, signal transduction-associated protein 3KH domain containing, RNA binding, signal transduction associated 3RNA-binding protein T-StarSam68-like phosphotyrosine protein, T-STARsam68-like mammalian protein 2
	Modification date	20200313	20200313
	UniProtAcc	.	O75525
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000340635, ENST00000360047, ENST00000405755, ENST00000502484, ENST00000502575, ENST00000503258, ENST00000507116, ENST00000546160, ENST00000503947, ENST00000317118, ENST00000358923,	ENST00000522578, ENST00000355849, ENST00000520981,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	40 X 32 X 12=15360	11 X 10 X 10=1100
	# samples	56	14
	** MAII score	log2(56/15360*10)=-4.77760757866355 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1100*10)=-2.97400479146706 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PDE4D [Title/Abstract] AND KHDRBS3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PDE4D(58476421)-KHDRBS3(136533480), # samples:3
Anticipated loss of major functional domain due to fusion event.	PDE4D-KHDRBS3 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. PDE4D-KHDRBS3 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. PDE4D-KHDRBS3 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. PDE4D-KHDRBS3 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. PDE4D-KHDRBS3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. PDE4D-KHDRBS3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target 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

Fusion gene breakpoints across PDE4D (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 KHDRBS3 (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	LUSC	TCGA-63-A5MY-01A	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+
ChimerDB4	LUSC	TCGA-63-A5MY	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+

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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)
ENST00000340635	PDE4D	chr5	58476421	-	ENST00000355849	KHDRBS3	chr8	136533480	+	2463	984	176	1936	586
ENST00000340635	PDE4D	chr5	58476421	-	ENST00000520981	KHDRBS3	chr8	136533480	+	1863	984	176	1336	386
ENST00000360047	PDE4D	chr5	58476421	-	ENST00000355849	KHDRBS3	chr8	136533480	+	2003	524	31	1476	481
ENST00000360047	PDE4D	chr5	58476421	-	ENST00000520981	KHDRBS3	chr8	136533480	+	1403	524	31	876	281
ENST00000507116	PDE4D	chr5	58476421	-	ENST00000355849	KHDRBS3	chr8	136533480	+	2231	752	7	1704	565
ENST00000507116	PDE4D	chr5	58476421	-	ENST00000520981	KHDRBS3	chr8	136533480	+	1631	752	7	1104	365
ENST00000546160	PDE4D	chr5	58476421	-	ENST00000355849	KHDRBS3	chr8	136533480	+	2104	625	0	1577	525
ENST00000546160	PDE4D	chr5	58476421	-	ENST00000520981	KHDRBS3	chr8	136533480	+	1504	625	0	977	325
ENST00000502575	PDE4D	chr5	58476421	-	ENST00000355849	KHDRBS3	chr8	136533480	+	2222	743	49	1695	548
ENST00000502575	PDE4D	chr5	58476421	-	ENST00000520981	KHDRBS3	chr8	136533480	+	1622	743	49	1095	348
ENST00000503258	PDE4D	chr5	58476421	-	ENST00000355849	KHDRBS3	chr8	136533480	+	2614	1135	717	2087	456
ENST00000503258	PDE4D	chr5	58476421	-	ENST00000520981	KHDRBS3	chr8	136533480	+	2014	1135	717	1487	256
ENST00000405755	PDE4D	chr5	58476421	-	ENST00000355849	KHDRBS3	chr8	136533480	+	2050	571	102	1523	473
ENST00000405755	PDE4D	chr5	58476421	-	ENST00000520981	KHDRBS3	chr8	136533480	+	1450	571	102	923	273

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
ENST00000340635	ENST00000355849	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.003212649	0.9967873
ENST00000340635	ENST00000520981	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.002309082	0.9976909
ENST00000360047	ENST00000355849	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000187144	0.9998129
ENST00000360047	ENST00000520981	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000244932	0.9997551
ENST00000507116	ENST00000355849	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000689682	0.9993104
ENST00000507116	ENST00000520981	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000277201	0.9997228
ENST00000546160	ENST00000355849	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000197702	0.9998023
ENST00000546160	ENST00000520981	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000114428	0.99988556
ENST00000502575	ENST00000355849	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000667263	0.9993327
ENST00000502575	ENST00000520981	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000251872	0.9997482
ENST00000503258	ENST00000355849	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000202823	0.99979717
ENST00000503258	ENST00000520981	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000700246	0.99929976
ENST00000405755	ENST00000355849	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000199718	0.99980026
ENST00000405755	ENST00000520981	PDE4D	chr5	58476421	-	KHDRBS3	chr8	136533480	+	0.000208955	0.9997911

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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

>63743_63743_1_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000340635_KHDRBS3_chr8_136533480_ENST00000355849_length(amino acids)=586AA_BP=74
MEAEGSSAPARAGSGEGSDSAGGATLKAPKHLWRHEQHHQYPLRQPQFRLLHPHHHLPPPPPPSPQPQPQCPLQPPPPPPLPPPPPPPGA
ARGRYASSGATGRVRHRGYSDTERYLYCRAMDRTSYAVETGHRPGLKKSRMSWPSSFQGLRRFDVDNGTSAGRSPLDPMTSPGSGLILQA
NFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITE
IEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKY
FHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPAPAITRGRGGVT
ARPVGVVVPRGTPTPRGVLSTRGPVSRGRGLLTPRARGVPPTGYRPPPPPPTQETYGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSGAD

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

>63743_63743_2_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000340635_KHDRBS3_chr8_136533480_ENST00000520981_length(amino acids)=386AA_BP=74
MEAEGSSAPARAGSGEGSDSAGGATLKAPKHLWRHEQHHQYPLRQPQFRLLHPHHHLPPPPPPSPQPQPQCPLQPPPPPPLPPPPPPPGA
ARGRYASSGATGRVRHRGYSDTERYLYCRAMDRTSYAVETGHRPGLKKSRMSWPSSFQGLRRFDVDNGTSAGRSPLDPMTSPGSGLILQA
NFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITE
IEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEE

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

>63743_63743_3_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000360047_KHDRBS3_chr8_136533480_ENST00000355849_length(amino acids)=481AA_BP=163
MLKQESWNSSVKITTCNVGDKKNINDRRSANMMHVNNFPFRRHSWICFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRS
DSDYDLSPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKY
IDVVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFA
PPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPAPAITRGRGGVTARPVGVVVPRGTPTP
RGVLSTRGPVSRGRGLLTPRARGVPPTGYRPPPPPPTQETYGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDS

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

>63743_63743_4_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000360047_KHDRBS3_chr8_136533480_ENST00000520981_length(amino acids)=281AA_BP=163
MLKQESWNSSVKITTCNVGDKKNINDRRSANMMHVNNFPFRRHSWICFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRS
DSDYDLSPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKY
IDVVINKNMKLGQKVLIPVKQFPKDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARTAK

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

>63743_63743_5_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000405755_KHDRBS3_chr8_136533480_ENST00000355849_length(amino acids)=473AA_BP=155
MGILASSLKMAFVWDPLGATVPGPSTRAKSRLRFSKSYSFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSP
KSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKN
MKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYAR
MGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPAPAITRGRGGVTARPVGVVVPRGTPTPRGVLSTRG
PVSRGRGLLTPRARGVPPTGYRPPPPPPTQETYGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTN

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

>63743_63743_6_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000405755_KHDRBS3_chr8_136533480_ENST00000520981_length(amino acids)=273AA_BP=155
MGILASSLKMAFVWDPLGATVPGPSTRAKSRLRFSKSYSFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSP
KSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKN
MKLGQKVLIPVKQFPKDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARTAKGVYRDQPY

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

>63743_63743_7_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000502575_KHDRBS3_chr8_136533480_ENST00000355849_length(amino acids)=548AA_BP=230
MDISGTVSEGTTLPWILASCTKLTRKMAQQTSPDTLTVPEVDNPHCPNPWLNEDLVKSLRENLLQHEKSKTARKSVSPKLSPVISPRNSP
RLLRRMLLSSNIPKQRRFTVAHTCFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHG
DDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFP
KFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPD
YNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPAPAITRGRGGVTARPVGVVVPRGTPTPRGVLSTRGPVSRGRGLLTPRARG
VPPTGYRPPPPPPTQETYGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARTAKGVY

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

>63743_63743_8_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000502575_KHDRBS3_chr8_136533480_ENST00000520981_length(amino acids)=348AA_BP=230
MDISGTVSEGTTLPWILASCTKLTRKMAQQTSPDTLTVPEVDNPHCPNPWLNEDLVKSLRENLLQHEKSKTARKSVSPKLSPVISPRNSP
RLLRRMLLSSNIPKQRRFTVAHTCFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHG
DDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFP

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

>63743_63743_9_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000503258_KHDRBS3_chr8_136533480_ENST00000355849_length(amino acids)=456AA_BP=138
MSIIMKPRSRSTSSLRTAEAVCFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHGDD
LIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKF
NFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN
DEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPAPAITRGRGGVTARPVGVVVPRGTPTPRGVLSTRGPVSRGRGLLTPRARGVP
PTGYRPPPPPPTQETYGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARTAKGVYRD

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

>63743_63743_10_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000503258_KHDRBS3_chr8_136533480_ENST00000520981_length(amino acids)=256AA_BP=138
MSIIMKPRSRSTSSLRTAEAVCFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHGDD
LIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKD

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

>63743_63743_11_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000507116_KHDRBS3_chr8_136533480_ENST00000355849_length(amino acids)=565AA_BP=247
MRQATECTNSSRLRPASLDISGTVSEGTTLPWILASCTKLTRKMAQQTSPDTLTVPEVDNPHCPNPWLNEDLVKSLRENLLQHEKSKTAR
KSVSPKLSPVISPRNSPRLLRRMLLSSNIPKQRRFTVAHTCFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDL
SPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVIN
KNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAY
ARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPAPAITRGRGGVTARPVGVVVPRGTPTPRGVLST
RGPVSRGRGLLTPRARGVPPTGYRPPPPPPTQETYGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEW

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

>63743_63743_12_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000507116_KHDRBS3_chr8_136533480_ENST00000520981_length(amino acids)=365AA_BP=247
MRQATECTNSSRLRPASLDISGTVSEGTTLPWILASCTKLTRKMAQQTSPDTLTVPEVDNPHCPNPWLNEDLVKSLRENLLQHEKSKTAR
KSVSPKLSPVISPRNSPRLLRRMLLSSNIPKQRRFTVAHTCFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDL
SPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVIN
KNMKLGQKVLIPVKQFPKDYDDGYGTAYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARTAKGVYRDQ

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

>63743_63743_13_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000546160_KHDRBS3_chr8_136533480_ENST00000355849_length(amino acids)=525AA_BP=207
MKRNTCDLLSRSKSASEETLHSSNEEEDPFRGMEPYLVRRLSCRNIQLPPLAFRQLEQADLKSESENIQRPTSLPLKILPLIAITSAESS
GFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFA
ALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEET
LTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENA
DVPVVRGKPTLRTRGVPAPAITRGRGGVTARPVGVVVPRGTPTPRGVLSTRGPVSRGRGLLTPRARGVPPTGYRPPPPPPTQETYGEYDY

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

>63743_63743_14_PDE4D-KHDRBS3_PDE4D_chr5_58476421_ENST00000546160_KHDRBS3_chr8_136533480_ENST00000520981_length(amino acids)=325AA_BP=207
MKRNTCDLLSRSKSASEETLHSSNEEEDPFRGMEPYLVRRLSCRNIQLPPLAFRQLEQADLKSESENIQRPTSLPLKILPLIAITSAESS
GFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFA
ALTNLQDRAPSKRSPMCNQPSINKATITEIEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKDYDDGYGTAYDEQSYDSYDNSY

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

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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/chr5:58476421/chr8:136533480)
- 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
.	KHDRBS3 O75525
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: RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Binds preferentially to the 5'-[AU]UAAA-3' motif in vitro. Binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. Binds poly(A). RNA-binding abilities are down-regulated by tyrosine kinase PTK6 (PubMed:10564820, PubMed:19561594, PubMed:26758068). Involved in splice site selection of vascular endothelial growth factor (PubMed:15901763). In vitro regulates CD44 alternative splicing by direct binding to purine-rich exonic enhancer (By similarity). Can regulate alternative splicing of neurexins NRXN1-3 in the laminin G-like domain 6 containing the evolutionary conserved neurexin alternative spliced segment 4 (AS4) involved in neurexin selective targeting to postsynaptic partners such as neuroligins and LRRTM family members (PubMed:26758068). Targeted, cell-type specific splicing regulation of NRXN1 at AS4 is involved in neuronal glutamatergic synapse function and plasticity (By similarity). May regulate expression of KHDRBS2/SLIM-1 in defined brain neuron populations by modifying its alternative splicing (By similarity). Can bind FABP9 mRNA (By similarity). May play a role as a negative regulator of cell growth. Inhibits cell proliferation. {ECO:0000250\|UniProtKB:Q9JLP1, ECO:0000250\|UniProtKB:Q9R226, ECO:0000269\|PubMed:10564820, ECO:0000269\|PubMed:15901763, ECO:0000269\|PubMed:19561594, ECO:0000269\|PubMed:26758068}.; FUNCTION: (Microbial infection) Involved in post-transcriptional regulation of HIV-1 gene expression. {ECO:0000269\|PubMed:11741900}.

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

PDE4D

chr5:58476421

chr8:136533480

ENST00000340635

42_88

269.3333333333333

810.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000360047

42_88

133.33333333333334

674.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000405755

42_88

147.33333333333334

688.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000502484

42_88

208.33333333333334

749.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000502575

42_88

205.33333333333334

220.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000503258

42_88

139.33333333333334

680.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000507116

42_88

205.33333333333334

746.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000546160

42_88

208.33333333333334

749.0

Compositional bias

Note=Pro-rich

Tgene

KHDRBS3

chr5:58476421

chr8:136533480

ENST00000355849

250_261

29.333333333333332

347.0

Compositional bias

Note=Pro-rich

Tgene

KHDRBS3

chr5:58476421

chr8:136533480

ENST00000355849

266_316

29.333333333333332

347.0

Compositional bias

Note=Tyr-rich

Tgene

KHDRBS3

chr5:58476421

chr8:136533480

ENST00000355849

61_127

29.333333333333332

347.0

Domain

Note=KH

- 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

PDE4D

chr5:58476421

chr8:136533480

ENST00000317118

42_88

519.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000358923

42_88

508.0

Compositional bias

Note=Pro-rich

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000317118

386_715

519.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000340635

386_715

269.3333333333333

810.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000358923

386_715

508.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000360047

386_715

133.33333333333334

674.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000405755

386_715

147.33333333333334

688.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000502484

386_715

208.33333333333334

749.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000502575

386_715

205.33333333333334

220.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000503258

386_715

139.33333333333334

680.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000507116

386_715

205.33333333333334

746.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000546160

386_715

208.33333333333334

749.0

Domain

PDEase

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000317118

462_466

519.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000340635

462_466

269.3333333333333

810.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000358923

462_466

508.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000360047

462_466

133.33333333333334

674.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000405755

462_466

147.33333333333334

688.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000502484

462_466

208.33333333333334

749.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000502575

462_466

205.33333333333334

220.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000503258

462_466

139.33333333333334

680.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000507116

462_466

205.33333333333334

746.0

Nucleotide binding

cAMP

Hgene

PDE4D

chr5:58476421

chr8:136533480

ENST00000546160

462_466

208.33333333333334

749.0

Nucleotide binding

cAMP

Tgene

KHDRBS3

chr5:58476421

chr8:136533480

ENST00000355849

1_160

29.333333333333332

347.0

Region

Involved in homodimerization

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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)
PDB file >>>1245_PDE4D_58476421_KHDRBS3_136533480_1245_PDE4D_58476421_KHDRBS3_136533480_ranked_0.pdb	PDE4D	58476421	58476421	ENST00000520981	KHDRBS3	chr8	136533480	+	MEAEGSSAPARAGSGEGSDSAGGATLKAPKHLWRHEQHHQYPLRQPQFRLLHPHHHLPPPPPPSPQPQPQCPLQPPPPPPLPPPPPPPGA ARGRYASSGATGRVRHRGYSDTERYLYCRAMDRTSYAVETGHRPGLKKSRMSWPSSFQGLRRFDVDNGTSAGRSPLDPMTSPGSGLILQA NFVHSQRRESFLYRSDSDYDLSPKSMSRNSSIASDIHGDDLIVTPFAQVLASLRTVRNNFAALTNLQDRAPSKRSPMCNQPSINKATITE IEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKY FHLNDDLHVLIEVFAPPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPAPAITRGRGGVT ARPVGVVVPRGTPTPRGVLSTRGPVSRGRGLLTPRARGVPPTGYRPPPPPPTQETYGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSGAD	586

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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.

PDE4D_pLDDT.png

KHDRBS3_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

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
PDE4D
KHDRBS3

- 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 PDE4D-KHDRBS3

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to PDE4D-KHDRBS3

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