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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PKDCC-CXXC5

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PKDCC-CXXC5
FusionPDB ID: 65688
FusionGDB2.0 ID: 65688
HgeneTgene
Gene symbol

PKDCC

CXXC5

Gene ID

91461

51523

Gene nameprotein kinase domain containing, cytoplasmicCXXC finger protein 5
SynonymsRLSDF|SGK493|VlkCF5|HSPC195|RINF|WID
Cytomap

2p21

5q31.2

Type of geneprotein-codingprotein-coding
Descriptionextracellular tyrosine-protein kinase PKDCCprotein kinase domain containing, cytoplasmic homologprotein kinase domain-containing protein, cytoplasmicprotein kinase-like protein SgK493sugen kinase 493vertebrate lonesome kinaseCXXC-type zinc finger protein 5CXXC finger 5 proteinWT1-induced Inhibitor of Dishevelledputative MAPK-activating protein PM08putative NF-kappa-B-activating protein 102retinoid-inducible nuclear factor
Modification date2020032820200313
UniProtAcc.

Q7LFL8

Ensembl transtripts involved in fusion geneENST idsENST00000480099, ENST00000294964, 
ENST00000302517, ENST00000511048, 
ENST00000515038, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score1 X 1 X 1=14 X 3 X 4=48
# samples 15
** MAII scorelog2(1/1*10)=3.32192809488736log2(5/48*10)=0.0588936890535686
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PKDCC [Title/Abstract] AND CXXC5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PKDCC(42284537)-CXXC5(139062465), # samples:1
Anticipated loss of major functional domain due to fusion event.PKDCC-CXXC5 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.
PKDCC-CXXC5 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.
PKDCC-CXXC5 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.
PKDCC-CXXC5 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.
PKDCC-CXXC5 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PKDCC-CXXC5 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PKDCC-CXXC5 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
PKDCC-CXXC5 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PKDCC-CXXC5 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
PKDCC-CXXC5 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePKDCC

GO:0018108

peptidyl-tyrosine phosphorylation

25171405

TgeneCXXC5

GO:0000122

negative regulation of transcription by RNA polymerase II

23303788


check buttonFusion gene breakpoints across PKDCC (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CXXC5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4OVTCGA-61-2111-01APKDCCchr2

42284537

+CXXC5chr5

139062465

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000294964PKDCCchr242284537+ENST00000511048CXXC5chr5139062465+228915761801703507

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000294964ENST00000511048PKDCCchr242284537+CXXC5chr5139062465+0.087692170.9123078

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Fusion Amino Acid Sequences


check button 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

>65688_65688_1_PKDCC-CXXC5_PKDCC_chr2_42284537_ENST00000294964_CXXC5_chr5_139062465_ENST00000511048_length(amino acids)=507AA_BP=465
MRRRRAAVAAGFCASFLLGSVLNVLFAPGSEPPRPGQSPEPSPAPGPGRRGGRGELARQIRARYEEVQRYSRGGPGPGAGRPERRRLMDL
APGGPGLPRPRPPWARPLSDGAPGWPPAPGPGSPGPGPRLGCAALRNVSGAQYMGSGYTKAVYRVRLPGGAAVALKAVDFSGHDLGSCVR
EFGVRRGCYRLAAHKLLKEMVLLERLRHPNVLQLYGYCYQDSEDIPDTLTTITELGAPVEMIQLLQTSWEDRFRICLSLGRLLHHLAHSP
LGSVTLLDFRPRQFVLVDGELKVTDLDDARVEETPCAGSTDCILEFPARNFTLPCSAQGWCEGMNEKRNLYNAYRFFFTYLLPHSAPPSL
RPLLDSIVNATGELAWGVDETLAQLEKVLHLYRSGQYLQNSTASSSTEYQCIPDSTIPQEDYRCWPSYHHGSCLLSVFNLAEAVDVCESH

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:42284537/chr5:139062465)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CXXC5

Q7LFL8

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: May indirectly participate in activation of the NF-kappa-B and MAPK pathways. Acts as a mediator of BMP4-mediated modulation of canonical Wnt signaling activity in neural stem cells (By similarity). Required for DNA damage-induced ATM phosphorylation, p53 activation and cell cycle arrest. Involved in myelopoiesis. Transcription factor. Binds to the oxygen responsive element of COX4I2 and represses its transcription under hypoxia conditions (4% oxygen), as well as normoxia conditions (20% oxygen) (PubMed:23303788). May repress COX4I2 transactivation induced by CHCHD2 and RBPJ (PubMed:23303788). Binds preferentially to DNA containing cytidine-phosphate-guanosine (CpG) dinucleotides over CpH (H=A, T, and C), hemimethylated-CpG and hemimethylated-hydroxymethyl-CpG (PubMed:29276034). {ECO:0000250|UniProtKB:Q5XIQ3, ECO:0000269|PubMed:19182210, ECO:0000269|PubMed:19557330, ECO:0000269|PubMed:23303788, ECO:0000269|PubMed:29276034}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePKDCCchr2:42284537chr5:139062465ENST00000294964+6728_128465.3333333333333494.0Compositional biasNote=Pro-rich
HgenePKDCCchr2:42284537chr5:139062465ENST00000294964+67144_152465.3333333333333494.0Nucleotide bindingATP
TgeneCXXC5chr2:42284537chr5:139062465ENST000003025170314_180323.0Compositional biasNote=Poly-Ser
TgeneCXXC5chr2:42284537chr5:139062465ENST000005110480314_180323.0Compositional biasNote=Poly-Ser
TgeneCXXC5chr2:42284537chr5:139062465ENST0000030251703257_2620323.0MotifNuclear localization signal
TgeneCXXC5chr2:42284537chr5:139062465ENST0000051104803257_2620323.0MotifNuclear localization signal
TgeneCXXC5chr2:42284537chr5:139062465ENST0000030251703256_2970323.0Zinc fingerCXXC-type
TgeneCXXC5chr2:42284537chr5:139062465ENST0000051104803256_2970323.0Zinc fingerCXXC-type

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePKDCCchr2:42284537chr5:139062465ENST00000294964+67138_493465.3333333333333494.0DomainProtein kinase


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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PKDCC
CXXC5


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to PKDCC-CXXC5


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

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Related Diseases to PKDCC-CXXC5


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

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource