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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 28852

FusionGeneSummary for PRPF18_CCDC3

check button Fusion gene summary
Fusion gene informationFusion gene name: PRPF18_CCDC3
Fusion gene ID: 28852
HgeneTgene
Gene symbol

PRPF18

CCDC3

Gene ID

8559

83643

Gene namepre-mRNA processing factor 18coiled-coil domain containing 3
SynonymsPRP18|hPrp18-
Cytomap

10p13

10p13

Type of geneprotein-codingprotein-coding
Descriptionpre-mRNA-splicing factor 18PRP18 homologPRP18 pre-mRNA processing factor 18 homologPRP18 pre-mRNA processing factor 18 homolog(PRPF18)coiled-coil domain-containing protein 3fat/vessel-derived secretory proteinfavine
Modification date2018052320180329
UniProtAcc

Q99633

Q9BQI4

Ensembl transtripts involved in fusion geneENST00000378572, ENST00000378825, 
ENST00000378839, 
Fusion gene scores* DoF score4 X 4 X 3=483 X 3 X 3=27
# samples 43
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PRPF18 [Title/Abstract] AND CCDC3 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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

check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUADTCGA-49-AAR0-01APRPF18chr10

13629152

+CCDC3chr10

12940679

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shitENST00000378572ENST00000378825PRPF18chr10

13629152

+CCDC3chr10

12940679

-
In-frameENST00000378572ENST00000378839PRPF18chr10

13629152

+CCDC3chr10

12940679

-

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FusionProtFeatures for PRPF18_CCDC3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PRPF18

Q99633

CCDC3

Q9BQI4

Participates in the second step of pre-mRNA splicing.{ECO:0000269|PubMed:9000057}. Negatively regulates TNF-alpha-induced pro-inflammatoryresponse in endothelial cells (ECs) via inhibition of TNF-alpha-induced NF-kappaB activation in ECs (PubMed:25193116). Positivelyregulates lipid accumulation in adipose cells (By similarity).{ECO:0000250|UniProtKB:Q9D6Y1, ECO:0000269|PubMed:25193116}.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for PRPF18_CCDC3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_PRPF18_ENST00000378572_chr10_13629152_+_CCDC3_ENST00000378839_chr10_12940679_-_110aa
MDILKSEILRKRQLVEDRNLLVLMCSSVQKALFEEEDHVKKLQQKVATLEKRNRQLRERVKKVKRSLRQARKKGRHLELANQKLSEKLAA


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_PRPF18_ENST00000378572_chr10_13629152_+_CCDC3_ENST00000378839_chr10_12940679_-_330nt
ATGGACATTCTGAAATCAGAGATCCTTCGGAAGCGGCAGCTGGTGGAGGACAGGAACCTGCTGGTGCTCATGTGCTCCTCGGTGCAGAAG
GCCTTGTTTGAGGAGGAGGACCACGTCAAGAAACTGCAGCAGAAAGTGGCCACCCTGGAGAAGCGCAACCGGCAGCTCCGGGAGCGAGTG
AAGAAGGTCAAGAGGTCCTTGCGGCAGGCGCGTAAGAAGGGCCGCCACCTGGAGCTGGCGAACCAGAAACTCAGTGAGAAGCTGGCGGCG


* Fusion transcript sequences (Full-length transcript).
>In-frame_PRPF18_ENST00000378572_chr10_13629152_+_CCDC3_ENST00000378839_chr10_12940679_-_2279nt
CTCTCTCATCCCAGCTTCCGCCGGAAGCGGCTCCTGTCAGTTGTTCTCAGGTGTTTGGGCTTGTTGTTCCGTATACTCAGTGGGTTCGCG
GCCGCCGGCCCAGTGAGGCTGGGTTCGAGGAGCTGGAGCGGGAAACTGGAGCTTAAATTCTGGCGGCGAGATGGACATTCTGAAATCAGA
GATCCTTCGGAAGCGGCAGCTGGTGGAGGACAGGAACCTGCTGGTGCTCATGTGCTCCTCGGTGCAGAAGGCCTTGTTTGAGGAGGAGGA
CCACGTCAAGAAACTGCAGCAGAAAGTGGCCACCCTGGAGAAGCGCAACCGGCAGCTCCGGGAGCGAGTGAAGAAGGTCAAGAGGTCCTT
GCGGCAGGCGCGTAAGAAGGGCCGCCACCTGGAGCTGGCGAACCAGAAACTCAGTGAGAAGCTGGCGGCGGGCGCGCTGCCGCACATCAA
TGCCCGGGGGCCCGTGCGCCCCCCCTACCTGCGGGGGTAACGGGCCTGGGGGCTGCCAGGTGTGCAGGGCCAATCCTGACGGTAATTGAG
AATGAGTGAGGTTTCGTACATGCAGCTATTTCAAGGGTTGTAAGAGTTTTTGTTTTTAATCACGCATTTGGTAGAGTCTAAATGGATAAA
ATGCAAGGCTTGCTTTCCCCTTGGGTGCTGGCCTCAATGTCAGACCCCACGCGCTGCCCCTTCCTGGCCTGACCCCAGACGCAGTGCCTG
GCAGTCCAGAGGCAGTGGGATCCCTGAGTGCTGAATGCTCGCCTGCAGAGCAGCCCAGAAAGAGCCCTGACTGGGGAGAGAACATTTTAG
AATCTCTAGTGTAAAAGACATCAACGTGCTTAGCCTTTATTTCAGAAAAAAATCAGGGTGGTTCCCAGCTCCCCAGTCCAGGACAACCAT
TAGTCCTGATGAGTGAGCTGACGCTGGTGCTGGAACCTGCTGGCACCTCACTGGCCACATCTTTGGAAGGGGATGGTGGCCTTGCATCCA
AGATGCCTGAAAATCAGCACGTGCAGGGCCTCCCTATCCAGCCAGCATTTTCCTTCCAGCTGAGGCAGGTGAAGACTTCATAAGCTCATC
ACAGGGGAGGGAATTAGGAGCAGGGCAGCAGGTAATTAAACAAGATAAATTATACCTGATTTCCAACACCAGCTACAAAGAGTTGAAGAT
GATACCTATGGGTCGCGTTAACACAGGGGGCAACTGCCTTGATCGGCCTGCCATGGGTCATCAGACTGCTTCCTAAATTGAGAGAAACTG
AGCAATCTCTCAGCCACTGCTATAGTCTAACTTCTTGTTTGCTGAGTAATTGTTTCTAATGTCTCTGAACTCAAAGTGAGGTGCTCCAAG
ACGCTGTGAACTTCTGCAAAGACACCTCCTTACCTACTGGGATCACGTGACCTGACCTCACTCCCAGCCAGGCTCCCAAAGGGCTCATTC
CAGCCATTCCAATCTCTTCTTCTTTATGCAAACACTTTTCCCCCACAACAAGCCTTGTTTGTTCCGATAGGAATACGTGTACGTCAGTGC
ACTTGTCCTTACGTCAGTTCCTTACACCACCAAAGCACTTCACCTTTCTGGAAATAAAACTTTTAAGACACTACTATAAGTAAAAATGAG
AGTATTCACTAGACTTATTGCTCAGGCACATTTGAGTGGGTCCCAGCTGTGTGATTAAGAAGTCAACTGGGTGGCCTTTTCTGGGTTATC
TTCTGATCATGGCCTTTCAACCCAACAAGGGCCCTTCCCTGCTCTTCCACCAGTAAAGGCTCCTGGCCTCTCATCAGGATCTGCCCCCCA
GAGACCCCCCCCAGACACTGCAGGGCCTGGTGATGCTGTCCTCTGTACCGGAAATGGCAGGCACTGTCAGATTTCCACTCTTCTGCCTTT
AGGAAGGCTGGGTGCTTCTTGCTCTGACAGCCAGTCTGGGGAGATGACTCTTACGTTGCTTGAGTCTTGGTGGCAGGCTGCTGTCCACGG
GGGAGAAGTCTCTGCTCTGGACTGGACAGAAGAGAGACTTTTACCCTGGGGCACTCACACGGCCAAGCTTCTGCCACCACTTCATTAGCT
GTATTCTCCATAGTATGGTGAAATAGCAGGTGCGTCTTCTAGTTTATTCCTCCTGGGGACATTTCCTCAAAGCAGTTTTGCGCCCCCGCA
AGGGAATGGTCAGCCTAAGGGTAATGTACAGCCCGTGCTTGGAGAACCATGGAAGCTACACCCCTACAGGTGCATACTGTTCTGCTTTTC


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FusionGenePPI for PRPF18_CCDC3


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
PRPF18LSM4, GTF2B, YWHAZ, RHOUCCDC3


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for PRPF18_CCDC3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for PRPF18_CCDC3


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