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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: 31504

FusionGeneSummary for RNF19A_PABPC1

check button Fusion gene summary
Fusion gene informationFusion gene name: RNF19A_PABPC1
Fusion gene ID: 31504
HgeneTgene
Gene symbol

RNF19A

PABPC1

Gene ID

25897

26986

Gene namering finger protein 19A, RBR E3 ubiquitin protein ligasepoly(A) binding protein cytoplasmic 1
SynonymsRNF19PAB1|PABP|PABP1|PABPC2|PABPL1
Cytomap

8q22.2

8q22.3

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase RNF19Adouble ring-finger proteinprotein p38 interacting with transcription factor Sp1ring finger protein 19ring finger protein 19A, E3 ubiquitin protein ligasering-IBR-ring domain containing protein Dorfinpolyadenylate-binding protein 1poly(A) binding protein, cytoplasmic 2
Modification date2018052320180523
UniProtAcc

Q9NV58

P11940

Ensembl transtripts involved in fusion geneENST00000341084, ENST00000519449, 
ENST00000523255, 
ENST00000318607, 
ENST00000519004, ENST00000522387, 
ENST00000519596, 
Fusion gene scores* DoF score15 X 11 X 8=13207 X 8 X 3=168
# samples 198
** MAII scorelog2(19/1320*10)=-2.79646660591487
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RNF19A [Title/Abstract] AND PABPC1 [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
TgenePABPC1

GO:2000623

negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

18447585


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
TCGALDBLCATCGA-GV-A3JW-01ARNF19Achr8

101287181

-PABPC1chr8

101730508

-
* 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-shiftENST00000341084ENST00000318607RNF19Achr8

101287181

-PABPC1chr8

101730508

-
Frame-shiftENST00000341084ENST00000519004RNF19Achr8

101287181

-PABPC1chr8

101730508

-
Frame-shiftENST00000341084ENST00000522387RNF19Achr8

101287181

-PABPC1chr8

101730508

-
5CDS-intronENST00000341084ENST00000519596RNF19Achr8

101287181

-PABPC1chr8

101730508

-
Frame-shiftENST00000519449ENST00000318607RNF19Achr8

101287181

-PABPC1chr8

101730508

-
Frame-shiftENST00000519449ENST00000519004RNF19Achr8

101287181

-PABPC1chr8

101730508

-
Frame-shiftENST00000519449ENST00000522387RNF19Achr8

101287181

-PABPC1chr8

101730508

-
5CDS-intronENST00000519449ENST00000519596RNF19Achr8

101287181

-PABPC1chr8

101730508

-
intron-3CDSENST00000523255ENST00000318607RNF19Achr8

101287181

-PABPC1chr8

101730508

-
intron-3CDSENST00000523255ENST00000519004RNF19Achr8

101287181

-PABPC1chr8

101730508

-
intron-3CDSENST00000523255ENST00000522387RNF19Achr8

101287181

-PABPC1chr8

101730508

-
intron-intronENST00000523255ENST00000519596RNF19Achr8

101287181

-PABPC1chr8

101730508

-

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FusionProtFeatures for RNF19A_PABPC1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RNF19A

Q9NV58

PABPC1

P11940

E3 ubiquitin-protein ligase which accepts ubiquitin fromE2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form ofa thioester and then directly transfers the ubiquitin to targetedsubstrates, such as SNCAIP or CASR. Specifically ubiquitinatespathogenic SOD1 variants, which leads to their proteasomaldegradation and to neuronal protection.{ECO:0000269|PubMed:11237715, ECO:0000269|PubMed:12145308,ECO:0000269|PubMed:12750386, ECO:0000269|PubMed:15456787,ECO:0000269|PubMed:16513638}. Binds the poly(A) tail of mRNA, including that of itsown transcript. May be involved in cytoplasmic regulatoryprocesses of mRNA metabolism such as pre-mRNA splicing. Itsfunction in translational initiation regulation can either beenhanced by PAIP1 or repressed by PAIP2. Can probably bind tocytoplasmic RNA sequences other than poly(A) in vivo. Involved intranslationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translationaland decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved inregulation of nonsense-mediated decay (NMD) of mRNAs containingpremature stop codons; for the recognition of prematuretermination codons (PTC) and initiation of NMD a competitiveinteraction between UPF1 and PABPC1 with the ribosome-boundrelease factors is proposed. By binding to long poly(A) tails, mayprotect them from uridylation by ZCCHC6/ZCCHC11 and hencecontribute to mRNA stability (PubMed:25480299). Positivelyregulates the replication of dengue virus (DENV)(PubMed:26735137). {ECO:0000269|PubMed:11051545,ECO:0000269|PubMed:17212783, ECO:0000269|PubMed:18447585,ECO:0000269|PubMed:20573744, ECO:0000269|PubMed:25480299,ECO:0000269|PubMed:26735137}.

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 RNF19A_PABPC1


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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for RNF19A_PABPC1


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
RNF19AUBE2L3, UBE2L6, SOD1, CASR, VCP, SNCAIP, NUDT21, ILK, RPS6KA5, MAP3K7, C11orf58, ZAKPABPC1ANAPC5, EIF4A2, IKBKE, PINX1, DYNLL1, PUF60, BCAR3, PAN2, UPF1, ETF1, PAN3, CNOT7, TOB1, EIF4B, PXN, PAIP1, GNB2L1, PAIP2, EIF4A1, GSPT2, GSPT1, EIF4G1, EIF4G3, HNRNPA1, AIRE, GIGYF2, H2AFX, PRMT6, HNRNPD, HDAC5, STAU1, HNRNPK, YWHAG, PCBP1, PCBP2, SREK1, NDRG1, ELAVL1, ARRB2, SIRT7, ZFP36, NCL, SH3KBP1, TSG101, TNRC6A, TNRC6B, TNRC6C, ATXN2, IGBP1, PPP2CA, NFX1, PABPC1, UBR5, CUL3, CUL4A, CUL4B, CUL5, CUL2, CUL1, COPS5, COPS6, DCUN1D1, CAND1, NEDD8, CHAF1A, CNOT6, TOB2, MEX3B, MEX3A, MEX3C, BRCA1, SMAD3, PAIP2B, FBXO6, SYNCRIP, HNRNPU, HNRNPR, SNRNP200, DHX15, SNW1, ILF3, EEF1A1, RPS21, RPS4X, RPSA, RPS28, RPL4, RPL7, RPL7A, RPL13, RALY, SNRPD3, SART1, PRPF3, SNRPA, RPL5, EEF2, ATP6V1B2, ATP5A1, ESR1, HBB, USP10, G3BP1, FN1, VCAM1, U2AF1, RBM4, IFIT1, IFIT2, IFIT3, AGO1, AGO2, IL7R, UBL4A, ITGA4, MAPKAPK2, SMG1, RBM8A, CD81, IGSF8, ICAM1, RUVBL1, TERT, BAG3, CSF2, TARDBP, CLK3, SRPK2, SRPK1, CLK2, ITCH, WBP4, APBB1, PIN1, WWOX, APEX1, P4HB, GNPDA1, SGTA, UBA1, PSMD9, TMOD3, RPA1, RPA2, RPA3, HAUS1, CEP250, TP53, WWP2, SMG6, R3HCC1L, TDRD3, CUL7, OBSL1, CCDC8, ZMYND11, FBXW11, MAEL, ACAT2, CSTF2, DDX19A, EEF1G, FDPS, G3BP2, HSPA8, KIN, LUC7L2, MIF, MSI2, NHP2L1, ORC4, ALYREF, ATXN2L, BRIX1, CSTF3, DDX39A, DDX39B, EEF1A2, EIF4E, PFAS, PHGDH, POLE, RAE1, RPL13A, RPL18, RPL35, SFN, SKIV2L2, UAP1, PAPOLA, PAPOLB, PDCD6, PLRG1, PREP, PRPF8, RPL10A, RPL11, RPL14, RPL15, RPL17, RPL18A, RPL27, RPL27A, RPL3, RPL37A, RPL39, RPL6, RPLP0, RPLP2, RPS16, RPS3A, RPS6, RPS8, SERBP1, SF3A1, SUMO1, NTRK1, XPO1, HIST1H3E, RPL10, GAN, SKI, CRY1, MKRN1, MCM2, U2AF2, ELAVL2, TRA2A, SNRNP70, CYLD, COX15, DLD, DLST, DNM1L, HSD17B10, PARK7, PDHA1, VDAC1, TRIM25, PRNP, DCAF4L2


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 RNF19A_PABPC1


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 RNF19A_PABPC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgenePABPC1C0005695Bladder Neoplasm1CTD_human
TgenePABPC1C0007138Carcinoma, Transitional Cell1CTD_human
TgenePABPC1C1458155Mammary Neoplasms1CTD_human