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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: 26597

FusionGeneSummary for PDXK_RRP1B

check button Fusion gene summary
Fusion gene informationFusion gene name: PDXK_RRP1B
Fusion gene ID: 26597
HgeneTgene
Gene symbol

PDXK

RRP1B

Gene ID

8566

23076

Gene namepyridoxal kinaseribosomal RNA processing 1B
SynonymsC21orf124|C21orf97|HEL-S-1a|PKH|PNK|PRED79KIAA0179|NNP1L|Nnp1|PPP1R136|RRP1
Cytomap

21q22.3

21q22.3

Type of geneprotein-codingprotein-coding
Descriptionpyridoxal kinaseepididymis secretory sperm binding protein Li 1apyridoxal (pyridoxine, vitamin B6) kinasepyridoxamine kinasepyridoxine kinasevitamin B6 kinaseribosomal RNA processing protein 1 homolog BRRP1-like protein Bprotein phosphatase 1, regulatory subunit 136ribosomal RNA processing 1 homolog B
Modification date2018052320180523
UniProtAcc

O00764

Q14684

Ensembl transtripts involved in fusion geneENST00000398081, ENST00000468090, 
ENST00000291565, ENST00000327574, 
ENST00000476313, ENST00000467908, 
ENST00000340648, 
Fusion gene scores* DoF score7 X 7 X 8=3921 X 2 X 2=4
# samples 82
** MAII scorelog2(8/392*10)=-2.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/4*10)=2.32192809488736
Context

PubMed: PDXK [Title/Abstract] AND RRP1B [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
HgenePDXK

GO:0008283

cell proliferation

10930737

HgenePDXK

GO:0042823

pyridoxal phosphate biosynthetic process

9099727|10987144|17766369

TgeneRRP1B

GO:0010923

negative regulation of phosphatase activity

19389623

TgeneRRP1B

GO:0098586

cellular response to virus

26311876


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
TCGALDACCTCGA-OR-A5J7-01APDXKchr21

45178423

+RRP1Bchr21

45114774

+
TCGALDBRCATCGA-AR-A0TS-01APDXKchr21

45154004

+RRP1Bchr21

45089765

+
* 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
intron-3UTRENST00000398081ENST00000340648PDXKchr21

45178423

+RRP1Bchr21

45114774

+
3UTR-3UTRENST00000468090ENST00000340648PDXKchr21

45178423

+RRP1Bchr21

45114774

+
3UTR-3UTRENST00000291565ENST00000340648PDXKchr21

45178423

+RRP1Bchr21

45114774

+
intron-3UTRENST00000327574ENST00000340648PDXKchr21

45178423

+RRP1Bchr21

45114774

+
intron-3UTRENST00000476313ENST00000340648PDXKchr21

45178423

+RRP1Bchr21

45114774

+
3UTR-3UTRENST00000467908ENST00000340648PDXKchr21

45178423

+RRP1Bchr21

45114774

+
In-frameENST00000398081ENST00000340648PDXKchr21

45154004

+RRP1Bchr21

45089765

+
In-frameENST00000468090ENST00000340648PDXKchr21

45154004

+RRP1Bchr21

45089765

+
In-frameENST00000291565ENST00000340648PDXKchr21

45154004

+RRP1Bchr21

45089765

+
In-frameENST00000327574ENST00000340648PDXKchr21

45154004

+RRP1Bchr21

45089765

+
3UTR-3CDSENST00000476313ENST00000340648PDXKchr21

45154004

+RRP1Bchr21

45089765

+
intron-3CDSENST00000467908ENST00000340648PDXKchr21

45154004

+RRP1Bchr21

45089765

+

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FusionProtFeatures for PDXK_RRP1B


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

O00764

RRP1B

Q14684

Required for synthesis of pyridoxal-5-phosphate fromvitamin B6. Positively regulates DNA damage-induced apoptosis byacting as a transcriptional coactivator of proapoptotic targetgenes of the transcriptional activator E2F1 (PubMed:20040599).Likely to play a role in ribosome biogenesis by targetingserine/threonine protein phosphatase PP1 to the nucleolus(PubMed:20926688). Involved in regulation of mRNA splicing (Bysimilarity). Inhibits SIPA1 GTPase activity (By similarity).Involved in regulating expression of extracellular matrix genes(By similarity). Associates with chromatin and may play a role inmodulating chromatin structure (PubMed:19710015).{ECO:0000250|UniProtKB:Q91YK2, ECO:0000269|PubMed:19710015,ECO:0000269|PubMed:20040599, ECO:0000269|PubMed:20926688}. (Microbial infection) Following influenza A virus (IAV)infection, promotes viral mRNA transcription by facilitating thebinding of IAV RNA-directed RNA polymerase to capped mRNA.{ECO:0000269|PubMed:26311876}.

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
TgeneRRP1Bchr21:45154004chr21:45089765ENST00000340648+016402_40643759Compositional biasNote=Poly-Lys

- In-frame and not-retained protein feature among the 13 regional features.
>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePDXKchr21:45154004chr21:45089765ENST00000291565+211186_18747313Nucleotide bindingATP
HgenePDXKchr21:45154004chr21:45089765ENST00000291565+211223_23447313Nucleotide bindingATP
HgenePDXKchr21:45154004chr21:45089765ENST00000468090+210186_18747285Nucleotide bindingATP
HgenePDXKchr21:45154004chr21:45089765ENST00000468090+210223_23447285Nucleotide bindingATP


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FusionGeneSequence for PDXK_RRP1B


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 PDXK_RRP1B


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
PDXKELAVL1, CUL3, CUL1, COPS5, CAND1, BARD1, YWHAQ, MOV10, NXF1, ABAT, OGT, EIF4E, EZR, G6PD, HIBADH, HYI, ITPA, MDH1, OAT, SNX2, SOD1, RABIF, TPI1, ATOH1RRP1BPPP1CA, LUC7L3, YBX3, CUBN, DDX21, H1FX, HNRNPA1, IGKC, IGKV2-40, ILF3, LARP1, LUC7L2, NCL, NPM1, PARP1, PRPF4B, RPL10A, RPL4, RPL5, RPLP0, RSL1D1, SDF2L1, SRSF1, SRSF6, SLC22A11, ALYREF, TOP1, HDGF, ELAVL1, SIRT7, CUL3, ESR1, PPP1CC, APOA1, CSNK2A1, MPG, LSM1, MAPK14, SRPK3, CSNK2A2, TARBP2, TP53, CUL7, OBSL1, CCDC8, RNF2, ABCE1, RPL14, ILF2, PPP1R3A, NTRK1, IFI16, NUP107, SRPK2, HNRNPU, SORT1, BAG6, TRIM28, CBX5, PES1, SENP3, CDC14B, MAGEB10, RRP8, MECP2, SART3, RPL18A, PPP1R7, PPP1CB, MTF1


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 PDXK_RRP1B


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgenePDXKO00764DB00165PyridoxinePyridoxal kinasesmall moleculeapproved|investigational|nutraceutical|vet_approved

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RelatedDiseases for PDXK_RRP1B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePDXKC0038220Status Epilepticus1CTD_human