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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: 25823

FusionGeneSummary for PAK1_RAD9A

check button Fusion gene summary
Fusion gene informationFusion gene name: PAK1_RAD9A
Fusion gene ID: 25823
HgeneTgene
Gene symbol

PAK1

RAD9A

Gene ID

5585

5883

Gene nameprotein kinase N1RAD9 checkpoint clamp component A
SynonymsDBK|PAK-1|PAK1|PKN|PKN-ALPHA|PRK1|PRKCL1RAD9
Cytomap

19p13.12

11q13.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase N1protease-activated kinase 1protein kinase C-like 1protein kinase C-like PKNprotein kinase C-related kinase 1protein kinase PKN-alphaserine-threonine kinase Nserine/threonine protein kinase Ncell cycle checkpoint control protein RAD9ADNA repair exonuclease rad9 homolog ARAD9 homolog AhRAD9
Modification date2018052320180523
UniProtAcc

Q13153

Q99638

Ensembl transtripts involved in fusion geneENST00000356341, ENST00000530617, 
ENST00000278568, ENST00000528203, 
ENST00000525542, 
ENST00000307980, 
ENST00000535644, 
Fusion gene scores* DoF score21 X 8 X 8=13442 X 2 X 2=8
# samples 232
** MAII scorelog2(23/1344*10)=-2.54682737183439
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: PAK1 [Title/Abstract] AND RAD9A [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
HgenePAK1

GO:0006357

regulation of transcription by RNA polymerase II

12514133

HgenePAK1

GO:0006468

protein phosphorylation

17332740

HgenePAK1

GO:0035407

histone H3-T11 phosphorylation

18066052

TgeneRAD9A

GO:0006974

cellular response to DNA damage stimulus

9872989

TgeneRAD9A

GO:0071479

cellular response to ionizing radiation

21659603


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
TCGALDSKCMTCGA-EB-A82B-01APAK1chr11

77184597

-RAD9Achr11

67155006

+
* 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
5UTR-intronENST00000356341ENST00000307980PAK1chr11

77184597

-RAD9Achr11

67155006

+
5UTR-intronENST00000356341ENST00000535644PAK1chr11

77184597

-RAD9Achr11

67155006

+
intron-intronENST00000530617ENST00000307980PAK1chr11

77184597

-RAD9Achr11

67155006

+
intron-intronENST00000530617ENST00000535644PAK1chr11

77184597

-RAD9Achr11

67155006

+
5UTR-intronENST00000278568ENST00000307980PAK1chr11

77184597

-RAD9Achr11

67155006

+
5UTR-intronENST00000278568ENST00000535644PAK1chr11

77184597

-RAD9Achr11

67155006

+
intron-intronENST00000528203ENST00000307980PAK1chr11

77184597

-RAD9Achr11

67155006

+
intron-intronENST00000528203ENST00000535644PAK1chr11

77184597

-RAD9Achr11

67155006

+
intron-intronENST00000525542ENST00000307980PAK1chr11

77184597

-RAD9Achr11

67155006

+
intron-intronENST00000525542ENST00000535644PAK1chr11

77184597

-RAD9Achr11

67155006

+

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FusionProtFeatures for PAK1_RAD9A


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PAK1

Q13153

RAD9A

Q99638

Protein kinase involved in intracellular signalingpathways downstream of integrins and receptor-type kinases thatplays an important role in cytoskeleton dynamics, in celladhesion, migration, proliferation, apoptosis, mitosis, and invesicle-mediated transport processes. Can directly phosphorylateBAD and protects cells against apoptosis. Activated by interactionwith CDC42 and RAC1. Functions as GTPase effector that links theRho-related GTPases CDC42 and RAC1 to the JNK MAP kinase pathway.Phosphorylates and activates MAP2K1, and thereby mediatesactivation of downstream MAP kinases. Involved in thereorganization of the actin cytoskeleton, actin stress fibers andof focal adhesion complexes. Phosphorylates the tubulin chaperoneTBCB and thereby plays a role in the regulation of microtubulebiogenesis and organization of the tubulin cytoskeleton. Plays arole in the regulation of insulin secretion in response toelevated glucose levels. Part of a ternary complex that containsPAK1, DVL1 and MUSK that is important for MUSK-dependentregulation of AChR clustering during the formation of theneuromuscular junction (NMJ). Activity is inhibited in cellsundergoing apoptosis, potentially due to binding of CDC2L1 andCDC2L2. Phosphorylates MYL9/MLC2. Phosphorylates RAF1 at 'Ser-338'and 'Ser-339' resulting in: activation of RAF1, stimulation ofRAF1 translocation to mitochondria, phosphorylation of BAD byRAF1, and RAF1 binding to BCL2. Phosphorylates SNAI1 at 'Ser-246'promoting its transcriptional repressor activity by increasing itsaccumulation in the nucleus. In podocytes, promotes NR3C2 nuclearlocalization. Required for atypical chemokine receptor ACKR2-induced phosphorylation of LIMK1 and cofilin (CFL1) and for theup-regulation of ACKR2 from endosomal compartment to cellmembrane, increasing its efficiency in chemokine uptake anddegradation. In synapses, seems to mediate the regulation of F-actin cluster formation performed by SHANK3, maybe through CFL1phosphorylation and inactivation. Plays a role in RUFY3-mediatedfacilitating gastric cancer cells migration and invasion(PubMed:25766321). {ECO:0000269|PubMed:10551809,ECO:0000269|PubMed:11733498, ECO:0000269|PubMed:12624090,ECO:0000269|PubMed:12876277, ECO:0000269|PubMed:14585966,ECO:0000269|PubMed:15611088, ECO:0000269|PubMed:15831477,ECO:0000269|PubMed:15833848, ECO:0000269|PubMed:16278681,ECO:0000269|PubMed:17726028, ECO:0000269|PubMed:17989089,ECO:0000269|PubMed:22669945, ECO:0000269|PubMed:23633677,ECO:0000269|PubMed:25766321, ECO:0000269|PubMed:8805275,ECO:0000269|PubMed:9032240, ECO:0000269|PubMed:9395435,ECO:0000269|PubMed:9528787}. Component of the 9-1-1 cell-cycle checkpoint responsecomplex that plays a major role in DNA repair. The 9-1-1 complexis recruited to DNA lesion upon damage by the RAD17-replicationfactor C (RFC) clamp loader complex. Acts then as a sliding clampplatform on DNA for several proteins involved in long-patch baseexcision repair (LP-BER). The 9-1-1 complex stimulates DNApolymerase beta (POLB) activity by increasing its affinity for the3'-OH end of the primer-template and stabilizes POLB to thosesites where LP-BER proceeds; endonuclease FEN1 cleavage activityon substrates with double, nick, or gap flaps of distinctsequences and lengths; and DNA ligase I (LIG1) on long-patch baseexcision repair substrates. The 9-1-1 complex is necessary for therecruitment of RHNO1 to sites of double-stranded breaks (DSB)occurring during the S phase. RAD9A possesses 3'->5' doublestranded DNA exonuclease activity. Its phosphorylation by PRKCDmay be required for the formation of the 9-1-1 complex.{ECO:0000269|PubMed:10713044, ECO:0000269|PubMed:21659603}.

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 PAK1_RAD9A


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 PAK1_RAD9A


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
PAK1ARHGEF2, ARPC1B, AKT1, RAC1, CDC42, CDK11A, ERBB2, ABI3, DYNLL1, PKLR, PLCG1, PAK1IP1, LIMK1, CDK5, RAF1, HGS, NCK1, ARHGEF7, MYLK, BAIAP2, NCK2, BMX, RHOJ, PAK1, SH3KBP1, HSP90AA1, YWHAG, YWHAZ, DYRK1B, ZBTB18, ZC3H7A, ZNF823, ZNF83, MYNN, C5orf42, ZNF418, HIST1H4A, TGM2, ARHGEF6, ELF3, GNB1, MAP3K1, MYO6, TGFBR1, TGFBR2, APP, CRIPAK, CHORDC1, ESR1, BAD, HIST1H3A, LYN, DYNLL2, PAK2, FBXO28, GIT1, SORBS3, BRSK1, EGFR, PYCARD, GIT2, H2AFX, SLC25A41, TAS2R41, ILKAP, PPAT, RELA, RHOU, SNW1, ICAM1, LPXN, FSD1, OR2K2, SOX2, SETX, FGB, PPM1A, PPP2CA, PPP1CA, MAPK14RAD9ABCL2L1, AR, NR3C1, RAD1, HUS1, RAD17, HUS1B, CLSPN, HDAC1, ABL1, DNAJC7, BCL2, TOPBP1, RPA1, RPA2, FEN1, ATR, SETMAR, DNMT1, SF3B3, PCNA, COPS5, FEM1B, MSH2, MSH6, MSH3, ATRX, RHNO1, C10orf2, TRIM25


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 PAK1_RAD9A


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 PAK1_RAD9A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePAK1C0007134Renal Cell Carcinoma1CTD_human
HgenePAK1C0033687Proteinuria1CTD_human
HgenePAK1C1458155Mammary Neoplasms1CTD_human
TgeneRAD9AC0085183Neoplasms, Second Primary1CTD_human