FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

FusionGeneSummary

leaf

FusionProtFeature

leaf

FusionGeneSequence

leaf

FusionGenePPI

leaf

RelatedDrugs

leaf

RelatedDiseases

Fusion gene ID: 25843

FusionGeneSummary for PAK4_LSM4

check button Fusion gene summary
Fusion gene informationFusion gene name: PAK4_LSM4
Fusion gene ID: 25843
HgeneTgene
Gene symbol

PAK4

LSM4

Gene ID

10298

25804

Gene namep21 (RAC1) activated kinase 4LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
Synonyms-GRP|YER112W
Cytomap

19q13.2

19p13.11

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase PAK 4p21 protein (Cdc42/Rac)-activated kinase 4p21(CDKN1A)-activated kinase 4protein kinase related to S. cerevisiae STE20, effector for Cdc42HsU6 snRNA-associated Sm-like protein LSm4LSM4 U6 small nuclear RNA and mRNA degradation associatedLSM4 homolog, U6 small nuclear RNA associatedglycine-rich protein
Modification date2018052320180523
UniProtAcc

O96013

Q9Y4Z0

Ensembl transtripts involved in fusion geneENST00000599470, ENST00000321944, 
ENST00000358301, ENST00000597766, 
ENST00000593690, ENST00000599386, 
ENST00000435673, ENST00000360442, 
ENST00000593829, ENST00000252816, 
Fusion gene scores* DoF score13 X 4 X 6=3124 X 3 X 3=36
# samples 135
** MAII scorelog2(13/312*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/36*10)=0.473931188332412
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PAK4 [Title/Abstract] AND LSM4 [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
TCGALDOVTCGA-10-0927-01APAK4chr19

39616559

+LSM4chr19

18426875

-
* 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-3CDSENST00000599470ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-intronENST00000599470ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-3CDSENST00000321944ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-intronENST00000321944ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-3CDSENST00000358301ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-intronENST00000358301ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-
3UTR-3CDSENST00000597766ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
3UTR-intronENST00000597766ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-3CDSENST00000593690ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-intronENST00000593690ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-3CDSENST00000599386ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
5UTR-intronENST00000599386ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-
intron-3CDSENST00000435673ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
intron-intronENST00000435673ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-
intron-3CDSENST00000360442ENST00000593829PAK4chr19

39616559

+LSM4chr19

18426875

-
intron-intronENST00000360442ENST00000252816PAK4chr19

39616559

+LSM4chr19

18426875

-

Top

FusionProtFeatures for PAK4_LSM4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PAK4

O96013

LSM4

Q9Y4Z0

Serine/threonine protein kinase that plays a role in avariety of different signaling pathways including cytoskeletonregulation, cell migration, growth, proliferation or cellsurvival. Activation by various effectors including growth factorreceptors or active CDC42 and RAC1 results in a conformationalchange and a subsequent autophosphorylation on several serineand/or threonine residues. Phosphorylates and inactivates theprotein phosphatase SSH1, leading to increased inhibitoryphosphorylation of the actin binding/depolymerizing factorcofilin. Decreased cofilin activity may lead to stabilization ofactin filaments. Phosphorylates LIMK1, a kinase that also inhibitsthe activity of cofilin. Phosphorylates integrin beta5/ITGB5 andthus regulates cell motility. Phosphorylates ARHGEF2 and activatesthe downstream target RHOA that plays a role in the regulation ofassembly of focal adhesions and actin stress fibers. Stimulatescell survival by phosphorylating the BCL2 antagonist of cell deathBAD. Alternatively, inhibits apoptosis by preventing caspase-8binding to death domain receptors in a kinase independent manner.Plays a role in cell-cycle progression by controlling levels ofthe cell-cycle regulatory protein CDKN1A and by phosphorylatingRAN. {ECO:0000269|PubMed:11278822, ECO:0000269|PubMed:11313478,ECO:0000269|PubMed:14560027, ECO:0000269|PubMed:15660133,ECO:0000269|PubMed:20507994, ECO:0000269|PubMed:20631255,ECO:0000269|PubMed:20805321, ECO:0000269|PubMed:26607847}. Binds specifically to the 3'-terminal U-tract of U6snRNA.

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


Top

FusionGeneSequence for PAK4_LSM4


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).

Top

FusionGenePPI for PAK4_LSM4


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
PAK4LRRK1, YWHAG, YWHAQ, CDC42, YWHAZ, SFN, DLST, LIMK1, RAC1, ITGB5, RAN, TERF1, POT1, APP, YWHAE, FBXO25, SRPK2, SRPK1, LATS2, YWHAB, SH3RF2, HECW2, PAK6, PAK7, LRRC16A, ARHGEF11, SUPT5H, GGNBP2, KLHL42, TMPRSS11A, DDX6, NAA20, NAA25, ABL1, PPM1B, NTRK1, TMEM17, XPO1, RCC2, RHOU, PAK4, PXN, VCL, RHOV, HIST1H1A, SNW1, CDC5L, MMP2, ITGB3, ITGAV, CDH1, EGFR, PPM1A, PTPN4, PTPN7, STYX, CDK6, MTUS2, KCTD3, KIF13B, CBY1, RAB3IP, G3BP1LSM4SNRPE, XRN1, CALCOCO2, LSM1, LSM2, LSM3, LSM6, LSM7, LSM8, SMN1, USP15, USP4, PRPF4, SART3, MEPCE, RNU4ATAC, RNU6ATAC, TOP1, LSM5, DDX39B, PRPF18, VAC14, TCEA2, WDR44, PYROXD1, MTR, RMI2, GTF2B, RAD23A, SGTA, PPIB, PPIP5K1, HUWE1, SMU1, TOE1, SLC22A2, SMIM14, NMI, RHOXF2, COX5B, PLEKHA5, WWOX, PSTPIP1, IKZF1, ZBTB10, L3MBTL3, HNRNPR, KLC2, LRPPRC, PKN2, NAA38, SF3A3, SF3B3, SYNCRIP, ZMAT2, XPO1, SIN3B, PRPF3, SNRPN, ALYREF, RPL26L1, PPIH, OLA1, RPL32


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


Top

RelatedDrugs for PAK4_LSM4


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

Top

RelatedDiseases for PAK4_LSM4


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