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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: 20339

FusionGeneSummary for LSM4_ADRBK1

check button Fusion gene summary
Fusion gene informationFusion gene name: LSM4_ADRBK1
Fusion gene ID: 20339
HgeneTgene
Gene symbol

LSM4

ADRBK1

Gene ID

25804

156

Gene nameLSM4 homolog, U6 small nuclear RNA and mRNA degradation associatedG protein-coupled receptor kinase 2
SynonymsGRP|YER112WADRBK1|BARK1|BETA-ARK1
Cytomap

19p13.11

11q13.2

Type of geneprotein-codingprotein-coding
DescriptionU6 snRNA-associated Sm-like protein LSm4LSM4 U6 small nuclear RNA and mRNA degradation associatedLSM4 homolog, U6 small nuclear RNA associatedglycine-rich proteinbeta-adrenergic receptor kinase 1adrenergic beta receptor kinase 1beta-ARK-1
Modification date2018052320180522
UniProtAcc

Q9Y4Z0

Ensembl transtripts involved in fusion geneENST00000593829, ENST00000252816, 
ENST00000308595, ENST00000526285, 
ENST00000527176, 
Fusion gene scores* DoF score6 X 3 X 5=901 X 1 X 1=1
# samples 61
** MAII scorelog2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: LSM4 [Title/Abstract] AND ADRBK1 [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
TgeneADRBK1

GO:0007217

tachykinin receptor signaling pathway

17986524

TgeneADRBK1

GO:0031623

receptor internalization

20074556


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
TCGARVSKCMTCGA-D3-A8GB-06ALSM4chr19

18433828

-ADRBK1chr11

67046671

+
* 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-shiftENST00000593829ENST00000308595LSM4chr19

18433828

-ADRBK1chr11

67046671

+
Frame-shiftENST00000593829ENST00000526285LSM4chr19

18433828

-ADRBK1chr11

67046671

+
5CDS-intronENST00000593829ENST00000527176LSM4chr19

18433828

-ADRBK1chr11

67046671

+
Frame-shiftENST00000252816ENST00000308595LSM4chr19

18433828

-ADRBK1chr11

67046671

+
Frame-shiftENST00000252816ENST00000526285LSM4chr19

18433828

-ADRBK1chr11

67046671

+
5CDS-intronENST00000252816ENST00000527176LSM4chr19

18433828

-ADRBK1chr11

67046671

+

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FusionProtFeatures for LSM4_ADRBK1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LSM4

Q9Y4Z0

ADRBK1

Binds specifically to the 3'-terminal U-tract of U6snRNA. Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}.

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 LSM4_ADRBK1


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 LSM4_ADRBK1


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
LSM4SNRPE, 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, RPL32ADRBK1GNAQ, GNA15, PRKCB, PDE6G, SRC, PDCL, PDC, GIT2, GIT1, RHO, CAV1, CCR4, EDNRB, AGTR1, FSHR, ADRB2, PDGFRB, CSNK2B, HDAC6, MDM2, ARRB1, GNB1, KCNIP3, GRM1, SNCA, PEBP1, FBXO25, EPHA2, RASGRF1, HSP90AA1, HSP90AB1, ADRBK2, ACACA, MOV10, DDX6, DNAAF5, FERMT2, PAPOLA, PPWD1, PROSC, PTPRF, NARS2, RXRB, PRPF4, CTR9, SLAIN2, GNB2, GPR17, PPP1R16B, TBC1D14


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 LSM4_ADRBK1


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 LSM4_ADRBK1


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