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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: 19742

FusionGeneSummary for LIMS1_CCDC138

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMS1_CCDC138
Fusion gene ID: 19742
HgeneTgene
Gene symbol

LIMS1

CCDC138

Gene ID

3987

165055

Gene nameLIM zinc finger domain containing 1coiled-coil domain containing 138
SynonymsPINCH|PINCH-1|PINCH1-
Cytomap

2q12.3

2q13

Type of geneprotein-codingprotein-coding
DescriptionLIM and senescent cell antigen-like-containing domain protein 1LIM and senescent cell antigen-like domains 1LIM-type zinc finger domains 1particularly interesting new Cys-His protein 1renal carcinoma antigen NY-REN-48senescent cell antigencoiled-coil domain-containing protein 138
Modification date2018052220180519
UniProtAcc

P48059

Q96M89

Ensembl transtripts involved in fusion geneENST00000544547, ENST00000332345, 
ENST00000393310, ENST00000410093, 
ENST00000409441, ENST00000338045, 
ENST00000462817, ENST00000542845, 
ENST00000393314, 
ENST00000412964, 
ENST00000295124, ENST00000470608, 
Fusion gene scores* DoF score4 X 2 X 3=241 X 1 X 1=1
# samples 41
** MAII scorelog2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(1/1*10)=3.32192809488736
Context

PubMed: LIMS1 [Title/Abstract] AND CCDC138 [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
HgeneLIMS1

GO:0045892

negative regulation of transcription, DNA-templated

21390327


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-K4-A5RJ-01ALIMS1chr2

109151050

+CCDC138chr2

109421345

+
* 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-shiftENST00000544547ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
Frame-shiftENST00000544547ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
5CDS-intronENST00000544547ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000332345ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000332345ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000332345ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393310ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393310ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000393310ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000410093ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000410093ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000410093ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000409441ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000409441ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000409441ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000338045ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000338045ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000338045ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000462817ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000462817ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000462817ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000542845ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000542845ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000542845ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393314ENST00000412964LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-3CDSENST00000393314ENST00000295124LIMS1chr2

109151050

+CCDC138chr2

109421345

+
intron-intronENST00000393314ENST00000470608LIMS1chr2

109151050

+CCDC138chr2

109421345

+

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FusionProtFeatures for LIMS1_CCDC138


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LIMS1

P48059

CCDC138

Q96M89

Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cellsurface receptor tyrosine kinases and growth factor receptors.Involved in the regulation of cell survival, cell proliferationand cell differentiation.

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 LIMS1_CCDC138


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 LIMS1_CCDC138


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
LIMS1ILK, RBBP8, LPXN, EHMT2, ACP6, NCK2, STK11, HNRNPU, MBIP, MAPT, STUB1, RSU1, TYMS, MYO18A, PARVA, PARVB, CMAS, SRRT, RABGAP1, REPS1, MYH7, PXN, TRIP6, BMP2K, PARVG, KIF22, XRCC5, TMEM132A, SGOL1, ASPM, SNW1, CDC5L, MYH4CCDC138SAV1, STX12, DCTN2, BTRC, CEP63, KIAA0753, CCDC14, MED4, CEP290, CEP162, PCM1, SSX2IP, AHI1, OFD1, CC2D2A, CEP170, CEP104, CEP120, CEP152, SPICE1, CEP128, CEP135, CEP89, CNTRL, NINL, NIN, ODF2, RPGRIP1L, SCLT1, POC5, LCA5, SASS6, CENPJ, FGFR1OP, PTPN22, TPTE2, PAK7


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 LIMS1_CCDC138


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 LIMS1_CCDC138


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