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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: 19717

FusionGeneSummary for LIMA1_RGL1

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMA1_RGL1
Fusion gene ID: 19717
HgeneTgene
Gene symbol

LIMA1

RGL1

Gene ID

51474

64333

Gene nameLIM domain and actin binding 1Rho GTPase activating protein 9
SynonymsEPLIN|SREBP310C|RGL1
Cytomap

12q13.12

12q13.3

Type of geneprotein-codingprotein-coding
DescriptionLIM domain and actin-binding protein 11110021C24Rikepithelial protein lost in neoplasm betasterol regulatory element binding protein 3rho GTPase-activating protein 9rho-type GTPase-activating protein 9
Modification date2018052220180523
UniProtAcc

Q9UHB6

Q9NZL6

Ensembl transtripts involved in fusion geneENST00000552491, ENST00000547825, 
ENST00000552823, ENST00000394943, 
ENST00000341247, ENST00000552783, 
ENST00000552909, ENST00000552008, 
ENST00000304685, ENST00000536277, 
ENST00000360851, ENST00000539189, 
Fusion gene scores* DoF score7 X 5 X 5=1756 X 5 X 5=150
# samples 76
** MAII scorelog2(7/175*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/150*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LIMA1 [Title/Abstract] AND RGL1 [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
HgeneLIMA1

GO:0030835

negative regulation of actin filament depolymerization

12566430

HgeneLIMA1

GO:0031529

ruffle organization

12566430

HgeneLIMA1

GO:0051017

actin filament bundle assembly

12566430


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-13-0888-01ALIMA1chr12

50677203

-RGL1chr1

183849750

+
* 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-3CDSENST00000552491ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552491ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552491ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552491ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000547825ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000547825ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000547825ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000547825ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552823ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552823ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552823ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552823ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000394943ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000394943ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000394943ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000394943ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000341247ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000341247ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000341247ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
5UTR-3CDSENST00000341247ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552783ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552783ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552783ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552783ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552909ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552909ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552909ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552909ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552008ENST00000304685LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552008ENST00000536277LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552008ENST00000360851LIMA1chr12

50677203

-RGL1chr1

183849750

+
intron-3CDSENST00000552008ENST00000539189LIMA1chr12

50677203

-RGL1chr1

183849750

+

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FusionProtFeatures for LIMA1_RGL1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LIMA1

Q9UHB6

RGL1

Q9NZL6

Probable guanine nucleotide exchange factor.

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 LIMA1_RGL1


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 LIMA1_RGL1


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
LIMA1SVIL, ARRB1, ARRB2, LRRK2, UBXN6, APP, ATP6V1B1, PAXIP1, UBC, FMNL1, YWHAE, PAN2, YWHAQ, LRCH3, YWHAB, RPA3, RPA2, RPA1, TP53, SHMT2, MOV10, NXF1, CUL7, OBSL1, CCDC8, EZH2, SUZ12, RNF2, BMI1, EGFR, LUZP4, LRRC39, FNDC4, ZFP41, NTRK1, PTEN, HIST1H3E, ACTA1, ACTB, ACTG1, ACTN4, AP2A1, AP2A2, AP2B1, ANXA2, RHOA, DST, CALD1, CALM1, CAPZA1, CAPZB, CAV1, CD44, CDC42, CFL1, CFL2, AP2M1, CLTA, CLTB, CLTC, CPM, CSNK1G3, DAB2, DAPK3, DBN1, DSG2, EEF1D, STOM, EPS15, FER, FLNA, FLNB, FLOT2, GSN, ITPR3, JUP, KRAS, RPSA, LGALS1, ABLIM1, LYN, MYO1B, MYO1C, MYO1E, MYO5A, MYO5B, PIK3C2A, PLEC, PPP1CA, PPP1CC, TWF1, RAB1A, RAB5C, RAC1, RALA, RAP1A, RAP1B, SIPA1, SPTAN1, SPTBN1, TMOD1, TNFAIP1, TUBG1, CORO2A, YES1, LUZP1, CLTCL1, PICALM, SORBS2, EIF3H, IQGAP1, HIP1R, GPRC5A, PDLIM1, NUMBL, SH3BP5, CLINT1, TOMM20, SEC16A, WDR1, ARPC3, ARPC1B, FLOT1, BASP1, IPO7, AKAP2, TWF2, SYNPO, RRAS2, MPRIP, CYFIP1, COBL, CORO1C, ZDHHC5, PLEKHG3, DECR2, RAI14, TES, ZBTB20, PACSIN3, TMOD3, CAPZA2, CDK2, GAK, MYH9, PPP1CB, VCL, ACTR2, MAPRE1, GTSE1, ANLN, MYO5C, MYO19, MYO18A, BMP2K, PPP1R9A, DIABLO, CORO1B, ARHGAP21, DENND1A, RAP2C, AFAP1, INF2, AHNAK, EFHD2, CYBRD1, ARPC5L, KCTD10, PPP1R9B, STON2, SSH2, NEXN, SPECC1, FCHO2, MISP, CCDC50, UBXN2A, PPP1R18, TPRN, PCNXL3, BIRC3, CDH1, GSTK1, MYL6, GOPC, PLEKHG6, BCL7C, LSP1, KCTD3, KIF13B, ZBTB21, KSR1, GIGYF1, LRFN1, SH3PXD2A, SRGAP2, EIF4E2, SIPA1L1, MAGI1, TESK2, DCLK1, ZNF638, RTKN, MAST3, PPM1H, SRSF12, DENND4C, SYDE1, AGAP1, CDC25B, CDK16, FAM110B, USP21, MAPKAP1, FAM53C, ANKRD34A, CGN, FAM110A, HDAC4, NF1, CBY1, NADK, TBC1D25, TIAM1, PHLDB2, KIAA1804, RASAL2, LPIN3, CAMSAP2, GAB2, CDC25C, MELK, PLEKHA7, KIF1C, GIGYF2, NAV1, DEPDC1B, DENND4A, MLLT4, PTPN14, STARD13, RPTOR, SH3RF3, PLEKHA5, HDAC7, SH3BP4, EDC3, LARP1, OSBPL6, RAB3IP, INPP5E, PARK7, PDHA1, RNF168RGL1HRAS, APP, FBXL13


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 LIMA1_RGL1


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 LIMA1_RGL1


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