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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: 29945

FusionGeneSummary for RAB25_PMF1

check button Fusion gene summary
Fusion gene informationFusion gene name: RAB25_PMF1
Fusion gene ID: 29945
HgeneTgene
Gene symbol

RAB25

PMF1

Gene ID

57111

100527963

Gene nameRAB25, member RAS oncogene familyPMF1-BGLAP readthrough
SynonymsCATX-8|RAB11CPMF1
Cytomap

1q22

1q22

Type of geneprotein-codingprotein-coding
Descriptionras-related protein Rab-25PMF1-BGLAP proteinpolyamine-modulated factor 1
Modification date2018052320180519
UniProtAcc

P57735

Q6P1K2

Ensembl transtripts involved in fusion geneENST00000361084, ENST00000487325, 
ENST00000368279, ENST00000368273, 
ENST00000368277, ENST00000565805, 
ENST00000567140, 
Fusion gene scores* DoF score2 X 1 X 2=43 X 3 X 3=27
# samples 23
** MAII scorelog2(2/4*10)=2.32192809488736log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RAB25 [Title/Abstract] AND PMF1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationOncogene involved fusion gene, in-frame and retained their domain.
Tumor suppressor gene involved fusion gene, in-frame but not retained their domain.
Tumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
* 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
HgeneRAB25

GO:0008284

positive regulation of cell proliferation

15502842

HgeneRAB25

GO:0031268

pseudopodium organization

17925226


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
TCGALDLUSCTCGA-39-5037-01ARAB25chr1

156031234

+PMF1chr1

156202111

+
* 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-shitENST00000361084ENST00000368279RAB25chr1

156031234

+PMF1chr1

156202111

+
5CDS-intronENST00000361084ENST00000368273RAB25chr1

156031234

+PMF1chr1

156202111

+
5CDS-intronENST00000361084ENST00000368277RAB25chr1

156031234

+PMF1chr1

156202111

+
5CDS-intronENST00000361084ENST00000565805RAB25chr1

156031234

+PMF1chr1

156202111

+
5CDS-intronENST00000361084ENST00000567140RAB25chr1

156031234

+PMF1chr1

156202111

+
3UTR-3CDSENST00000487325ENST00000368279RAB25chr1

156031234

+PMF1chr1

156202111

+
3UTR-intronENST00000487325ENST00000368273RAB25chr1

156031234

+PMF1chr1

156202111

+
3UTR-intronENST00000487325ENST00000368277RAB25chr1

156031234

+PMF1chr1

156202111

+
3UTR-intronENST00000487325ENST00000565805RAB25chr1

156031234

+PMF1chr1

156202111

+
3UTR-intronENST00000487325ENST00000567140RAB25chr1

156031234

+PMF1chr1

156202111

+

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FusionProtFeatures for RAB25_PMF1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RAB25

P57735

PMF1

Q6P1K2

Involved in the regulation of cell survival. Promotesinvasive migration of cells in which it functions to localize andmaintain integrin alpha-V/beta-1 at the tips of extendingpseudopodia (PubMed:17925226). Involved in the regulation ofepithelial morphogenesis through the control of CLDN4 expressionand localization at tight junctions (By similarity). Mayselectively regulate the apical recycling pathway. Together withMYO5B regulates transcytosis (By similarity).{ECO:0000250|UniProtKB:E2RQ15, ECO:0000250|UniProtKB:P46629,ECO:0000250|UniProtKB:Q9WTL2, ECO:0000269|PubMed:17925226}.

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 RAB25_PMF1


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 RAB25_PMF1


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
RAB25PKIG, KPTN, AP2S1, RAB11FIP1, RAB11FIP2, RAB11FIP3, RAB11FIP5, ATP4A, MYO5B, OPTN, RAB11B, RAB11A, PDE4DIP, CDK15, FAM60APMF1NFE2L2, MIS12, DSN1, GDF9, KIAA1377, MED31, CRMP1, PTN, COPS6, GIT1, COPS7A, SUGT1, HSP90AA1, TCP10L, KDM1A, USHBP1, BUB1B, NSMCE1, NSL1, ZWINT, SGTB, SEC63, PGRMC2, ZRANB1, WDR45B, GNPAT, PPP1CC, ZMPSTE24, CMTM6, GFER, TALDO1, SPC24, SPC25, CASC5, NUF2, KIF21B, BICD2, RUFY2, GCC2, NDC80, ZC4H2, CEP89, FBXO28, RUFY1, TSNAX, ATG16L1, NRBF2, ALOX5, MLLT10, CENPC, RGPD8, STXBP4, MLF1, TRIM25, UBE2S


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 RAB25_PMF1


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 RAB25_PMF1


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