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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: 42375

FusionGeneSummary for YTHDC1_RBM25

check button Fusion gene summary
Fusion gene informationFusion gene name: YTHDC1_RBM25
Fusion gene ID: 42375
HgeneTgene
Gene symbol

YTHDC1

RBM25

Gene ID

91746

58517

Gene nameYTH domain containing 1RNA binding motif protein 25
SynonymsYT521|YT521-BNET52|RED120|RNPC7|S164|Snu71|fSAP94
Cytomap

4q13.2

14q24.2

Type of geneprotein-codingprotein-coding
DescriptionYTH domain-containing protein 1putative splicing factor YT521splicing factor YT521splicing factor YT521-BRNA-binding protein 25Arg/Glu/Asp-rich protein, 120 kDaRNA-binding region (RNP1, RRM) containing 7RNA-binding region-containing protein 7U1 small nuclear ribonucleoprotein 1SNRP homologarg/Glu/Asp-rich protein of 120 kDafunctional spliceosome-associ
Modification date2018051920180523
UniProtAcc

Q96MU7

P49756

Ensembl transtripts involved in fusion geneENST00000344157, ENST00000355665, 
ENST00000579690, ENST00000552105, 
ENST00000550485, 		ENST00000261973, 
ENST00000540173, ENST00000527432, 
ENST00000525321, ENST00000526754, 
ENST00000532483, 
Fusion gene scores* DoF score9 X 9 X 4=3246 X 10 X 5=300
# samples 911
** MAII scorelog2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/300*10)=-1.44745897697122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: YTHDC1 [Title/Abstract] AND RBM25 [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
HgeneYTHDC1

GO:0006376

mRNA splice site selection

20167602

HgeneYTHDC1

GO:0048024

regulation of mRNA splicing, via spliceosome

26876937

TgeneRBM25

GO:0000381

regulation of alternative mRNA splicing, via spliceosome

18663000

TgeneRBM25

GO:0042981

regulation of apoptotic process

18663000


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
ChiTaRS3.1CN350716YTHDC1chr4

33924

-RBM25chr14

73572681

+
* 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-3CDSENST00000344157ENST00000261973YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000344157ENST00000540173YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000344157ENST00000527432YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000344157ENST00000525321YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000344157ENST00000526754YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000344157ENST00000532483YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-3CDSENST00000355665ENST00000261973YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000355665ENST00000540173YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000355665ENST00000527432YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000355665ENST00000525321YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000355665ENST00000526754YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000355665ENST00000532483YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-3CDSENST00000579690ENST00000261973YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000579690ENST00000540173YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000579690ENST00000527432YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000579690ENST00000525321YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000579690ENST00000526754YTHDC1chr4

33924

-RBM25chr14

73572681

+
intron-intronENST00000579690ENST00000532483YTHDC1chr4

33924

-RBM25chr14

73572681

+
Frame-shiftENST00000552105ENST00000261973YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000552105ENST00000540173YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000552105ENST00000527432YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000552105ENST00000525321YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000552105ENST00000526754YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000552105ENST00000532483YTHDC1chr4

33924

-RBM25chr14

73572681

+
Frame-shiftENST00000550485ENST00000261973YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000550485ENST00000540173YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000550485ENST00000527432YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000550485ENST00000525321YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000550485ENST00000526754YTHDC1chr4

33924

-RBM25chr14

73572681

+
5CDS-intronENST00000550485ENST00000532483YTHDC1chr4

33924

-RBM25chr14

73572681

+

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FusionProtFeatures for YTHDC1_RBM25


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
YTHDC1

Q96MU7

RBM25

P49756

Regulator of alternative splicing that specificallyrecognizes and binds N6-methyladenosine (m6A)-containing RNAs(PubMed:26318451, PubMed:26876937, PubMed:25242552,PubMed:28984244). M6A is a modification present at internal sitesof mRNAs and some non-coding RNAs and plays a role in theefficiency of mRNA splicing, processing and stability(PubMed:26318451, PubMed:25242552). Acts as a key regulator ofexon-inclusion or exon-skipping during alternative splicing viainteraction with mRNA splicing factors SRSF3 and SRSF10(PubMed:26876937). Specifically binds m6A-containing mRNAs andpromotes recruitment of SRSF3 to its mRNA-binding elementsadjacent to m6A sites, leading to exon-inclusion duringalternative splicing (PubMed:26876937). In contrast, interactionwith SRSF3 prevents interaction with SRSF10, a splicing factorthat promotes exon skipping: this prevents SRSF10 from binding toits mRNA-binding sites close to m6A-containing regions, leading toinhibit exon skipping during alternative splicing(PubMed:26876937). May also regulate alternative splice siteselection (PubMed:20167602). Also involved in nuclear export ofm6A-containing mRNAs via interaction with SRSF3: interaction withSRSF3 facilitates m6A-containing mRNA-binding to both SRSF3 andNXF1, promoting mRNA nuclear export (PubMed:28984244). Alsorecognizes and binds m6A on other RNA molecules (PubMed:27602518).Involved in random X inactivation mediated by Xist RNA: recognizesand binds m6A-containing Xist and promotes transcriptionrepression activity of Xist (PubMed:27602518). Involved in S-adenosyl-L-methionine homeostasis by regulating expression ofMAT2A transcripts, probably by binding m6A-containing MAT2A mRNAs(By similarity). {ECO:0000250|UniProtKB:E9Q5K9,ECO:0000269|PubMed:20167602, ECO:0000269|PubMed:25242552,ECO:0000269|PubMed:26318451, ECO:0000269|PubMed:26876937,ECO:0000269|PubMed:27602518, ECO:0000269|PubMed:28984244}.

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 YTHDC1_RBM25


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 YTHDC1_RBM25


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


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 YTHDC1_RBM25


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 YTHDC1_RBM25


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