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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: 29831

FusionGeneSummary for R3HDM1_YTHDC1

check button Fusion gene summary
Fusion gene informationFusion gene name: R3HDM1_YTHDC1
Fusion gene ID: 29831
HgeneTgene
Gene symbol

R3HDM1

YTHDC1

Gene ID

23518

91746

Gene nameR3H domain containing 1YTH domain containing 1
SynonymsR3HDMYT521|YT521-B
Cytomap

2q21.3

4q13.2

Type of geneprotein-codingprotein-coding
DescriptionR3H domain-containing protein 1R3H domain (binds single-stranded nucleic acids) containingYTH domain-containing protein 1putative splicing factor YT521splicing factor YT521splicing factor YT521-B
Modification date2018051920180519
UniProtAcc

Q15032

Q96MU7

Ensembl transtripts involved in fusion geneENST00000409478, ENST00000329971, 
ENST00000264160, ENST00000410054, 
ENST00000409606, ENST00000443537, 
ENST00000344157, ENST00000355665, 
ENST00000579690, ENST00000552105, 
ENST00000550485, 
Fusion gene scores* DoF score3 X 3 X 1=95 X 5 X 2=50
# samples 35
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/50*10)=0
Context

PubMed: R3HDM1 [Title/Abstract] AND YTHDC1 [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
TgeneYTHDC1

GO:0006376

mRNA splice site selection

20167602

TgeneYTHDC1

GO:0048024

regulation of mRNA splicing, via spliceosome

26876937


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
ChiTaRS3.1BF798521R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
* 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
5CDS-intronENST00000409478ENST00000344157R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409478ENST00000355665R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409478ENST00000579690R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409478ENST00000552105R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409478ENST00000550485R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000329971ENST00000344157R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000329971ENST00000355665R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000329971ENST00000579690R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000329971ENST00000552105R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000329971ENST00000550485R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000264160ENST00000344157R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000264160ENST00000355665R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000264160ENST00000579690R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000264160ENST00000552105R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000264160ENST00000550485R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000410054ENST00000344157R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000410054ENST00000355665R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000410054ENST00000579690R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000410054ENST00000552105R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000410054ENST00000550485R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409606ENST00000344157R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409606ENST00000355665R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409606ENST00000579690R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409606ENST00000552105R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
5CDS-intronENST00000409606ENST00000550485R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
intron-intronENST00000443537ENST00000344157R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
intron-intronENST00000443537ENST00000355665R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
intron-intronENST00000443537ENST00000579690R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
intron-intronENST00000443537ENST00000552105R3HDM1chr2

136432942

+YTHDC1chr4

15815

-
intron-intronENST00000443537ENST00000550485R3HDM1chr2

136432942

+YTHDC1chr4

15815

-

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FusionProtFeatures for R3HDM1_YTHDC1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
R3HDM1

Q15032

YTHDC1

Q96MU7

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 R3HDM1_YTHDC1


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 R3HDM1_YTHDC1


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 R3HDM1_YTHDC1


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 R3HDM1_YTHDC1


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