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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: 21181

FusionGeneSummary for MBD3_PALM

check button Fusion gene summary
Fusion gene informationFusion gene name: MBD3_PALM
Fusion gene ID: 21181
HgeneTgene
Gene symbol

MBD3

PALM

Gene ID

53615

5064

Gene namemethyl-CpG binding domain protein 3paralemmin
Synonyms--
Cytomap

19p13.3

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionmethyl-CpG-binding domain protein 3paralemmin-1
Modification date2018052320180523
UniProtAcc

O95983

O75781

Ensembl transtripts involved in fusion geneENST00000590550, ENST00000434436, 
ENST00000592012, ENST00000156825, 
ENST00000585967, 		ENST00000264560, 
ENST00000338448, ENST00000593172, 
Fusion gene scores* DoF score3 X 3 X 3=276 X 3 X 5=90
# samples 36
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MBD3 [Title/Abstract] AND PALM [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
TgenePALM

GO:0007194

negative regulation of adenylate cyclase activity

16386234

TgenePALM

GO:0051491

positive regulation of filopodium assembly

14978216

TgenePALM

GO:0060160

negative regulation of dopamine receptor signaling pathway

16386234


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
TCGALDACCTCGA-OR-A5JY-01AMBD3chr19

1582621

-PALMchr19

726138

+
* 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-shiftENST00000590550ENST00000264560MBD3chr19

1582621

-PALMchr19

726138

+
Frame-shiftENST00000590550ENST00000338448MBD3chr19

1582621

-PALMchr19

726138

+
5CDS-intronENST00000590550ENST00000593172MBD3chr19

1582621

-PALMchr19

726138

+
Frame-shiftENST00000434436ENST00000264560MBD3chr19

1582621

-PALMchr19

726138

+
Frame-shiftENST00000434436ENST00000338448MBD3chr19

1582621

-PALMchr19

726138

+
5CDS-intronENST00000434436ENST00000593172MBD3chr19

1582621

-PALMchr19

726138

+
Frame-shiftENST00000592012ENST00000264560MBD3chr19

1582621

-PALMchr19

726138

+
Frame-shiftENST00000592012ENST00000338448MBD3chr19

1582621

-PALMchr19

726138

+
5CDS-intronENST00000592012ENST00000593172MBD3chr19

1582621

-PALMchr19

726138

+
Frame-shiftENST00000156825ENST00000264560MBD3chr19

1582621

-PALMchr19

726138

+
Frame-shiftENST00000156825ENST00000338448MBD3chr19

1582621

-PALMchr19

726138

+
5CDS-intronENST00000156825ENST00000593172MBD3chr19

1582621

-PALMchr19

726138

+
5UTR-3CDSENST00000585967ENST00000264560MBD3chr19

1582621

-PALMchr19

726138

+
5UTR-3CDSENST00000585967ENST00000338448MBD3chr19

1582621

-PALMchr19

726138

+
5UTR-intronENST00000585967ENST00000593172MBD3chr19

1582621

-PALMchr19

726138

+

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FusionProtFeatures for MBD3_PALM


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MBD3

O95983

PALM

O75781

Acts as transcriptional repressor and plays a role ingene silencing. Does not bind to DNA by itself (PubMed:12124384).Binds to DNA with a preference for sites containing methylated CpGdinucleotides (in vitro). Binds to a lesser degree DNA containingunmethylated CpG dinucleotides (PubMed:24307175). Recruits histonedeacetylases and DNA methyltransferases.{ECO:0000269|PubMed:10947852, ECO:0000269|PubMed:12124384,ECO:0000269|PubMed:18644863, ECO:0000269|PubMed:23361464,ECO:0000269|PubMed:24307175, ECO:0000269|PubMed:9774669}. Involved in plasma membrane dynamics and cell processformation. Isoform 1 and isoform 2 are necessary for axonal anddendritic filopodia induction, for dendritic spine maturation andsynapse formation in a palmitoylation-dependent manner.{ECO:0000269|PubMed:14978216}.

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 MBD3_PALM


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 MBD3_PALM


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
MBD3MBD3L1, MBD3, MBD2, CHD4, MTA2, HDAC1, HDAC2, AURKA, GATAD2A, GATAD2B, RBBP7, RBBP4, MECOM, TRIM27, MTA3, SRRM2, SIN3A, SMARCA2, TAF6, BCL11B, BCL11A, MBD3L2, BCL6, PCNT, DDX5, JUN, PARK7, HIC1, CDK2AP1, KDM1A, MTA1, TET1, SMARCA4, SOX2, KDM5B, ELAVL1, NR2C1, DNMT1, TAB2, CHD3, SMARCA5, BAZ1B, EWSR1, HNRNPM, FUS, IGBP1, INO80, DDX3X, DDB1, HIST3H3, MMS19, RARA, ZBTB16, CEP250, GOLGA2, ICA1, KRT15, SDCBP, ZNF277, TRIM54, RCN3, CEP76, ZNF219, PHF20L1, INSL3, FAM219A, ZBTB46, CHD5, KMT2A, ATF7, HIST1H3E, KPNA1, ZMYND8, NANOG, POU5F1, NFATC2, TXNIP, TCF19, L3MBTL2, ZBED1, ZNF800, CPNE5, UHRF2PALMPOT1, SLC25A41, HOXB5, FYTTD1, RABGGTB, TMEM185A, TMEM17, DBN1, FLNA, SYNPO, CTDSPL, PTPRG, MED21, GJB7, DUSP22, TRIM25


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 MBD3_PALM


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 MBD3_PALM


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMBD3C0004352Autistic Disorder1CTD_human