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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: 33052

FusionGeneSummary for SEC24B_MALAT1

check button Fusion gene summary
Fusion gene informationFusion gene name: SEC24B_MALAT1
Fusion gene ID: 33052
HgeneTgene
Gene symbol

SEC24B

MALAT1

Gene ID

10427

378938

Gene nameSEC24 homolog B, COPII coat complex componentmetastasis associated lung adenocarcinoma transcript 1
SynonymsSEC24HCN|LINC00047|NCRNA00047|NEAT2|PRO2853
Cytomap

4q25

11q13.1

Type of geneprotein-codingncRNA
Descriptionprotein transport protein Sec24BSEC24 related gene family, member Bsecretory protein 24hepcarcinlong intergenic non-protein coding RNA 47metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)nuclear enriched abundant transcript 2nuclear paraspeckle assembly transcript 2 (non-protein coding)
Modification date2018051920180527
UniProtAcc

O95487

Ensembl transtripts involved in fusion geneENST00000504968, ENST00000399100, 
ENST00000265175, 
ENST00000534336, 
Fusion gene scores* DoF score2 X 2 X 1=471 X 110 X 1=7810
# samples 2126
** MAII scorelog2(2/4*10)=2.32192809488736log2(126/7810*10)=-2.63189881464206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SEC24B [Title/Abstract] AND MALAT1 [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
HgeneSEC24B

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296


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
ChiTaRS3.1AV726458SEC24Bchr4

110384622

+MALAT1chr11

65270650

+
* 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-3UTRENST00000504968ENST00000534336SEC24Bchr4

110384622

+MALAT1chr11

65270650

+
5CDS-3UTRENST00000399100ENST00000534336SEC24Bchr4

110384622

+MALAT1chr11

65270650

+
5CDS-3UTRENST00000265175ENST00000534336SEC24Bchr4

110384622

+MALAT1chr11

65270650

+

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FusionProtFeatures for SEC24B_MALAT1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SEC24B

O95487

MALAT1

Component of the coat protein complex II (COPII) whichpromotes the formation of transport vesicles from the endoplasmicreticulum (ER). The coat has two main functions, the physicaldeformation of the endoplasmic reticulum membrane into vesiclesand the selection of cargo molecules for their transport to theGolgi complex (PubMed:17499046, PubMed:20427317, PubMed:18843296).Plays a central role in cargo selection within the COPII complexand together with SEC24A may have a different specificity comparedto SEC24C and SEC24D. May package preferentially cargos withcytoplasmic DxE or LxxLE motifs and may also recognizeconformational epitopes (PubMed:17499046, PubMed:18843296).{ECO:0000269|PubMed:17499046, ECO:0000269|PubMed:18843296,ECO:0000269|PubMed:20427317}. Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}.

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 SEC24B_MALAT1


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 SEC24B_MALAT1


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 SEC24B_MALAT1


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 SEC24B_MALAT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneMALAT1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneMALAT1C0023903Liver neoplasms1CTD_human
TgeneMALAT1C0027626Neoplasm Invasiveness1CTD_human
TgeneMALAT1C0027627Neoplasm Metastasis1CTD_human
TgeneMALAT1C0032460Polycystic Ovary Syndrome1CTD_human
TgeneMALAT1C0236663Alcohol withdrawal syndrome1PSYGENET
TgeneMALAT1C0279626Squamous cell carcinoma of esophagus1CTD_human