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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: 42232

FusionGeneSummary for XRN1_GNPTAB

check button Fusion gene summary
Fusion gene informationFusion gene name: XRN1_GNPTAB
Fusion gene ID: 42232
HgeneTgene
Gene symbol

XRN1

GNPTAB

Gene ID

54464

79158

Gene name5'-3' exoribonuclease 1N-acetylglucosamine-1-phosphate transferase subunits alpha and beta
SynonymsSEP1GNPTA|ICD
Cytomap

3q23

12q23.2

Type of geneprotein-codingprotein-coding
Description5'-3' exoribonuclease 1strand-exchange protein 1 homologN-acetylglucosamine-1-phosphotransferase subunits alpha/betaGlcNAc phosphotransferaseN-acetylglucosamine-1-phosphate transferase alpha and beta subunitsUDP-N-acetylglucosamine-1-phosphotransferase subunits alpha/betaUDP-N-acetylglucosamine-lysosomal-e
Modification date2018051920180523
UniProtAcc

Q8IZH2

Q3T906

Ensembl transtripts involved in fusion geneENST00000264951, ENST00000392981, 
ENST00000463916, ENST00000544157, 
ENST00000465074, 
ENST00000299314, 
ENST00000549940, ENST00000392919, 
ENST00000549165, 
Fusion gene scores* DoF score6 X 5 X 6=1807 X 8 X 4=224
# samples 79
** MAII scorelog2(7/180*10)=-1.36257007938471
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/224*10)=-1.31550182572793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: XRN1 [Title/Abstract] AND GNPTAB [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
TgeneGNPTAB

GO:0046835

carbohydrate phosphorylation

19955174|23733939


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
ChiTaRS3.1AI871771XRN1chr3

142029034

-GNPTABchr12

102139580

-
ChiTaRS3.1BE671625XRN1chr3

142029034

-GNPTABchr12

102139580

-
* 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-3UTRENST00000264951ENST00000299314XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000264951ENST00000549940XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000264951ENST00000392919XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000264951ENST00000549165XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-3UTRENST00000392981ENST00000299314XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000392981ENST00000549940XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000392981ENST00000392919XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000392981ENST00000549165XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-3UTRENST00000463916ENST00000299314XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000463916ENST00000549940XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000463916ENST00000392919XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000463916ENST00000549165XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-3UTRENST00000544157ENST00000299314XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000544157ENST00000549940XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000544157ENST00000392919XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000544157ENST00000549165XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-3UTRENST00000465074ENST00000299314XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000465074ENST00000549940XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000465074ENST00000392919XRN1chr3

142029034

-GNPTABchr12

102139580

-
intron-intronENST00000465074ENST00000549165XRN1chr3

142029034

-GNPTABchr12

102139580

-

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FusionProtFeatures for XRN1_GNPTAB


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
XRN1

Q8IZH2

GNPTAB

Q3T906

Major 5'-3' exoribonuclease involved in mRNA decay.Required for the 5'-3'-processing of the G4 tetraplex-containingDNA and RNA substrates. The kinetic of hydrolysis is faster for G4RNA tetraplex than for G4 DNA tetraplex and monomeric RNAtetraplex. Binds to RNA and DNA (By similarity). Plays a role inreplication-dependent histone mRNA degradation. May act as a tumorsuppressor protein in osteogenic sarcoma (OGS).{ECO:0000250|UniProtKB:P97789, ECO:0000269|PubMed:18172165}. Catalyzes the formation of mannose 6-phosphate (M6P)markers on high mannose type oligosaccharides in the Golgiapparatus. M6P residues are required to bind to the M6P receptors(MPR), which mediate the vesicular transport of lysosomal enzymesto the endosomal/prelysosomal compartment.{ECO:0000269|PubMed:19955174, ECO:0000269|PubMed:23733939,ECO:0000269|PubMed:28918368}.

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 XRN1_GNPTAB


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 XRN1_GNPTAB


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 XRN1_GNPTAB


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 XRN1_GNPTAB


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneGNPTABC0033788Pseudo-Hurler Polydystrophy14CTD_human;ORPHANET;UNIPROT
TgeneGNPTABC2673377MUCOLIPIDOSIS II ALPHA/BETA (disorder)10CTD_human;UNIPROT