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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: 32336

FusionGeneSummary for RTFDC1_CALR

check button Fusion gene summary
Fusion gene informationFusion gene name: RTFDC1_CALR
Fusion gene ID: 32336
HgeneTgene
Gene symbol

RTFDC1

CALR

Gene ID

811

Gene namecalreticulin
SynonymsCRT|HEL-S-99n|RO|SSA|cC1qR
Cytomap

19p13.13

Type of geneprotein-coding
DescriptioncalreticulinCRP55ERp60HACBPSicca syndrome antigen A (autoantigen Ro; calreticulin)calregulinendoplasmic reticulum resident protein 60epididymis secretory sperm binding protein Li 99ngrp60
Modification date20180527
UniProtAcc

Q9BY42

P27797

Ensembl transtripts involved in fusion geneENST00000023939, ENST00000395881, 
ENST00000357348, ENST00000484084, 
ENST00000435342, 
ENST00000316448, 
Fusion gene scores* DoF score5 X 4 X 3=6012 X 15 X 3=540
# samples 618
** MAII scorelog2(6/60*10)=0log2(18/540*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RTFDC1 [Title/Abstract] AND CALR [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
TgeneCALR

GO:0000122

negative regulation of transcription by RNA polymerase II

8107809

TgeneCALR

GO:0006611

protein export from nucleus

11149926

TgeneCALR

GO:0017148

negative regulation of translation

14726956

TgeneCALR

GO:0033144

negative regulation of intracellular steroid hormone receptor signaling pathway

8107809

TgeneCALR

GO:0034504

protein localization to nucleus

15998798

TgeneCALR

GO:0045665

negative regulation of neuron differentiation

8107809

TgeneCALR

GO:0045892

negative regulation of transcription, DNA-templated

8107809

TgeneCALR

GO:0048387

negative regulation of retinoic acid receptor signaling pathway

8107809


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
ChiTaRS3.1BC072002RTFDC1chr20

55089631

-CALRchr19

13049436

+
ChiTaRS3.1BU839262RTFDC1chr20

55089631

-CALRchr19

13049436

+
* 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-5UTRENST00000023939ENST00000316448RTFDC1chr20

55089631

-CALRchr19

13049436

+
intron-5UTRENST00000395881ENST00000316448RTFDC1chr20

55089631

-CALRchr19

13049436

+
intron-5UTRENST00000357348ENST00000316448RTFDC1chr20

55089631

-CALRchr19

13049436

+
intron-5UTRENST00000484084ENST00000316448RTFDC1chr20

55089631

-CALRchr19

13049436

+
intron-5UTRENST00000435342ENST00000316448RTFDC1chr20

55089631

-CALRchr19

13049436

+

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FusionProtFeatures for RTFDC1_CALR


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RTFDC1

Q9BY42

CALR

P27797

Calcium-binding chaperone that promotes folding,oligomeric assembly and quality control in the endoplasmicreticulum (ER) via the calreticulin/calnexin cycle. This lectininteracts transiently with almost all of the monoglucosylatedglycoproteins that are synthesized in the ER. Interacts with theDNA-binding domain of NR3C1 and mediates its nuclear export.Involved in maternal gene expression regulation. May participatein oocyte maturation via the regulation of calcium homeostasis (Bysimilarity). {ECO:0000250, ECO:0000269|PubMed:11149926,ECO:0000269|PubMed:7876246}.

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 RTFDC1_CALR


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 RTFDC1_CALR


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 RTFDC1_CALR


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCALRP27797DB00031TenecteplaseCalreticulinbiotechapproved
TgeneCALRP27797DB11093Calcium CitrateCalreticulinsmall moleculeapproved
TgeneCALRP27797DB11348Calcium PhosphateCalreticulinsmall moleculeapproved
TgeneCALRP27797DB00025Antihemophilic factor, human recombinantCalreticulinbiotechapproved|investigational
TgeneCALRP27797DB01065MelatoninCalreticulinsmall moleculeapproved|nutraceutical|vet_approved

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RelatedDiseases for RTFDC1_CALR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCALRC0033975Psychotic Disorders2PSYGENET
TgeneCALRC0036337Schizoaffective Disorder2PSYGENET
TgeneCALRC0349204Nonorganic psychosis2PSYGENET
TgeneCALRC0005586Bipolar Disorder1PSYGENET
TgeneCALRC0009404Colorectal Neoplasms1CTD_human
TgeneCALRC0025205Melanoma, Experimental1CTD_human
TgeneCALRC0027626Neoplasm Invasiveness1CTD_human
TgeneCALRC0033578Prostatic Neoplasms1CTD_human
TgeneCALRC0033937Psychoses, Drug1PSYGENET
TgeneCALRC0036349Paranoid Schizophrenia1PSYGENET
TgeneCALRC0036939Shared Paranoid Disorder1PSYGENET
TgeneCALRC0151744Myocardial Ischemia1CTD_human
TgeneCALRC0279626Squamous cell carcinoma of esophagus1CTD_human