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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: 20441

FusionGeneSummary for LYAR_CTBP1

check button Fusion gene summary
Fusion gene informationFusion gene name: LYAR_CTBP1
Fusion gene ID: 20441
HgeneTgene
Gene symbol

LYAR

CTBP1

Gene ID

55646

1487

Gene nameLy1 antibody reactiveC-terminal binding protein 1
SynonymsZC2HC2|ZLYARBARS|HADDTS
Cytomap

4p16.3

4p16.3

Type of geneprotein-codingprotein-coding
Descriptioncell growth-regulating nucleolar proteinLy1 antibody reactive homologC-terminal-binding protein 1brefeldin A-ribosylated substrate
Modification date2018051920180522
UniProtAcc

Q9NX58

Q13363

Ensembl transtripts involved in fusion geneENST00000343470, ENST00000452476, 
ENST00000382952, ENST00000290921, 
ENST00000510568, ENST00000515690, 
Fusion gene scores* DoF score4 X 4 X 2=328 X 7 X 8=448
# samples 412
** MAII scorelog2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(12/448*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LYAR [Title/Abstract] AND CTBP1 [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

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
TCGALDOVTCGA-25-2391-01ALYARchr4

4285348

-CTBP1chr4

1222131

-
* 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-shiftENST00000343470ENST00000382952LYARchr4

4285348

-CTBP1chr4

1222131

-
Frame-shiftENST00000343470ENST00000290921LYARchr4

4285348

-CTBP1chr4

1222131

-
5CDS-intronENST00000343470ENST00000510568LYARchr4

4285348

-CTBP1chr4

1222131

-
5CDS-intronENST00000343470ENST00000515690LYARchr4

4285348

-CTBP1chr4

1222131

-
Frame-shiftENST00000452476ENST00000382952LYARchr4

4285348

-CTBP1chr4

1222131

-
Frame-shiftENST00000452476ENST00000290921LYARchr4

4285348

-CTBP1chr4

1222131

-
5CDS-intronENST00000452476ENST00000510568LYARchr4

4285348

-CTBP1chr4

1222131

-
5CDS-intronENST00000452476ENST00000515690LYARchr4

4285348

-CTBP1chr4

1222131

-

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FusionProtFeatures for LYAR_CTBP1


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

Q9NX58

CTBP1

Q13363

Plays a role in the maintenance of the appropriateprocessing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and theirsubsequent processing to produce 18S and 28S rRNAs(PubMed:24495227). Also acts at the level of transcriptionregulation. Along with PRMT5, binds the gamma-globin (HBG1/HBG2)promoter and represses its expression (PubMed:25092918). Inneuroblastoma cells, may also repress the expression of oxidativestress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and SNORD41that encodes a small nucleolar RNA (PubMed:28686580).Preferentially binds to a DNA motif containing 5'-GGTTAT-3'(PubMed:25092918). Stimulates phagocytosis of photoreceptor outersegments by retinal pigment epithelial cells (By similarity).Prevents nucleolin/NCL self-cleavage, maintaining a normal steady-state level of NCL protein in undifferentiated embryonic stemcells (ESCs), which in turn is essential for ESC self-renewal (Bysimilarity). {ECO:0000250|UniProtKB:Q08288,ECO:0000269|PubMed:24495227, ECO:0000269|PubMed:25092918,ECO:0000269|PubMed:28686580}. Corepressor targeting diverse transcription regulatorssuch as GLIS2 or BCL6. Has dehydrogenase activity. Involved incontrolling the equilibrium between tubular and stacked structuresin the Golgi complex. Functions in brown adipose tissue (BAT)differentiation. {ECO:0000269|PubMed:12419229,ECO:0000269|PubMed:15542832, ECO:0000269|PubMed:18212045,ECO:0000269|PubMed:19103759, ECO:0000269|PubMed:9858600}.

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 LYAR_CTBP1


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 LYAR_CTBP1


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
LYARRPL23A, MYBBP1A, TWF2, KRT85, DHX57, RPL3, TSR1, BRIX1, KRT31, RPS9, GTPBP4, RPL18A, DHX9, RPS3A, RPL21, NAT10, NPM1, GNL2, DDX27, EIF3I, KRT82, EBNA1BP2, RPL31, KPNA1, SRP14, DDX21, ZHX1, ZBTB16, NOP56, OAS3, EIF2AK2, HDGF, TERF1, TERF2, CUL3, CUL1, COPS5, CAND1, GRK5, ESR1, MDC1, PAXIP1, VCP, FGF18, CD2, PHF20L1, ADSSL1, PRKRA, SDCBP2, BEND7, PHF6, RNF2, PRR11, ILF2, EPB41L3, ERCC4, IFI16, CEP152, HNRNPU, NCBP1, RPL10, RFWD3, FAM83H, RNF138, ZNF746, RPL37A, MAGEB10, RPL30, NCL, BRD1CTBP1PNN, IKZF1, SMAD6, RBBP8, TGIF1, NRIP1, MDM2, HDAC1, HDAC3, HDAC4, HDAC5, HDAC9, BRCA1, HDAC2, KAT2B, GEMIN2, TBP, GTF2B, FOXP1, FOXP2, KMT2A, CBX4, MECOM, IKZF4, CTBP2, ZEB1, ACTL6B, HTT, TBL1X, ZNF217, RCOR1, SATB1, CTBP1, TCF4, LCOR, TP53, HIC1, EHMT2, EHMT1, WIZ, APC, PLK1, TUBG1, HSD11B2, TCF7L2, KDM1A, CREBBP, EP300, KAT2A, SP1, RREB1, CDYL, UBE2I, BCORL1, SERPINH1, BCL3, AKT1, HIST3H3, SPEN, ZBP1, SOBP, ZNF219, LCORL, CHD3, RBBP5, CTNNA1, SOX2, ELAVL1, ZEB2, TERF2IP, TERF2, TFAP4, ATXN1L, BCL6, NCOR2, ECT2, CTNNB1, KLF4, DNMT1, RUNX1, BAG3, THAP11, HEMGN, NME2, ORC4, ARNT2, NOL4L, KLF12, MARCH10, CDC23, FUNDC1, IKZF2, KLF3, LNX1, PIAS2, RAI2, RNF111, ZBTB18, CEP68, NOL4, DGCR6, SNRPN, CRY2, HOXB5, PRKAA1, MAPK9, PLCB1, BCAS3, TSHZ3, DMRTB1, EGFR, HIC2, PRDM2, ZNF516, DYRK1A, TRPS1, C10orf12, BCOR, FBXO11, RCOR2, RCOR3, C2orf44, RBL1, INA, RB1, E2F7, TRMT61B, FOXK1, C15orf39, AMPD2, TOR2A, ADSS, ATIC, CARM1, CTH, ECHS1, FKBP1A, GAPDH, DUT, HYI, SSNA1, WDR1, NTRK1, MED23, OFD1, FBF1, KCNIP3, KLF8, NFATC1, NFATC2, MTMR7, RBM14-RBM4, IGFBP1, CHD4, NISCH, KIAA0430, HELZ, PCGF5, SOWAHA, PAN2, EIF4ENIF1, FANCC, FANCA, FANCF, FANCG, FANCL, FANCE, FANCD2, 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 LYAR_CTBP1


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 LYAR_CTBP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCTBP1C0009404Colorectal Neoplasms1CTD_human