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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: 12966

FusionGeneSummary for FARSA_LYL1

check button Fusion gene summary
Fusion gene informationFusion gene name: FARSA_LYL1
Fusion gene ID: 12966
HgeneTgene
Gene symbol

FARSA

LYL1

Gene ID

2193

4066

Gene namephenylalanyl-tRNA synthetase subunit alphaLYL1, basic helix-loop-helix family member
SynonymsCML33|FARSL|FARSLA|FRSA|PheHAbHLHa18
Cytomap

19p13.13

19p13.13

Type of geneprotein-codingprotein-coding
Descriptionphenylalanine--tRNA ligase alpha subunitpheRSphenylalanine tRNA ligase 1, alpha, cytoplasmicphenylalanine--tRNA ligase alpha chainphenylalanine-tRNA synthetase alpha-subunitphenylalanine-tRNA synthetase-like, alpha subunitphenylalanyl-tRNA synthetasprotein lyl-1class A basic helix-loop-helix protein 18lymphoblastic leukemia associated hematopoiesis regulator 1lymphoblastic leukemia derived sequence 1
Modification date2018052320180523
UniProtAcc

Q9Y285

P12980

Ensembl transtripts involved in fusion geneENST00000588025, ENST00000423140, 
ENST00000314606, 
ENST00000264824, 
Fusion gene scores* DoF score4 X 4 X 4=641 X 1 X 1=1
# samples 41
** MAII scorelog2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: FARSA [Title/Abstract] AND LYL1 [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
HgeneFARSA

GO:0006432

phenylalanyl-tRNA aminoacylation

20223217

HgeneFARSA

GO:0051290

protein heterotetramerization

20223217

TgeneLYL1

GO:0006355

regulation of transcription, DNA-templated

10023675

TgeneLYL1

GO:0045893

positive regulation of transcription, DNA-templated

18160048


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
TCGARVSTADTCGA-CG-4443-01AFARSAchr19

13039156

-LYL1chr19

13210548

-
* 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-shitENST00000588025ENST00000264824FARSAchr19

13039156

-LYL1chr19

13210548

-
Frame-shitENST00000423140ENST00000264824FARSAchr19

13039156

-LYL1chr19

13210548

-
Frame-shitENST00000314606ENST00000264824FARSAchr19

13039156

-LYL1chr19

13210548

-

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FusionProtFeatures for FARSA_LYL1


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

Q9Y285

LYL1

P12980


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 FARSA_LYL1


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 FARSA_LYL1


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
FARSAUSP11, USP32, UBC, EIF2AK2, UNC93B1, CUL3, CUL1, FBXO6, A2M, ECSIT, APOE, RNF32, FARSB, EEF2, CFTR, PAN2, TDGF1, GORAB, PUS1, RPLP0, WWOX, ASB4, ABI3, EGFR, ESR1, CCT6B, NTRK1, CDC42, IRF2BP1, KIAA0368, OGT, PRPS1, PSMG2, TARS, OFD1, XRCC3, MCM2, NF2, RC3H1, WWP2, ZNF746, CYLD, DLD, SDHALYL1NFKB1, TCF4, NFKBIA, LMO1, LMO2, TCF3, TRIM33, TAL1, RHOU


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 FARSA_LYL1


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 FARSA_LYL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneLYL1C0023448Lymphoid leukemia1CTD_human
TgeneLYL1C0023467Leukemia, Myelocytic, Acute1CTD_human
TgeneLYL1C3463824MYELODYSPLASTIC SYNDROME1CTD_human