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Fusion gene ID: 30306 |
FusionGeneSummary for RALY_MAP1LC3A |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RALY_MAP1LC3A | Fusion gene ID: 30306 | Hgene | Tgene | Gene symbol | RALY | MAP1LC3A | Gene ID | 22913 | 84557 |
| Gene name | RALY heterogeneous nuclear ribonucleoprotein | microtubule associated protein 1 light chain 3 alpha | |
| Synonyms | HNRPCL2|P542 | ATG8E|LC3|LC3A|MAP1ALC3|MAP1BLC3 | |
| Cytomap | 20q11.22 | 20q11.22 | |
| Type of gene | protein-coding | protein-coding | |
| Description | RNA-binding protein RalyRNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog)RNA-binding protein (autoantigenic)RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)autoantigen p542heterogeneous nuclear r | microtubule-associated proteins 1A/1B light chain 3AMAP1 light chain 3-like protein 1MAP1A/1B light chain 3 AMAP1A/MAP1B LC3 AMAP1A/MAP1B light chain 3 Aautophagy-related ubiquitin-like modifier LC3 Amicrotubule-associated proteins 1A/1B light chain | |
| Modification date | 20180523 | 20180527 | |
| UniProtAcc | Q9UKM9 | Q9H492 | |
| Ensembl transtripts involved in fusion gene | ENST00000375114, ENST00000246194, ENST00000493399, | ENST00000374837, ENST00000360668, ENST00000397709, ENST00000476428, | |
| Fusion gene scores | * DoF score | 17 X 10 X 11=1870 | 5 X 4 X 5=100 |
| # samples | 20 | 5 | |
| ** MAII score | log2(20/1870*10)=-3.22496636500027 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RALY [Title/Abstract] AND MAP1LC3A [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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Tgene | MAP1LC3A | GO:0009267 | cellular response to starvation | 28223137 |
| Tgene | MAP1LC3A | GO:0016236 | macroautophagy | 28223137 |
| Tgene | MAP1LC3A | GO:0097352 | autophagosome maturation | 28223137 |
| 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 type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | LD | BRCA | TCGA-D8-A1XD-01A | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 5UTR-3CDS | ENST00000375114 | ENST00000374837 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| 5UTR-3CDS | ENST00000375114 | ENST00000360668 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| 5UTR-3CDS | ENST00000375114 | ENST00000397709 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| 5UTR-intron | ENST00000375114 | ENST00000476428 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| 5UTR-3CDS | ENST00000246194 | ENST00000374837 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| 5UTR-3CDS | ENST00000246194 | ENST00000360668 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| 5UTR-3CDS | ENST00000246194 | ENST00000397709 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| 5UTR-intron | ENST00000246194 | ENST00000476428 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| intron-3CDS | ENST00000493399 | ENST00000374837 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| intron-3CDS | ENST00000493399 | ENST00000360668 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| intron-3CDS | ENST00000493399 | ENST00000397709 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
| intron-intron | ENST00000493399 | ENST00000476428 | RALY | chr20 | 32581937 | + | MAP1LC3A | chr20 | 33147012 | + |
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FusionProtFeatures for RALY_MAP1LC3A |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RALY | MAP1LC3A |
| RNA-binding protein that acts as a transcriptionalcofactor for cholesterol biosynthetic genes in the liver. Bindsthe lipid-responsive non-coding RNA LeXis and is required forLeXis-mediated effect on cholesterogenesis (By similarity). May bea heterogeneous nuclear ribonucleoprotein (hnRNP)(PubMed:9376072). {ECO:0000250|UniProtKB:Q64012,ECO:0000269|PubMed:9376072}. | Ubiquitin-like modifier involved in formation ofautophagosomal vacuoles (autophagosomes) (PubMed:20713600,PubMed:24290141). Whereas LC3s are involved in elongation of thephagophore membrane, the GABARAP/GATE-16 subfamily is essentialfor a later stage in autophagosome maturation (PubMed:20713600).{ECO:0000269|PubMed:20713600, ECO:0000269|PubMed:24290141}. |
| Retention 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 . * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for RALY_MAP1LC3A |
| 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 RALY_MAP1LC3A |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| RALY | SPG7, WDR62, USP45, TADA2A, YWHAQ, CAND1, PCBP1, RBMX, PABPC1, HNRNPM, HNRNPU, HNRNPH1, SYNCRIP, HNRNPR, SNRNP40, HNRNPC, RBM39, RNPS1, DHX9, HNRNPA0, MED16, HSP90AB2P, HNRNPD, MED1, ERLIN1, RPS20, FMNL1, FN1, VCAM1, HNRNPK, QKI, KHDRBS1, CELF1, SOX2, TARDBP, PARK2, RPA3, RPA2, RPA1, LIN28A, LIN28B, SHMT2, MOV10, NXF1, PHF6, CUL7, OBSL1, EZH2, SUZ12, EED, RNF2, BMI1, PSME3, RPL6, RALYL, HNRNPA1, ILF2, NTRK1, HNRNPUL2, PRPF8, RANGAP1, RANBP2, SPICE1, HIST1H3E, MATR3, TEAD2, FOXA3, FOXB1, FOXD4, FOXE1, FOXL1, FOXP3, FOXS1, SNW1, CDC5L, U2AF2, ELAVL2, STRBP, APOBEC3D, C11orf57, ZC3H18, STAU1, DGCR8, FBXW11, ZFC3H1, SNRNP70, SNIP1, RPL7, COX15, HSD17B10, FOXA1, TRIM25, BRCA1, LMNA | MAP1LC3A | KIF15, SQSTM1, MAP1B, FYCO1, MAP1A, STK4, NSMAF, ATG7, CLINT1, GBAS, STK3, NIPSNAP1, HADHA, HADHB, ATG4B, TMEM160, PRKCI, ATG3, KEAP1, CLTC, RASSF5, RAB3GAP1, RAB3GAP2, CLTA, PDCD6IP, PIK3C2A, SAFB2, MAP1LC3B, PRKAG2, DVL2, CALCOCO2, VCP, CASP8, UBQLN1, OPTN, NBR1, SNCA, TBC1D1, TBC1D2, TBC1D2B, TBC1D5, TBC1D7, TBC1D9, TBC1D9B, TBC1D10A, TBC1D10B, RABGAP1, TBC1D16, TBC1D17, RABGAP1L, TBC1D25, WDFY3, PRPF40A, PIAS4, GABARAPL1, PINK1, RAB33B, ULK1, ATG13, MAP1S, HTT, APP, BNIP3L, UBQLN4, PSMD4, SYNPO2, SERBP1, CLTCL1, HNRNPU, HSPA5, DDX5, VPRBP, HSPA1A, RPL4, TUBA1B, HSPA2, HNRNPM, TUBB4B, PELP1, TUBB, DDX17, SAFB, ASAP2, PADI3, HNRNPH1, MATR3, IPO5, EGFR, RRBP1, EPRS, PGAP1, RDH12, EPHA7, SRPK1, UBC, ATG101, LGALS3, EPAS1, TOLLIP, TNIP1, KXD1, FUNDC1, FAM134C, CBX5, AKAP13, RTKN, TP53INP2, GPSM1, TP53INP1, MEFV, TRIM21, CLU, CHDH, BCL10, MDM2, NOTCH1, PLIN1, CAV1, LMNB1 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for RALY_MAP1LC3A |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for RALY_MAP1LC3A |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RALY | C0236733 | Amphetamine-Related Disorders | 1 | CTD_human |
| Tgene | MAP1LC3A | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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