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Fusion gene ID: 31720 |
FusionGeneSummary for RORA_PTPN9 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RORA_PTPN9 | Fusion gene ID: 31720 | Hgene | Tgene | Gene symbol | RORA | PTPN9 | Gene ID | 6095 | 5780 |
| Gene name | RAR related orphan receptor A | protein tyrosine phosphatase, non-receptor type 9 | |
| Synonyms | NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA | MEG2|PTPMEG2 | |
| Cytomap | 15q22.2 | 15q24.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nuclear receptor ROR-alphaROR-alphanuclear receptor RZR-alphanuclear receptor subfamily 1 group F member 1retinoic acid receptor-related orphan receptor alpharetinoid-related orphan receptor alphathyroid hormone nuclear receptor alpha variant 4tran | tyrosine-protein phosphatase non-receptor type 9PTPase-MEG2protein-tyrosine phosphatase MEG2 | |
| Modification date | 20180523 | 20180520 | |
| UniProtAcc | P35398 | P43378 | |
| Ensembl transtripts involved in fusion gene | ENST00000335670, ENST00000309157, ENST00000261523, ENST00000449337, ENST00000560004, | ENST00000306726, ENST00000564970, | |
| Fusion gene scores | * DoF score | 8 X 3 X 5=120 | 3 X 3 X 3=27 |
| # samples | 8 | 3 | |
| ** MAII score | log2(8/120*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: RORA [Title/Abstract] AND PTPN9 [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 |
| Hgene | RORA | GO:0006355 | regulation of transcription, DNA-templated | 9328355 |
| Hgene | RORA | GO:0030522 | intracellular receptor signaling pathway | 19965867 |
| Hgene | RORA | GO:0036315 | cellular response to sterol | 19965867 |
| Hgene | RORA | GO:0045893 | positive regulation of transcription, DNA-templated | 7926749 |
| Hgene | RORA | GO:0045944 | positive regulation of transcription by RNA polymerase II | 17545671|19955433 |
| Tgene | PTPN9 | GO:0010977 | negative regulation of neuron projection development | 27655914 |
| Tgene | PTPN9 | GO:0035335 | peptidyl-tyrosine dephosphorylation | 27655914 |
| Tgene | PTPN9 | GO:1903078 | positive regulation of protein localization to plasma membrane | 27655914 |
| 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 | RV | SARC | TCGA-SI-AA8B-01A | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| * 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 |
| intron-3CDS | ENST00000335670 | ENST00000306726 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| intron-intron | ENST00000335670 | ENST00000564970 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| intron-3CDS | ENST00000309157 | ENST00000306726 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| intron-intron | ENST00000309157 | ENST00000564970 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| intron-3CDS | ENST00000261523 | ENST00000306726 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| intron-intron | ENST00000261523 | ENST00000564970 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| In-frame | ENST00000449337 | ENST00000306726 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| 5CDS-intron | ENST00000449337 | ENST00000564970 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| intron-3CDS | ENST00000560004 | ENST00000306726 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
| intron-intron | ENST00000560004 | ENST00000564970 | RORA | chr15 | 60884586 | - | PTPN9 | chr15 | 75798344 | - |
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FusionProtFeatures for RORA_PTPN9 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RORA | PTPN9 |
| Nuclear receptor that binds DNA as a monomer to RORresponse elements (RORE) containing a single core motif half-site5'-AGGTCA-3' preceded by a short A-T-rich sequence. Key regulatorof embryonic development, cellular differentiation, immunity,circadian rhythm as well as lipid, steroid, xenobiotics andglucose metabolism. Considered to have intrinsic transcriptionalactivity, have some natural ligands like oxysterols that act asagonists (25-hydroxycholesterol) or inverse agonists (7-oxygenatedsterols), enhancing or repressing the transcriptional activity,respectively. Recruits distinct combinations of cofactors totarget genes regulatory regions to modulate their transcriptionalexpression, depending on the tissue, time and promoter contexts.Regulates genes involved in photoreceptor development includingOPN1SW, OPN1SM and ARR3 and skeletal muscle development withMYOD1. Required for proper cerebellum development, regulates SHHgene expression, among others, to induce granule cellsproliferation as well as expression of genes involved in calcium-mediated signal transduction. Regulates the circadian expressionof several clock genes, including CLOCK, ARNTL/BMAL1, NPAS2 andCRY1. Competes with NR1D1 for binding to their shared DNA responseelement on some clock genes such as ARNTL/BMAL1, CRY1 and NR1D1itself, resulting in NR1D1-mediated repression or RORA-mediatedactivation of clock genes expression, leading to the circadianpattern of clock genes expression. Therefore influences the periodlength and stability of the clock. Regulates genes involved inlipid metabolism such as apolipoproteins APOA1, APOA5, APOC3 andPPARG. In liver, has specific and redundant functions with RORC aspositive or negative modulator of expression of genes encodingphase I and phase II proteins involved in the metabolism oflipids, steroids and xenobiotics, such as CYP7B1 and SULT2A1.Induces a rhythmic expression of some of these genes. In addition,interplays functionally with NR1H2 and NR1H3 for the regulation ofgenes involved in cholesterol metabolism. Also involved in theregulation of hepatic glucose metabolism through the modulation ofG6PC and PCK1. In adipose tissue, plays a role as negativeregulator of adipocyte differentiation, probably acting throughdual mechanisms. May suppress CEBPB-dependent adipogenesis throughdirect interaction and PPARG-dependent adipogenesis throughcompetition for DNA-binding. Downstream of IL6 and TGFB andsynergistically with RORC isoform 2, is implicated in the lineagespecification of uncommitted CD4(+) T-helper (T(H)) cells intoT(H)17 cells, antagonizing the T(H)1 program. Probably regulatesIL17 and IL17F expression on T(H) by binding to the essentialenhancer conserved non-coding sequence 2 (CNS2) in the IL17-IL17Flocus. Involved in hypoxia signaling by interacting with andactivating the transcriptional activity of HIF1A. May inhibit cellgrowth in response to cellular stress. May exert an anti-inflammatory role by inducing CHUK expression and inhibiting NF-kappa-B signaling. {ECO:0000269|PubMed:10478845,ECO:0000269|PubMed:11053433, ECO:0000269|PubMed:11252722,ECO:0000269|PubMed:11554739, ECO:0000269|PubMed:12467577,ECO:0000269|PubMed:14570920, ECO:0000269|PubMed:15781255,ECO:0000269|PubMed:15790933, ECO:0000269|PubMed:16462772,ECO:0000269|PubMed:17512500, ECO:0000269|PubMed:18005000,ECO:0000269|PubMed:18354202, ECO:0000269|PubMed:18658046,ECO:0000269|PubMed:19965867, ECO:0000269|PubMed:21499262,ECO:0000269|PubMed:7926749, ECO:0000269|PubMed:9328355,ECO:0000269|PubMed:9862959}. | Protein-tyrosine phosphatase that could participate inthe transfer of hydrophobic ligands or in functions of the Golgiapparatus. {ECO:0000269|PubMed:19167335}. |
| 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 RORA_PTPN9 |
| 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. |
| >In-frame_RORA_ENST00000449337_chr15_60884586_-_PTPN9_ENST00000306726_chr15_75798344_-_391aa MMYFVIAAMKDSNIKDIXGHAASAQGVSSRKPGWVRQNXSRHLEFPVPTPGERPPRSLRXDHPVLPPSCLRLGLSTCSRSPCYDHPRVGG LCXCQAKARNLXGIXRHSSXEPCWHFPLFHVSRKPREKPLWGCTLPGPNXSEANKAKWPYSDRLHQCQFHGWLQAEECLHWHTRSFGEYL SXFLAHGMGAKSLGDCHDHPLXGRRQEKVWPVLAFRKRLSDPIWLPHSDQSRRGEHESLXENNARNSQHRGTAETPGDPLPVLELARLWC PFLSSFPHXLLESGQKPAESGCEQHGSTLQRAVPXATHCGPLQCRHWQDRYLLLTGHLPGTAGGAWHPXCVPDGVTHEDPEGLQHPDPXA |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| >In-frame_RORA_ENST00000449337_chr15_60884586_-_PTPN9_ENST00000306726_chr15_75798344_-_1174nt ATGATGTATTTTGTGATCGCAGCGATGAAAGATTCAAATATTAAAGACATCTGAGGTCACGCAGCATCTGCCCAGGGAGTGTCTTCCAGA AAACCTGGGTGGGTACGTCAAAATTGATCTCGCCACTTGGAATTTCCAGTTCCTACCCCAGGTGAACGGCCACCCAGATCCCTTCGATGA GATCATCCTGTTCTCCCTCCCTCCTGCCTTAGACTGGGACTCAGTACATGTTCCAGGTCCCCATGCTATGACCATCCAAGAGTTGGTGGA CTATGTTAATGCCAGGCAAAAGCAAGGAATCTATGAGGAATATGAAGACATTCGTCGTGAGAACCCTGTTGGCACTTTCCACTGTTCCAT GTCTCCAGGAAACCTAGAGAAAAACCGTTATGGGGATGTACCCTGCCTGGACCAAACTAGAGTGAAGCTAACAAAGCGAAGTGGCCATAC TCAGACAGATTACATCAATGCCAGTTTCATGGATGGCTACAAGCAGAAGAATGCTTACATTGGCACACAAGGTCCTTTGGAGAATACCTA TCGTGATTTCTGGCTCATGGTATGGGAGCAAAAAGTCTTGGTGATTGTCATGACCACCCGCTTTGAGGAAGGCGGCAGGAGAAAGTGTGG CCAGTACTGGCCTTTAGAAAAAGACTCTCGGATCCGATTTGGCTTCCTCACAGTGACCAATCTAGGCGTGGAGAACATGAATCATTATAA GAAAACAACGCTAGAAATTCACAACACAGAGGAACGGCAGAAACGCCAGGTGACCCACTTCCAGTTCTTGAGCTGGCCAGACTATGGTGT CCCTTCCTCAGCAGCTTCCCTCATTGACTTCTTGAGAGTGGTCAGAAACCAGCAGAGTCTGGCTGTGAGCAACATGGGAGCACGCTCCAA AGGGCAGTGCCCTGAGCCACCCATTGTGGTCCATTGCAGTGCAGGCATTGGCAGGACAGGTACCTTCTGCTCACTGGACATCTGCCTGGC ACAGCTGGAGGAGCTTGGCACCCTTAATGTGTTCCAGACGGTGTCACGCATGAGGACCCAGAGGGCCTTCAGCATCCAGACCCCTGAGCA GTACTATTTTTGCTACAAGGCCATCCTGGAGTTCGCAGAGAAGGAGGGCATGGTATCCTCTGGCCAAAACCTGCTGGCCGTGGAGAGTCA |
| * Fusion transcript sequences (Full-length transcript). |
| >In-frame_RORA_ENST00000449337_chr15_60884586_-_PTPN9_ENST00000306726_chr15_75798344_-_2946nt TCTCGGCGGGCGGGCAGCTGCGGCAGCTGCTGCTGTGGCTCGGGCGGCGGCGGCGCGGCGGCGGCAGAGGGGGCTCCGGGGTCGGACCAT CCGCTCTCCCTGCGCTCTCCGCACCGCGGCTTAAATGATGTATTTTGTGATCGCAGCGATGAAAGATTCAAATATTAAAGACATCTGAGG TCACGCAGCATCTGCCCAGGGAGTGTCTTCCAGAAAACCTGGGTGGGTACGTCAAAATTGATCTCGCCACTTGGAATTTCCAGTTCCTAC CCCAGGTGAACGGCCACCCAGATCCCTTCGATGAGATCATCCTGTTCTCCCTCCCTCCTGCCTTAGACTGGGACTCAGTACATGTTCCAG GTCCCCATGCTATGACCATCCAAGAGTTGGTGGACTATGTTAATGCCAGGCAAAAGCAAGGAATCTATGAGGAATATGAAGACATTCGTC GTGAGAACCCTGTTGGCACTTTCCACTGTTCCATGTCTCCAGGAAACCTAGAGAAAAACCGTTATGGGGATGTACCCTGCCTGGACCAAA CTAGAGTGAAGCTAACAAAGCGAAGTGGCCATACTCAGACAGATTACATCAATGCCAGTTTCATGGATGGCTACAAGCAGAAGAATGCTT ACATTGGCACACAAGGTCCTTTGGAGAATACCTATCGTGATTTCTGGCTCATGGTATGGGAGCAAAAAGTCTTGGTGATTGTCATGACCA CCCGCTTTGAGGAAGGCGGCAGGAGAAAGTGTGGCCAGTACTGGCCTTTAGAAAAAGACTCTCGGATCCGATTTGGCTTCCTCACAGTGA CCAATCTAGGCGTGGAGAACATGAATCATTATAAGAAAACAACGCTAGAAATTCACAACACAGAGGAACGGCAGAAACGCCAGGTGACCC ACTTCCAGTTCTTGAGCTGGCCAGACTATGGTGTCCCTTCCTCAGCAGCTTCCCTCATTGACTTCTTGAGAGTGGTCAGAAACCAGCAGA GTCTGGCTGTGAGCAACATGGGAGCACGCTCCAAAGGGCAGTGCCCTGAGCCACCCATTGTGGTCCATTGCAGTGCAGGCATTGGCAGGA CAGGTACCTTCTGCTCACTGGACATCTGCCTGGCACAGCTGGAGGAGCTTGGCACCCTTAATGTGTTCCAGACGGTGTCACGCATGAGGA CCCAGAGGGCCTTCAGCATCCAGACCCCTGAGCAGTACTATTTTTGCTACAAGGCCATCCTGGAGTTCGCAGAGAAGGAGGGCATGGTAT CCTCTGGCCAAAACCTGCTGGCCGTGGAGAGTCAGTAACTCTCCTACGAACCTCCTACCTGTTGGCCAGCCTTCCTTAAACTACCCTGGA CACCGCTGAGCCTATAGGTTGCCATCAGTTACGCTGAAGCCATGGATCAACTTCTTTCTTGTGTCTCCCAGCACACGTGTGCACGCAAGG CAGCCTTTCCCTTTGGCTAGATAAATGTGGTGAAATTGCCACTAGAAAGGGCCAGTAGCAATGTGTTCTTAATTCCTAGCATCTGCTATC AAACTGTGCCTTATTAAAACCAAATTGTGGCTATTGATTTTTGCTAGGGTCCCCGAGGTAAGTGGGGAAGGAACCTCCCTCCTCCTTTCT CCCGCCATTCTTTTTCTGAGGTCTCCTGTCTCCCACTCCTTCCCTTTCCTAGGATTTTATGGGGAGGTTTGATGAGCATTTGCCTTTCTC CCCAGAGAGCTTGACCAAGTTACATATTCTAGAGATCGTCCTGAGTGCCAAGCACGTTTATAAGTAGGGCGTGTATTCCAGTCCTTTCTG TCATTCTGTGTGTGTGTGTGTGTGCACTTATGTGTATGGGTCCATATGTACGTGTGTATATAATATATATTGTATGTGATAATATGATCG TATTCTATAAATACATATACACACGATACTCCTTTCCAGAAGTTCCTGGGGCTCCGTGTTGCAGTTCAGGACTCCTTGCTTCTTGGACCC TACTATTTATCCTGGACTAGCTTGGGTTGGTGATCATGTCTCCTCTTGTCAGGCTACAGAGTGGTGGAAGAGGACACACACACATCTCCT CCATGTTCCTGCCACAGGGCCCCTTCCTTAAGTAATGACTTATCTCCTTCCAGTTGCCACCTGTTGGAGCCAAGAATGTATTAGTTTGTG GTGACACTGGGTTAGCTCAGCATGGATTTCCCTTATCCGATGATTTTTCTACATTTACTTGGCCAATTTGGGGAACAGACCTCCACTGTG ATTCCATACTCTCTCTTTGCTTTCACTATCCCAGGGATGGGAGGCGGAGGGTAGAGATGAACTCACTGAGCAGCCAGAGCCAAATGCAAT CGGTACGAATCTTAGAAGGAAGGAGGGGGAGCCCAGGTATGAGAAAGAAAAAACCACTAAGAAAATACCTCCCTGGGAGGATGAGCTGGG GCCCTTTTTCTTTTGCTGGATGGTTCCTTTATGCAGCTTGGCCCTGTCTACCGAGATGCCCATCTCTTCCTGCCTGCTAGCCTGCTAGAC CCTCAAACTGGGTGGGTTCTGTGTCAATAAAAAGCTTCACCCCCTGGCTGAGTGAGGTGGTCCCCTGCAATCACTGTTTGTCCCCTACCC ACCCAACCTGTCCCTGCCTGCTCCCAGCCCACTCATCCTTATGTGCTAGGGATAAATCAAGAGTCCTCAGCACTCCACATTCCCAAAAAA TCCCAGGAACTCCTAAACCTTCCCCTGTGACAGAAGATGAGGTTGGCAGCTGATCAGACCTCAATAATTTTATACTGTAATAAGCTCTTT GAATGTGTATATTATTATTTTTTACAATCATTTCATTTTGTATTTAATATCAATGGACTGAGTCTGATTCAGAAAATAATTGTAATGTTC |
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FusionGenePPI for RORA_PTPN9 |
| 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 |
| RORA | PSMC5, EP300, MYOD1, CEBPB, RUVBL1, LRIF1, ZXDC, PROX1, PNRC1, NCOA1, COPS5, PNRC2, LMO3, NR0B1, EZH2, VPRBP, DDB1, PTBP1, SMARCD3, NSD1, GFAP, CSNK1E, BHLHE41 | PTPN9 | RTN3, GHR, MYC, TP53BP1, VCP, AGTRAP, REEP6, MAL2, CMTM5, ENO1, MOV10, NXF1, NTRK1, CREB3, LZTR1, PC, EYA1, RAD51C, FAM26D, VSIG8, C5AR2, MDK, PDCD1, PTPN9, GEMIN8, FSIP1, SMN1, DDX20, GEMIN4, PMPCA, SLC39A7, STRAP, TUBA3C, AAR2, SMN2, TUBA3D, LMNA |
| - 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 RORA_PTPN9 |
| 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 RORA_PTPN9 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RORA | C0005586 | Bipolar Disorder | 5 | PSYGENET |
| Hgene | RORA | C0011581 | Depressive disorder | 3 | PSYGENET |
| Hgene | RORA | C0004352 | Autistic Disorder | 2 | CTD_human |
| Hgene | RORA | C0011570 | Mental Depression | 2 | PSYGENET |
| Hgene | RORA | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| Hgene | RORA | C0085159 | Seasonal Affective Disorder | 1 | PSYGENET |
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