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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: 31720

FusionGeneSummary for RORA_PTPN9

check button Fusion gene summary
Fusion gene informationFusion gene name: RORA_PTPN9
Fusion gene ID: 31720
HgeneTgene
Gene symbol

RORA

PTPN9

Gene ID

6095

5780

Gene nameRAR related orphan receptor Aprotein tyrosine phosphatase, non-receptor type 9
SynonymsNR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRAMEG2|PTPMEG2
Cytomap

15q22.2

15q24.2

Type of geneprotein-codingprotein-coding
Descriptionnuclear 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 4trantyrosine-protein phosphatase non-receptor type 9PTPase-MEG2protein-tyrosine phosphatase MEG2
Modification date2018052320180520
UniProtAcc

P35398

P43378

Ensembl transtripts involved in fusion geneENST00000335670, ENST00000309157, 
ENST00000261523, ENST00000449337, 
ENST00000560004, 
ENST00000306726, 
ENST00000564970, 
Fusion gene scores* DoF score8 X 3 X 5=1203 X 3 X 3=27
# samples 83
** MAII scorelog2(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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneRORA

GO:0006355

regulation of transcription, DNA-templated

9328355

HgeneRORA

GO:0030522

intracellular receptor signaling pathway

19965867

HgeneRORA

GO:0036315

cellular response to sterol

19965867

HgeneRORA

GO:0045893

positive regulation of transcription, DNA-templated

7926749

HgeneRORA

GO:0045944

positive regulation of transcription by RNA polymerase II

17545671|19955433

TgenePTPN9

GO:0010977

negative regulation of neuron projection development

27655914

TgenePTPN9

GO:0035335

peptidyl-tyrosine dephosphorylation

27655914

TgenePTPN9

GO:1903078

positive regulation of protein localization to plasma membrane

27655914


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
TCGARVSARCTCGA-SI-AA8B-01ARORAchr15

60884586

-PTPN9chr15

75798344

-
* 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-3CDSENST00000335670ENST00000306726RORAchr15

60884586

-PTPN9chr15

75798344

-
intron-intronENST00000335670ENST00000564970RORAchr15

60884586

-PTPN9chr15

75798344

-
intron-3CDSENST00000309157ENST00000306726RORAchr15

60884586

-PTPN9chr15

75798344

-
intron-intronENST00000309157ENST00000564970RORAchr15

60884586

-PTPN9chr15

75798344

-
intron-3CDSENST00000261523ENST00000306726RORAchr15

60884586

-PTPN9chr15

75798344

-
intron-intronENST00000261523ENST00000564970RORAchr15

60884586

-PTPN9chr15

75798344

-
In-frameENST00000449337ENST00000306726RORAchr15

60884586

-PTPN9chr15

75798344

-
5CDS-intronENST00000449337ENST00000564970RORAchr15

60884586

-PTPN9chr15

75798344

-
intron-3CDSENST00000560004ENST00000306726RORAchr15

60884586

-PTPN9chr15

75798344

-
intron-intronENST00000560004ENST00000564970RORAchr15

60884586

-PTPN9chr15

75798344

-

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FusionProtFeatures for RORA_PTPN9


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

P35398

PTPN9

P43378

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}.

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 RORA_PTPN9


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.
>In-frame_RORA_ENST00000449337_chr15_60884586_-_PTPN9_ENST00000306726_chr15_75798344_-_391aa
MMTFVIAAMKDSNIKDI_GHAASAQGVSSRKPGWVRQN_SRHLEFPVPTPGERPPRSLR_DHPVLPPSCLRLGLSTCSRSPCTDHPRVGG
LC_CQAKARNL_GI_RHSS_EPCWHFPLFHVSRKPREKPLWGCTLPGPN_SEANKAKWPYSDRLHQCQFHGWLQAEECLHWHTRSFGEYL
S_FLAHGMGAKSLGDCHDHPL_GRRQEKVWPVLAFRKRLSDPIWLPHSDQSRRGEHESL_ENNARNSQHRGTAETPGDPLPVLELARLWC
PFLSSFPH_LLESGQKPAESGCEQHGSTLQRAVP_ATHCGPLQCRHWQDRYLLLTGHLPGTAGGAWHP_CVPDGVTHEDPEGLQHPDP_A


* 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


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
RORAPSMC5, EP300, MYOD1, CEBPB, RUVBL1, LRIF1, ZXDC, PROX1, PNRC1, NCOA1, COPS5, PNRC2, LMO3, NR0B1, EZH2, VPRBP, DDB1, PTBP1, SMARCD3, NSD1, GFAP, CSNK1E, BHLHE41PTPN9RTN3, 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


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 RORA_PTPN9


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 RORA_PTPN9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRORAC0005586Bipolar Disorder5PSYGENET
HgeneRORAC0011581Depressive disorder3PSYGENET
HgeneRORAC0004352Autistic Disorder2CTD_human
HgeneRORAC0011570Mental Depression2PSYGENET
HgeneRORAC0038356Stomach Neoplasms1CTD_human
HgeneRORAC0085159Seasonal Affective Disorder1PSYGENET