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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ORMDL3 Gene

protein-coding   GIFtS: 53
GCID: GC17M038077

ORM1-like 3 (S. cerevisiae)

(Previous name: ORM1 (S. cerevisiae)-like 3 )
 Explore 8 diseases affiliated with
ORMDL3 via our new
 Human Malady Compendium 
Biological research products
for ORMDL3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
ORM1-Like 3 (S. Cerevisiae)1 2
ORM1 (S. Cerevisiae)-Like 31
ORM1-Like Protein 32

External Ids:    HGNC: 160381   Entrez Gene: 941032   Ensembl: ENSG000001720577   OMIM: 6100755   UniProtKB: Q8N1383   

Export aliases for ORMDL3 gene to outside databases

Previous GC identifers: GC17P037421 GC17U900023 GC17M037987 GC17M038452 GC17M035330 GC17M033871


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: ORML3_HUMAN, Q8N138
Function: Negative regulator of sphingolipid synthesis. May indirectly regulate endoplasmic reticulum-mediated Ca(+2)
signaling




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NC_018928.1  NT_010783.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ORMDL3 gene promoter:
         COUP-TF1   C/EBPbeta   COUP   HNF-4alpha2   AP-4   LCR-F1   HNF-4alpha1   c-Ets-1   COUP-TF   HOXA5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidORMDL3 promoter sequence
   Search SABiosciences Chromatin IP Primers for ORMDL3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ORMDL3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q12   Ensembl cytogenetic band:  17q12   HGNC cytogenetic band: 17q12

ORMDL3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ORMDL3 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M038077:  view genomic region     (about GC identifiers)

Start:
38,077,294 bp from pter      End:
38,083,854 bp from pter
Size:
6,561 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: ORML3_HUMAN, Q8N138 (See protein sequence)
Recommended Name: ORM1-like protein 3  
Size: 153 amino acids; 17495 Da
Subunit: Interacts with SPTLC1
Subcellular location: Endoplasmic reticulum membrane; Multi-pass membrane protein
Miscellaneous: SNPs on 17q21 locus that are associated with childhood asthma also show a consistent and strong
association with transcript levels of ORMDL3, indicating that genetic variants regulating ORMDL3 expression are
determinants of susceptibility to childhood asthma
Secondary accessions: B3KS83 Q6UY83
Alternative splicing: 2 isoforms:  Q8N138-1   Q8N138-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ORMDL3: NX_Q8N138

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8N138

  • ORMDL3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_644809.1  
    ENSEMBL proteins: 
     ENSP00000304858   ENSP00000464693   ENSP00000462961   ENSP00000377724   ENSP00000464455  
     ENSP00000464298  

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    Uscn Proteins for ORMDL3

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783endoplasmic reticulum IDA12093374
    GO:0016021integral to membrane IEA--
    GO:0035339SPOTS complex IDA--


    ORMDL3 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ORMDL3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007203 ORMDL

    Graphical View of Domain Structure for InterPro Entry Q8N138

    ProtoNet protein and cluster: Q8N138

    1 Blocks protein family: IPB007203 ORMDL

    UniProtKB/Swiss-Prot: ORML3_HUMAN, Q8N138
    Similarity: Belongs to the ORM family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: ORML3_HUMAN, Q8N138
    Function: Negative regulator of sphingolipid synthesis. May indirectly regulate endoplasmic reticulum-mediated Ca(+2)
    signaling

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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--


    ORMDL3 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for ORMDL3:
     G0/1 arrest  Increased G1 DNA content 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ORMDL3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    5/12 Interacting proteins for ORMDL3 (Q8N1382, 3 ENSP000003048584) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SPTLC1O152693, ENSP000002625544I2D: score=1 STRING: ENSP00000262554
    GTF2H1P327803I2D: score=5 
    EEF1A1P681043I2D: score=3 
    SPTSSAENSP000002981304STRING: ENSP00000298130
    SPTSSBENSP000003520974STRING: ENSP00000352097
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006672ceramide metabolic process IMP--


    ORMDL3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ORMDL3
    Search CenterWatch for drugs/clinical trials and news about ORMDL3 / ORML3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for ORMDL3 gene: 
    NM_139280.2  

    Unigene Cluster for ORMDL3:

    ORM1-like 3 (S. cerevisiae)
    Hs.514151  [show with all ESTs]
    Unigene Representative Sequence: AK093063
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000304046(uc002htj.2) ENST00000579695(uc002htk.2) ENST00000579287
    ENST00000581284 ENST00000394169(uc002hti.1) ENST00000584220 ENST00000584000
    ENST00000582052

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    hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-429 hsa-miR-106a hsa-miR-449a hsa-miR-372 hsa-miR-93
    SwitchGear 3'UTR luciferase reporter plasmidORMDL3 3' UTR sequence
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    Additional cDNA sequence: 

    AF151043.1 AF373101.1 AF373102.1 AF395708.1 AJ308027.1 AK074811.1 AK075212.1 AK093063.1 
    AY357943.1 BC000638.1 BC017087.1 BC018837.1 BC050710.1 BC054042.1 BC071833.1 

    6 DOTS entries:

    DT.75123827  DT.99960637  DT.101983962  DT.120892836  DT.40230348  DT.95172328 

    24/324 AceView cDNA sequences (see all 324):

    CF264690 AX775843 BE073479 AF119884 AW961240 AF258572 BP872262 C02557 
    BG831510 CF264907 BX479594 NM_018530 BM712955 BC017087 AW089705 AW074190 
    BX538068 BC071833 BQ008854 AF395708 AW973329 AW591603 AX747896 AK093063 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for ORMDL3 (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c · 8d · 8e · 8f ^ 9
    SP1:                                                                                                            
    SP2:                    -     -     -     -                                                                     
    SP3:                    -     -     -     -                                                                     
    SP4:                    -     -     -     -                                                                     
    SP5:                          -     -     -                                                                     


    ECgene alternative splicing isoforms for ORMDL3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ORMDL3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTTCTGTTAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See ORMDL3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ORMDL3

    SOURCE GeneReport for Unigene cluster: Hs.514151

    UniProtKB/Swiss-Prot: ORML3_HUMAN, Q8N138
    Tissue specificity: Widely expressed. Expressed in adult and fetal heart, brain, lung, liver, skeletal muscle and
    kidney. Expressed in adult pancreas and placenta and in fetal spleen abd thymus

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for ORMDL3 gene from 6/25 species (see all 25)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves ORMDL31 ORM1-like 3 (S. cerevisiae) 84.75(n)
    92.81(a)
      426131  XM_003642808.1  XP_003642856.1 
    lizard
    (Anolis carolinensis)
    Reptilia ORMDL36
    --
    91(a)
    1 ↔ 1
    6(68818737-68836782)
    zebrafish
    (Danio rerio)
    Actinopterygii ormdl31 ORM1-like 3 (S. cerevisiae) 81.92(n)
    92.16(a)
      450067  NM_001006087.1  NP_001006087.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta ORMDL1 CG14577-PA 56.58(n)
    50(a)
      40404  NM_168929.2  NP_730669.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G012301 ORMDL-like protein 49.77(n)
    43.66(a)
      839331  NM_100006.3  NP_563622.1 
    rice
    (Oryza sativa)
    Liliopsida Os04g05677001 hypothetical protein 51.28(n)
    41.96(a)
      4336696  NM_001060122.1  NP_001053587.1 


    ENSEMBL Gene Tree for ORMDL3 (if available)
    TreeFam Gene Tree for ORMDL3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ORMDL3 gene
    ORMDL12  ORMDL22  
    2 SIMAP similar genes for ORMDL3 using alignment to 4 protein entries:     ORML3_HUMAN (see all proteins):
    ORMDL1    ORMDL2

    ORMDL3 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for ORMDL3
    PGOHUM00000238349


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/136 NCBI SNPs in ORMDL3 are shown (see all 136    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1122609321,2
    C,F,--38077185(+) CCTCCC/TGCCAC 1 -- int12Minor allele frequency- T:0.50NA 4
    rs1902534681,2
    --38077190(+) TGCCAA/CCGTCA 1 -- int10--------
    rs1458098341,2
    --38077298(+) GGAAAC/GAGAAA 1 -- ut310--------
    rs10446751,2
    H--38077332(-) GTATTC/TTGAGA 1 -- ut31 ese37Minor allele frequency- T:0.05MN NS EA NA 606
    rs1417120281,2
    --38077366(+) ATTCAC/TACTTT 1 -- ut310--------
    rs31695721,2
    C,F,H,--38077412(-) NNNNCC/TGTGTA 1 -- ut31 ese313Minor allele frequency- T:0.02MN NS EA NA 1562
    rs22788941,2
    C,F,H,--38077423(+) GGAGAT/CGCAGG 1 -- ut31 ese311Minor allele frequency- C:0.03EA NA NS 2154
    rs1469585761,2
    --38077426(+) GATGCA/GGGGTC 1 -- ut310--------
    rs79421,2
    C,F,H,--38077464(+) TCTCCC/TGTTCC 1 -- ut3128Minor allele frequency- G:0.00EA NA MN NS WA CSA 1321
    rs769863941,2
    C--38077477(+) TGGACC/TCCTGG 1 -- ut310--------

    HapMap Linkage Disequilibrium report for ORMDL3 (38077294 - 38083854 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for ORMDL3: --
    Human Gene Mutation Database (HGMD): ORMDL3

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    ORMDL3 for disorders           About GeneDecksing

    OMIM gene information: 610075    OMIM disorders: --

    UniProtKB/Swiss-Prot: ORML3_HUMAN, Q8N138
  • Genetic variations in ORMDL3 are associated with susceptibility to asthma (ASTHMA) [MIM:600807]. The most
  • common chronic disease affecting children and young adults. It is a complex genetic disorder with a heterogeneous
    phenotype, largely attributed to the interactions among many genes and between these genes and the environment. It is
    characterized by recurrent attacks of paroxysmal dyspnea, with weezing due to spasmodic contraction of the bronchi

    8 diseases for ORMDL3:    About MalaCards
    primary biliary cirrhosis    ankylosing spondylitis    spondylitis    atopy
    crohn's disease    rabies    asthma    obesity

    1 disease from the University of Copenhagen DISEASES database for ORMDL3:
    Asthma
    Human Genome Epidemiology (HuGE) Navigator: ORMDL3 (18 documents)

    Export disorders for ORMDL3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for ORMDL3 gene, integrated from 9 sources (see all 50):
    (articles sorted by number of sources associating them with ORMDL3)
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    1. Genetic variation in ORM1-like 3 (ORMDL3) and gasdermin-like (GSDML) and childhood asthma. (PubMed id 19133921)1, 2, 9 Wu H....London S.J. (2009)
    2. Orm family proteins mediate sphingolipid homeostasis. (PubMed id 20182505)1, 2 Breslow D.K....Weissman J.S. (2010)
    3. The asthma-associated ORMDL3 gene product regulates e ndoplasmic reticulum-mediated calcium signaling and cellular stress. (PubMed id 19819884)1, 2 Cantero-Recasens G....Vicente R. (2010)
    4. A polymorphism controlling ORMDL3 expression is associated with asthma that is poorly controlled by current medications. (PubMed id 18395550)1, 2 Tavendale R....Palmer C.N. (2008)
    5. ORMDL3 variants associated with asthma susceptibility in North Americans of European ancestry. (PubMed id 18760456)1, 2 Sleiman P.M....Hakonarson H. (2008)
    6. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. (PubMed id 17611496)1, 2 Moffatt M.F....Cookson W.O. (2007)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    9. ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins. (PubMed id 12093374)1, 2 Hjelmqvist L....Gonzalez-Duarte R. (2002)
    10. ORMDL3 is an inducible lung epithelial gene regulating metalloproteases, chemokines, OAS, and ATF6. (PubMed id 23011799)1 Miller M....Broide D.H. (2012)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 94103 HGNC: 16038 AceView: GSDMLandORMDL3 Ensembl:ENSG00000172057 euGenes: HUgn94103
    ECgene: ORMDL3 H-InvDB: ORMDL3

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ORMDL3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for ORMDL3 gene:
    Search GeneIP for patents involving ORMDL3

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