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

ORMDL1 Gene

protein-coding   GIFtS: 50
GCID: GC02M190634

ORM1-like 1 (S. cerevisiae)

(Previous name: ORM1 (S. cerevisiae)-like 1 )
 Explore 2 diseases affiliated with
ORMDL1 via our new
 Human Malady Compendium 
Biological research products
for ORMDL1
    

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

Aliases
ORM1-Like 1 (S. Cerevisiae)1 2
ORM1 (S. Cerevisiae)-Like 11
Adoplin-13
ORM1-Like Protein 12
Adoplin-13

External Ids:    HGNC: 160361   Entrez Gene: 941012   Ensembl: ENSG000001286997   OMIM: 6100735   UniProtKB: Q9P0S33   

Export aliases for ORMDL1 gene to outside databases

Previous GC identifers: GC00U991061 GC02U900735 GC02M190460 GC02M190343 GC02M182494


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

UniProtKB/Swiss-Prot: ORML1_HUMAN, Q9P0S3
Function: Negative regulator of sphingolipid synthesis




(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_000002.11  NC_018913.1  NT_005403.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ORMDL1 gene promoter:
         STAT1   GATA-3   STAT1beta   STAT1alpha   GATA-2   GATA-1   YY1   STAT2   c-Myb   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): ORMDL1 promoter sequence
   Search SABiosciences Chromatin IP Primers for ORMDL1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ORMDL1


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

Entrez Gene cytogenetic band: 2q32   Ensembl cytogenetic band:  2q32.2   HGNC cytogenetic band: 2q32

ORMDL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ORMDL1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M190634:  view genomic region     (about GC identifiers)

Start:
190,634,993 bp from pter      End:
190,649,097 bp from pter
Size:
14,105 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: ORML1_HUMAN, Q9P0S3 (See protein sequence)
Recommended Name: ORM1-like protein 1  
Size: 153 amino acids; 17371 Da
Subcellular location: Endoplasmic reticulum membrane; Multi-pass membrane protein
Secondary accessions: B2R8W3 D3DPH9

Explore the universe of human proteins at neXtProt for ORMDL1: NX_Q9P0S3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9P0S3

  • ORMDL1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001121622.1  NP_057551.1  

    ENSEMBL proteins: 
     ENSP00000376161   ENSP00000326869   ENSP00000376160   ENSP00000386253   ENSP00000407234  
     ENSP00000402074  

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    Novus Biologicals ORMDL1 Protein
    Novus Biologicals ORMDL1 Lysates
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for ORMDL1

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005789endoplasmic reticulum membrane IDA12093374
    GO:0016021integral to membrane IEA--


    ORMDL1 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

    ORMDL1 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007203 ORMDL

    Graphical View of Domain Structure for InterPro Entry Q9P0S3

    ProtoNet protein and cluster: Q9P0S3

    1 Blocks protein family: IPB007203 ORMDL

    UniProtKB/Swiss-Prot: ORML1_HUMAN, Q9P0S3
    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: ORML1_HUMAN, Q9P0S3
    Function: Negative regulator of sphingolipid synthesis

    miRNA
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    hsa-miR-520d-5p hsa-miR-130a* hsa-miR-487a hsa-miR-23c hsa-miR-154* hsa-miR-3667-3p hsa-miR-23b hsa-miR-320e
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ORMDL1

    1 GenomeRNAi human phenotype for ORMDL1:
     Decreased Wnt reporter activit 


    (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 ORMDL1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    5/8 Interacting proteins for ORMDL1 (Q9P0S33 ENSP000003268694) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TMBIM4Q9HC243, ENSP000003509654I2D: score=1 STRING: ENSP00000350965
    CREB3O438893I2D: score=1 
    MEOX2P502223I2D: score=1 
    UBCENSP000003448184STRING: ENSP00000344818
    SACM1LENSP000003737134STRING: ENSP00000373713
    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--


    ORMDL1 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 ORMDL1
    Search CenterWatch for drugs/clinical trials and news about ORMDL1 / ORML1 

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 ORMDL1 gene (2 alternative transcripts): 
    NM_001128150.1  NM_016467.4  

    Unigene Cluster for ORMDL1:

    ORM1-like 1 (S. cerevisiae)
    Hs.700632  [show with all ESTs]
    Unigene Representative Sequence: NM_016467
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000392350(uc002ure.4) ENST00000325795(uc002urb.4 uc002urd.4)
    ENST00000496543 ENST00000392349 ENST00000409519 ENST00000442547 ENST00000458355


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    8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate ORMDL1 (see all 10):
    hsa-miR-520d-5p hsa-miR-130a* hsa-miR-487a hsa-miR-23c hsa-miR-154* hsa-miR-3667-3p hsa-miR-23b hsa-miR-320e
    SwitchGear 3'UTR luciferase reporter plasmidORMDL1 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for ORMDL1 (see all 4)
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ORMDL1
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    Additional cDNA sequence: 

    AB064959.1 AB064960.1 AF151036.1 AF395704.1 AK074756.1 AK075160.1 AK313533.1 BC005200.1 
    CR936635.1 

    18 DOTS entries:

    DT.95268270  DT.100845867  DT.100845865  DT.100845864  DT.117163  DT.100732575  DT.120935947  DT.120935967 
    DT.95282748  DT.95282749  DT.100802626  DT.100845866  DT.99944317  DT.120935956  DT.120936025  DT.95282745 
    DT.100845862  DT.120935998 

    24/274 AceView cDNA sequences (see all 274):

    CR602229 BM545732 BX386186 T35220 BM787040 AI923278 AI128400 BM511712 
    BM714393 BX115168 CR620006 AA359968 AA443819 AA281316 BQ574014 BX101051 
    AA926866 N93556 BQ004335 AW002693 AA743830 AL514284 AW102929 AI439400 

    GeneLoc Exon Structure

    5/12 Alternative Splicing Database (ASD) splice patterns (SP) for ORMDL1 (see all 12)    About this scheme

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

    ExUns: 6f
    SP1:      
    SP2:      
    SP3:      
    SP4:      
    SP5:      


    ECgene alternative splicing isoforms for ORMDL1

    (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

    ORMDL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TAAACCGGAA

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

    About this image
    See ORMDL1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ORMDL1

    SOURCE GeneReport for Unigene cluster: Hs.700632

    UniProtKB/Swiss-Prot: ORML1_HUMAN, Q9P0S3
    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. Expressed at intermediate level in
    pancreas, placenta and brain but low in skeletal muscle and lung

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    In Situ
    Assay Products:
     

     
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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 ORMDL1 gene from 6/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves ORMDL11 ORM1-like 1 (S. cerevisiae) 81.26(n)
    96.08(a)
      423981  XM_001231892.2  XP_001231893.1 
    lizard
    (Anolis carolinensis)
    Reptilia ORMDL16
    --
    97(a)
    1 ↔ 1
    2(135058037-135066116)
    zebrafish
    (Danio rerio)
    Actinopterygii ormdl11 ORM1-like 1 (S. cerevisiae) 78.43(n)
    92.81(a)
      368632  NM_200093.1  NP_956387.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta ORMDL6
    ORMDL
    47(a)
    1 → many
    3L(21628405-21629351)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G012306
    AT5G420006
    ORMDL domain-containing protein
    39(a)
    38(a)
    many ↔ many
    many ↔ many
    1(97456-99240)
    5(16799354-16801028)
    rice
    (Oryza sativa)
    Liliopsida --
    --
    (see all 3)
    ORM1, putative, expressed
    (see all 3)
    38(a)
    37(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    7(15601027-15603594)
    4(28336743-28340891)


    ENSEMBL Gene Tree for ORMDL1 (if available)
    TreeFam Gene Tree for ORMDL1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ORMDL1 gene
    ORMDL22  ORMDL32  
    2 SIMAP similar genes for ORMDL1 using alignment to 2 protein entries:     ORML1_HUMAN (see all proteins):
    ORMDL3    ORMDL2

    ORMDL1 for paralogs           About GeneDecksing



    (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

    10/201 NCBI SNPs in ORMDL1 are shown (see all 201    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs12251071,2
    C,F,H,--190634538(-) TACTAC/TTGTGG 2 -- int127Minor allele frequency- T:0.02NS EA NA WA CSA 2240
    rs1876226491,2
    --190634539(+) CACAAC/TAGTAA 2 -- int10--------
    rs12251061,2
    C,A,H,--190634549(-) CTTGCG/AGCAAT 2 -- int113Minor allele frequency- A:0.02NA WA CSA EA 376
    rs1907951401,2
    --190634778(+) CTAACA/GTAATT 2 -- int10--------
    rs1838378181,2
    --190634961(+) TTGTTA/GCTTTA 2 -- int10--------
    rs1453498501,2
    --190634973(+) TTTTAC/TGAATT 2 -- int10--------
    rs1883318021,2
    --190635002(+) CTTGAA/CAAATG 2 -- ut310--------
    rs1140990161,2
    C,F,--190635063(+) ACCAAC/TGAAAA 2 -- ut311Minor allele frequency- T:0.02WA 118
    rs1159916491,2
    --190635068(+) CGAAAA/CATTTT 2 -- ut311Minor allele frequency- C:0.01NA 120
    rs1929281521,2
    --190635069(+) GAAAAA/CTTTTA 2 -- ut310--------

    HapMap Linkage Disequilibrium report for ORMDL1 (190634993 - 190649097 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for ORMDL1: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing ORMDL1
    DNA2.0 Custom Variant and Variant Library Synthesis for ORMDL1

    (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

    ORMDL1 for disorders           About GeneDecksing

    OMIM gene information: 610073    OMIM disorders: --

    2 diseases for ORMDL1:    About MalaCards
    loeys-dietz syndrome    ehlers-danlos syndrome

    1 disease from the University of Copenhagen DISEASES database for ORMDL1:
    Loeys-Dietz syndrome

    Export disorders for ORMDL1 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 ORMDL1 gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with ORMDL1)
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    1. ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins. (PubMed id 12093374)1, 2, 3 Hjelmqvist L....Gonzalez-Duarte R. (2002)
    2. A family of membrane proteins associated with presenilin expression and gamma-secretase function. (PubMed id 17928364)1, 2, 9 Araki W....Tabira T. (2008)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)1, 2 Zhang Q.-H.... Chen Z. (2000)
    5. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    6. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    7. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    8. Orm family proteins mediate sphingolipid homeostasis. (PubMed id 20182505)2 Breslow D.K....Weissman J.S. (2010)
    9. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    10. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 94101 HGNC: 16036 AceView: ORMDL1 Ensembl:ENSG00000128699 euGenes: HUgn94101
    ECgene: ORMDL1 H-InvDB: ORMDL1

    (According to HUGE)
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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 ORMDL1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ORMDL1 gene:
    Search GeneIP for patents involving ORMDL1

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