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

ORM2 Gene

protein-coding   GIFtS: 46
GCID: GC09P117092

orosomucoid 2

 Explore 9 diseases affiliated with
ORM2 via our new
 Human Malady Compendium 
Biological research products
for ORM2
    

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

Aliases
Orosomucoid 21 2     OMD 22 3
AGP21 2 3     Alpha-1-Acid Glycoprotein 22
AGP-B1 2     Alpha-1-Acid Glycoprotein, Type 22
AGP-B'1 2     Orosomucoid-23
AGP 22 3     Orosomucoid-23

External Ids:    HGNC: 84991   Entrez Gene: 50052   Ensembl: ENSG000002282787   OMIM: 1386105   UniProtKB: P196523   

Export aliases for ORM2 gene to outside databases

Previous GC identifers: GC09U990059 GC09P108818 GC09P022004 GC09P112462 GC09P112468 GC09P114165 GC09P114171 GC09P116131 GC09P086697


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

Entrez Gene summary for ORM2:
This gene encodes a key acute phase plasma protein. Because of its increase due to acute inflammation, this protein is
classified as an acute-phase reactant. The specific function of this protein has not yet been determined; however, it
may be involved in aspects of immunosuppression. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: A1AG2_HUMAN, P19652
Function: Functions as transport protein in the blood stream. Binds various hydrophobic ligands in the interior of its
beta-barrel domain. Also binds synthetic drugs and influences their distribution and availability. Appears to function
in modulating the activity of the immune system during the acute-phase reaction




(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_000009.11  NC_018920.1  NT_008470.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ORM2 gene promoter:
         STAT1   NCX/Ncx   RREB-1   NRSF form 1   Lmo2   NRSF form 2   Pax-4a   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidORM2 promoter sequence
   Search SABiosciences Chromatin IP Primers for ORM2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ORM2


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

Entrez Gene cytogenetic band: 9q32   Ensembl cytogenetic band:  9q32   HGNC cytogenetic band: 9q31-qter

ORM2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ORM2 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P117092:  view genomic region     (about GC identifiers)

Start:
117,092,069 bp from pter      End:
117,095,536 bp from pter
Size:
3,468 bases      Orientation:
plus 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: A1AG2_HUMAN, P19652 (See protein sequence)
Recommended Name: Alpha-1-acid glycoprotein 2 precursor  
Size: 201 amino acids; 23603 Da
Subcellular location: Secreted
Sequence caution: Sequence=CAA29873.2; Type=Erroneous gene model prediction; Sequence=CAA29874.1; Type=Erroneous gene
model prediction;
4 PDB 3D structures from and Proteopedia for ORM2:
3APU (3D)        3APV (3D)        3APW (3D)        3APX (3D)    
Secondary accessions: B2R5L2 Q16571 Q5T538 Q6IB74

Explore the universe of human proteins at neXtProt for ORM2: NX_P19652

Post-translational modifications:

  • N-glycosylated. N-glycan heterogeneity at Asn-33: Hex5HexNAc4 (minor), Hex6HexNAc5 (major) and dHex1Hex6HexNAc5 (minor)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P19652

  • ORM2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_000599.1  
    ENSEMBL proteins: 
     ENSP00000394936   ENSP00000407099  

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    Novus Biologicals ORM2 Protein
    Novus Biologicals ORM2 Lysates
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for ORM2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space IEA--


    ORM2 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

    ORM2 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR012674 Calycin
     IPR011038 Calycin-like
     IPR001500 A1A_glycop
     IPR000566 Lipocln_cytosolic_FA-bd_dom

    Graphical View of Domain Structure for InterPro Entry P19652

    ProtoNet protein and cluster: P19652

    2 Blocks protein families:
    IPB001500 Alpha-1-acid glycoprotein signature
    IPB002345 Lipocalin signature


    UniProtKB/Swiss-Prot: A1AG2_HUMAN, P19652
    Domain: Contains a beta-barrel that binds various ligands in its interior
    Similarity: Belongs to the calycin superfamily. Lipocalin 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: A1AG2_HUMAN, P19652
    Function: Functions as transport protein in the blood stream. Binds various hydrophobic ligands in the interior of its
    beta-barrel domain. Also binds synthetic drugs and influences their distribution and availability. Appears to function
    in modulating the activity of the immune system during the acute-phase reaction
    Induction: Synthesis is controlled by glucocorticoids, interleukin-1 and interleukin-6, It increases 5- to 50-fold upon
    inflammation

         Genatlas biochemistry entry for ORM2:
    orosomucoid 2 (lipocalin family,outlier group),abundant in plasma

    miRNA
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    Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for ORM2

    2 GenomeRNAi human phenotypes for ORM2:
     Decreased viability  Synthetic lethal with c-Myc af 


    (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 ORM2

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for ORM2 (ENSP000003949364) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CYP39A1ENSP000002750164STRING: ENSP00000275016
    PRDX6ENSP000003420264STRING: ENSP00000342026
    STK3ENSP000003905004STRING: ENSP00000390500
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002682regulation of immune system process IEA--
    GO:0006810transport IEA--
    GO:0006953acute-phase response IEA--


    ORM2 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 ORM2
    Search CenterWatch for drugs/clinical trials and news about ORM2 / A1AG2 

    (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 ORM2 gene: 
    NM_000608.2  

    Unigene Cluster for ORM2:

    Orosomucoid 2
    Hs.719954  [show with all ESTs]
    Unigene Representative Sequence: BG565280
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000431067(uc004bil.3) ENST00000412657

    miRNA
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    Inhib. RNA
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    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for ORM2 (see all 4)
    OriGene shRNA RFP: ORM2
    OriGene siRNA: ORM2
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ORM2
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ORM2

    Additional cDNA sequence: 

    AK303760.1 AK312226.1 BC015964.1 BC056239.1 CR456930.1 

    13 DOTS entries:

    DT.92463996  DT.100670839  DT.92464010  DT.121186696  DT.450404  DT.95175806  DT.65286353  DT.92464001 
    DT.92464008  DT.95158975  DT.86840646  DT.92463997  DT.92464007 

    24/657 AceView cDNA sequences (see all 657):

    AV682753 CB124856 AV645952 T69622 AA345746 BG562529 AA345520 CB148255 
    AA344271 AA344010 AA313164 BC056239 AA345342 BQ446130 AA343509 AA344117 
    T64422 CR607356 AA344049 BG562428 BC026238 T28642 AW963039 D17069 

    GeneLoc Exon Structure


    (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

    ORM2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    About this image

    ORM2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Mesendoderm-like cells (Generation of mesend...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See ORM2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ORM2

    SOURCE GeneReport for Unigene cluster: Hs.719954

    UniProtKB/Swiss-Prot: A1AG2_HUMAN, P19652
    Tissue specificity: Expressed by the liver and secreted in plasma

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    In Situ
    Assay Products:
     

     
    Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for ORM2

    (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 human and mouse.

    Orthologs for ORM2 gene from 1/4 species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Orm25 orosomucoid 2   --   4 (33.96 cM) 63362449 


    ENSEMBL Gene Tree for ORM2 (if available)
    TreeFam Gene Tree for ORM2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ORM2 gene
    ORM12  
    1 SIMAP similar gene for ORM2 using alignment to 2 protein entries:     A1AG2_HUMAN (see all proteins):
    ORM1

    ORM2 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

    UniProtKB/Swiss-Prot: A1AG2_HUMAN, P19652
    Polymorphism: Many different variants of ORM2 are known


    10/152 NCBI SNPs in ORM2 are shown (see all 152    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs64780751,2
    C,F,A,--117090116(+) GCCACG/AAAGGG 1 -- us2k11Minor allele frequency- A:0.17WA 118
    rs1508110371,2
    --117090246(+) GCTGCA/GTACAC 1 -- us2k10--------
    rs37620571,2
    C,H,--117090376(-) ATGCTG/CTAGTC 1 -- us2k12Minor allele frequency- C:0.17EA NA 1486
    rs1135218891,2
    --117090407(+) CACTGC/TTGTGC 1 -- us2k12Minor allele frequency- T:0.04CSA WA 119
    rs37620561,2
    C,--117090434(-) TCGGTA/GTCCCC 1 -- us2k11Minor allele frequency- G:0.00CSA 1
    rs70395141,2
    C,--117090437(+) GACACC/TGAGCT 1 -- us2k10--------
    rs1443114741,2
    --117090516(+) AGAACC/GTAAAA 1 -- us2k10--------
    rs26368841,2
    C,F,A,H,,--117090539(+) TTTCAA/GTGTTA 1 -- us2k18Minor allele frequency- G:0.03NS EA NA WA 542
    rs37620551,2
    C,F,H,--117090575(-) TCCTCA/GGTATG 1 -- us2k18Minor allele frequency- G:0.02EA NS CSA WA NA 2122
    rs1143297931,2
    --117090586(+) GGATCC/TGCTGA 1 -- us2k11Minor allele frequency- T:0.01WA 118

    HapMap Linkage Disequilibrium report for ORM2 (117092069 - 117095536 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 8 variations for ORM2
         8 CNVs: 70782 53884 53071 100763 29804 5263 8632 5264

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for ORM2

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

    ORM2 for disorders           About GeneDecksing

    OMIM gene information: 138610    OMIM disorders: --

    9 diseases for ORM2:    About MalaCards
    chronic myeloid leukemia    myeloid leukemia    sjogren's syndrome    hepatitis b
    hepatocellular carcinoma    leukemia    hepatitis    immunodeficiency
    carcinoma

    1 Novoseek disease relationship for ORM2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    inflammation 0 1 12528117 (1)

    Human Genome Epidemiology (HuGE) Navigator: ORM2 (4 documents)

    Export disorders for ORM2 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 ORM2 gene, integrated from 9 sources (see all 47):
    (articles sorted by number of sources associating them with ORM2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Structure and characterisation of a duplicated human alpha 1 acid glycoprotein gene. (PubMed id 2970990)1, 2, 3 Merritt C.M. and Board P.G. (1988)
    2. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)1, 2 Liu T.... Smith R.D. (2005)
    3. A proteomic analysis of human bile. (PubMed id 15084671)1, 2 Kristiansen T.Z.... Pandey A. (2004)
    4. Screening for N-glycosylated proteins by liquid chromatography mass spectrometry. (PubMed id 14760718)1, 2 Bunkenborg J.... Wisniewski J.R. (2004)
    5. A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation. (PubMed id 15253437)1, 2 Hagglund P.... Roepstorff P. (2004)
    6. 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)
    7. Analysis of the five glycosylation sites of human alpha 1-acid glycoprotein. (PubMed id 1567356)1, 2 Treuheit M.J.... Halsall H.B. (1992)
    8. Structure and expression of the genes coding for human alpha 1-acid glycoprotein. (PubMed id 2822385)1, 2 Dente L.... Cortese R. (1987)
    9. The disulfide bonds of alpha1-acid glycoprotein. (PubMed id 4603214)1, 2 Schmid K.... Nanno S. (1974)
    10. Structure of alpha 1-acid glycoprotein. The complete amino acid sequence, multiple amino acid substitutions, and homology with the immunoglobulins. (PubMed id 4711474)1, 3 Schmid K.... Nanno S. (1973)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 5005 HGNC: 8499 AceView: ORM1andORM2 Ensembl:ENSG00000228278 euGenes: HUgn5005
    ECgene: ORM2 H-InvDB: ORM2

    (According to HUGE)
    About This Section
      --

    (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 ORM2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for ORM2 gene:
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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