Human Gene ORM1 (ENST00000259396.9_3) from GENCODE V47lift37
  Description: orosomucoid 1 (from RefSeq NM_000607.4)
Gencode Transcript: ENST00000259396.9_3
Gencode Gene: ENSG00000229314.6_4
Transcript (Including UTRs)
   Position: hg19 chr9:117,085,378-117,088,759 Size: 3,382 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr9:117,085,414-117,088,637 Size: 3,224 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:117,085,378-117,088,759)mRNA (may differ from genome)Protein (201 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: A1AG1_HUMAN
DESCRIPTION: RecName: Full=Alpha-1-acid glycoprotein 1; Short=AGP 1; AltName: Full=Orosomucoid-1; Short=OMD 1; Flags: Precursor;
FUNCTION: Functions as transport protein in the blood stream. Binds various ligands in the interior of its beta-barrel domain. Also binds synthetic drugs and influences their distribution and availability in the body. Appears to function in modulating the activity of the immune system during the acute-phase reaction.
INTERACTION: P05121:SERPINE1; NbExp=4; IntAct=EBI-976767, EBI-953978;
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Expressed by the liver and secreted in plasma.
INDUCTION: Synthesis is controlled by glucocorticoids, interleukin-1 and interleukin-6, It increases 5- to 50-fold upon inflammation.
DOMAIN: Contains a beta-barrel that binds various ligands in its interior.
PTM: N-glycosylated. N-glycan heterogeneity at Asn-33: Hex5HexNAc4 (minor), Hex6HexNAc5 (major) and dHex1Hex6HexNAc5 (minor).
POLYMORPHISM: Three common alleles of ORM1 are known. ORM1*F1 has Gln-38/Val-174; ORM1*F2 has Gln-38/Met-174 and ORM1*S has Arg- 38/Val-174. The sequence shown is that of allele ORM1*F1.
SIMILARITY: Belongs to the calycin superfamily. Lipocalin family.
SEQUENCE CAUTION: Sequence=CAA29229.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ORM1
Diseases sorted by gene-association score: dry eye syndrome (3), pediatric multiple sclerosis (2), odontogenic myxoma (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7046.51 RPKM in Liver
Total median expression: 7085.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.4036-0.150 Picture PostScript Text
3' UTR -31.40122-0.257 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001500 - A1A_glycop
IPR012674 - Calycin
IPR011038 - Calycin-like
IPR000566 - Lipocln_cytosolic_FA-bd_dom

Pfam Domains:
PF00061 - Lipocalin / cytosolic fatty-acid binding protein family

SCOP Domains:
50814 - Lipocalins
55681 - Class II aaRS and biotin synthetases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3KQ0 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P02763
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0002576 platelet degranulation
GO:0002682 regulation of immune system process
GO:0006953 acute-phase response
GO:0006954 inflammatory response
GO:0032715 negative regulation of interleukin-6 production
GO:0032720 negative regulation of tumor necrosis factor production
GO:0043312 neutrophil degranulation
GO:0050716 positive regulation of interleukin-1 secretion
GO:0050718 positive regulation of interleukin-1 beta secretion
GO:1904469 positive regulation of tumor necrosis factor secretion

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0031012 extracellular matrix
GO:0031093 platelet alpha granule lumen
GO:0035580 specific granule lumen
GO:0070062 extracellular exosome
GO:0072562 blood microparticle
GO:1904724 tertiary granule lumen


-  Descriptions from all associated GenBank mRNAs
  KJ897282 - Synthetic construct Homo sapiens clone ccsbBroadEn_06676 ORM1 gene, encodes complete protein.
X02544 - Human mRNA for alpha1-acid glycoprotein (orosomucoid).
JD534556 - Sequence 515580 from Patent EP1572962.
JD366017 - Sequence 347041 from Patent EP1572962.
JD383017 - Sequence 364041 from Patent EP1572962.
AK316207 - Homo sapiens cDNA, FLJ79106 complete cds, weakly similar to Alpha-1-acid glycoprotein 1 precursor.
AK312035 - Homo sapiens cDNA, FLJ92312, Homo sapiens orosomucoid 1 (ORM1), mRNA.
BC026238 - Homo sapiens orosomucoid 1, mRNA (cDNA clone MGC:22246 IMAGE:4767956), complete cds.
BC007032 - Homo sapiens cDNA clone IMAGE:4071534, containing frame-shift errors.
JD537172 - Sequence 518196 from Patent EP1572962.
BC104818 - Homo sapiens orosomucoid 1, mRNA (cDNA clone MGC:132478 IMAGE:8143821), complete cds.
BC104820 - Homo sapiens orosomucoid 1, mRNA (cDNA clone MGC:132480 IMAGE:8143823), complete cds.
BC143313 - Homo sapiens orosomucoid 1, mRNA (cDNA clone MGC:176835 IMAGE:9051818), complete cds.
BC143314 - Homo sapiens orosomucoid 1, mRNA (cDNA clone MGC:176836 IMAGE:9051819), complete cds.
M13692 - Human alpha-1 acid glycoprotein mRNA, complete cds.
AB463987 - Synthetic construct DNA, clone: pF1KB6888, Homo sapiens ORM1 gene for orosomucoid 1, without stop codon, in Flexi system.
CU693168 - Synthetic construct Homo sapiens gateway clone IMAGE:100022096 5' read ORM1 mRNA.
BT019790 - Homo sapiens orosomucoid 1 mRNA, complete cds.
EU794584 - Homo sapiens epididymis secretory sperm binding protein Li 153w (HEL-S-153w) mRNA, complete cds.
BC014367 - Homo sapiens mRNA similar to orosomucoid 1 (cDNA clone IMAGE:3934516).
JD317862 - Sequence 298886 from Patent EP1572962.
JD137666 - Sequence 118690 from Patent EP1572962.
JD433524 - Sequence 414548 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P02763 (Reactome details) participates in the following event(s):

R-HSA-6798749 Exocytosis of specific granule lumen proteins
R-HSA-481007 Exocytosis of platelet alpha granule contents
R-HSA-6798745 Exocytosis of tertiary granule lumen proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-114608 Platelet degranulation
R-HSA-168249 Innate Immune System
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-168256 Immune System
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: A1AG1_HUMAN, AGP1, B7ZKQ5, ENST00000259396.1, ENST00000259396.2, ENST00000259396.3, ENST00000259396.4, ENST00000259396.5, ENST00000259396.6, ENST00000259396.7, ENST00000259396.8, NM_000607, P02763, Q5T539, Q5U067, Q8TC16, uc317ggm.1, uc317ggm.2
UCSC ID: ENST00000259396.9_3
RefSeq Accession: NM_000607.4
Protein: P02763 (aka A1AG1_HUMAN or A1AG_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.