Human Gene SAA1 (ENST00000356524.9_4) from GENCODE V47lift37
  Description: serum amyloid A1, transcript variant 2 (from RefSeq NM_199161.5)
Gencode Transcript: ENST00000356524.9_4
Gencode Gene: ENSG00000173432.13_9
Transcript (Including UTRs)
   Position: hg19 chr11:18,287,811-18,291,514 Size: 3,704 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr11:18,288,435-18,291,402 Size: 2,968 Coding Exon Count: 3 

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 (chr11:18,287,811-18,291,514)mRNA (may differ from genome)Protein (122 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SAA1_HUMAN
DESCRIPTION: RecName: Full=Serum amyloid A-1 protein; Short=SAA; Contains: RecName: Full=Amyloid protein A; AltName: Full=Amyloid fibril protein AA; Contains: RecName: Full=Serum amyloid protein A(2-104); Contains: RecName: Full=Serum amyloid protein A(3-104); Contains: RecName: Full=Serum amyloid protein A(2-103); Contains: RecName: Full=Serum amyloid protein A(2-102); Contains: RecName: Full=Serum amyloid protein A(4-101); Flags: Precursor;
FUNCTION: Major acute phase reactant. Apolipoprotein of the HDL complex.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Expressed by the liver; secreted in plasma.
INDUCTION: Upon cytokine stimulation.
PTM: This protein is the precursor of amyloid protein A, which is formed by the removal of approximately 24 residues from the C- terminal end.
MASS SPECTROMETRY: Mass=11702; Mass_error=14; Method=MALDI; Range=19-122; Source=PubMed:12973732;
MASS SPECTROMETRY: Mass=11682.7; Method=MALDI; Range=19-122; Source=PubMed:12606051;
MASS SPECTROMETRY: Mass=11526.5; Method=MALDI; Range=20-122; Source=PubMed:12606051;
MASS SPECTROMETRY: Mass=11439.6; Method=MALDI; Range=21-122; Source=PubMed:12606051;
MASS SPECTROMETRY: Mass=11363.6; Method=MALDI; Range=20-121; Source=PubMed:12606051;
MASS SPECTROMETRY: Mass=11235.6; Method=MALDI; Range=20-120; Source=PubMed:12606051;
MASS SPECTROMETRY: Mass=10872.6; Method=MALDI; Range=22-119; Source=PubMed:12606051;
MASS SPECTROMETRY: Mass=8337.5; Mass_error=0.8; Method=Electrospray; Range=19-94; Note=With variants Ala-70, Val- 75, Asn-78 and 86-Leu-Thr-87; Source=PubMed:1463770;
MASS SPECTROMETRY: Mass=8390.9; Mass_error=0.2; Method=Electrospray; Range=19-94; Note=With variant Ala-70; Source=PubMed:1463770;
POLYMORPHISM: At least 5 different SAA1 alleles have been described: SAA1.1 (SAA1alpha), SAA1.2 (SAA1beta), SAA1.3 (SAA1gamma), SAA1.4 (SAA1delta), SAA1.5 (also named SAA1beta but which differs from SAA1.2). We use here the revised nomenclature described in PubMed:10211414. The sequence shown is that of SAA1.1.
DISEASE: Note=Reactive, secondary amyloidosis is characterized by the extracellular accumulation in various tissues of the SAA1 protein. These deposits are highly insoluble and resistant to proteolysis; they disrupt tissue structure and compromise function.
DISEASE: Note=Elevated serum SAA1 protein levels may be associated with lung cancer.
SIMILARITY: Belongs to the SAA family.

-  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: SAA1
Diseases sorted by gene-association score: amyloidosis aa* (45), amyloidosis (23), splenic artery aneurysm (17), familial mediterranean fever, ar (14), bronchus cancer (14), arthritis (11), hyper-igd syndrome (10), subclavian artery aneurysm (8), familial cold autoinflammatory syndrome (8), amyloidosis, familial visceral (7), blepharochalasis (6), rheumatoid arthritis (6), ochronosis (6), hermansky-pudlak syndrome 5 (6), atherosclerosis (5), fetal erythroblastosis (5), acute contagious conjunctivitis (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 5869.61 RPKM in Liver
Total median expression: 7663.40 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 -1.8037-0.049 Picture PostScript Text
3' UTR -32.00112-0.286 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
IPR000096 - Serum_amyloid_A

Pfam Domains:
PF00277 - Serum amyloid A protein

ModBase Predicted Comparative 3D Structure on P0DJI8
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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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001664 G-protein coupled receptor binding
GO:0008201 heparin binding
GO:0042056 chemoattractant activity

Biological Process:
GO:0000187 activation of MAPK activity
GO:0006898 receptor-mediated endocytosis
GO:0006953 acute-phase response
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0019221 cytokine-mediated signaling pathway
GO:0030168 platelet activation
GO:0030593 neutrophil chemotaxis
GO:0044267 cellular protein metabolic process
GO:0045087 innate immune response
GO:0045785 positive regulation of cell adhesion
GO:0048246 macrophage chemotaxis
GO:0048247 lymphocyte chemotaxis
GO:0050708 regulation of protein secretion
GO:0050715 positive regulation of cytokine secretion
GO:0050716 positive regulation of interleukin-1 secretion
GO:0050728 negative regulation of inflammatory response
GO:0050918 positive chemotaxis

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005881 cytoplasmic microtubule
GO:0034364 high-density lipoprotein particle
GO:0070062 extracellular exosome
GO:0071682 endocytic vesicle lumen


-  Descriptions from all associated GenBank mRNAs
  X51444 - Human mRNA for serum amyloid A (SAA) protein partial, clone pAS6.
BC007022 - Homo sapiens serum amyloid A1, mRNA (cDNA clone MGC:12369 IMAGE:4071612), complete cds.
BC105796 - Homo sapiens serum amyloid A1, mRNA (cDNA clone MGC:111216 IMAGE:4722684), complete cds.
DQ892344 - Synthetic construct clone IMAGE:100004974; FLH186961.01X; RZPDo839C0472D serum amyloid A1 (SAA1) gene, encodes complete protein.
DQ892439 - Synthetic construct Homo sapiens clone IMAGE:100005069; FLH263493.01X; RZPDo839D0571D serum amyloid A1 (SAA1) gene, encodes complete protein.
DQ895549 - Synthetic construct Homo sapiens clone IMAGE:100010009; FLH186957.01L; RZPDo839C0462D serum amyloid A1 (SAA1) gene, encodes complete protein.
EU176517 - Synthetic construct Homo sapiens clone IMAGE:100011602; FLH263705.01L; RZPDo839A0571D serum amyloid A1 (SAA1) gene, encodes complete protein.
KJ901721 - Synthetic construct Homo sapiens clone ccsbBroadEn_11115 SAA1 gene, encodes complete protein.
AB590374 - Synthetic construct DNA, clone: pFN21AE1532, Homo sapiens SAA1 gene for serum amyloid A1, without stop codon, in Flexi system.
CR542241 - Homo sapiens full open reading frame cDNA clone RZPDo834A0126D for gene SAA1, serum amyloid A1; complete cds, without stopcodon.
M10906 - Human serum amyloid A (SAA) mRNA.
M23698 - Homo sapiens serum amyloid A1 (SAA1) mRNA, complete cds.
X51443 - Human mRNA for serum amyloid A protein partial, clone pAS4.
X51441 - Human mRNA for serum amyloid A (SAA) protein partial, clone pAS3-alpha.
X51442 - Human mRNA for serum amyloid A (SAA) protein partial, clone pAS3-beta.
X51439 - Human mRNA for serum amyloid A (SAA) protein partial, clone pAS1.
JD054287 - Sequence 35311 from Patent EP1572962.
JD025381 - Sequence 6405 from Patent EP1572962.
JD035314 - Sequence 16338 from Patent EP1572962.

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

Protein P0DJI8 (Reactome details) participates in the following event(s):

R-HSA-391913 FPR2 binds FPR2 ligands
R-HSA-879411 Advanced glycosylation end product-specific receptor (AGER/RAGE) is a multiligand receptor
R-HSA-2197646 SCARB1 (SR-BI, CLA-1) binds ligands
R-HSA-749454 The Ligand:GPCR:Gi complex dissociates
R-HSA-749452 The Ligand:GPCR:Gq complex dissociates
R-HSA-879362 AGER binds ERK1/2
R-NUL-997411 AGER binds rat ERK1/2
R-HSA-749456 Liganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi
R-HSA-749448 Liganded Gq-activating GPCRs bind inactive heterotrimeric Gq
R-HSA-380073 Liganded Gi-activating GPCR acts as a GEF for Gi
R-HSA-379048 Liganded Gq/11-activating GPCRs act as GEFs for Gq/11
R-HSA-444473 Formyl peptide receptors bind formyl peptides and many other ligands
R-HSA-879415 Advanced glycosylation endproduct receptor signaling
R-HSA-3000471 Scavenging by Class B Receptors
R-HSA-6785807 Interleukin-4 and 13 signaling
R-HSA-977225 Amyloid fiber formation
R-HSA-418594 G alpha (i) signalling events
R-HSA-416476 G alpha (q) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-168249 Innate Immune System
R-HSA-2173782 Binding and Uptake of Ligands by Scavenger Receptors
R-HSA-449147 Signaling by Interleukins
R-HSA-392499 Metabolism of proteins
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-168256 Immune System
R-HSA-5653656 Vesicle-mediated transport
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-372790 Signaling by GPCR
R-HSA-500792 GPCR ligand binding
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: E9PQD6, ENST00000356524.1, ENST00000356524.2, ENST00000356524.3, ENST00000356524.4, ENST00000356524.5, ENST00000356524.6, ENST00000356524.7, ENST00000356524.8, NM_199161, P02735, P02736, P02737, P0DJI8, Q16730, Q16834, Q16835, Q16879, Q3KRB3, Q6FG67, Q96QN0, Q9UCK9, Q9UCL0, SAA1_HUMAN, uc317zpg.1, uc317zpg.2
UCSC ID: ENST00000356524.9_4
RefSeq Accession: NM_199161.5
Protein: P0DJI8 (aka SAA1_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.