Human Gene APOA2 (ENST00000367990.7_8) from GENCODE V47lift37
  Description: apolipoprotein A2 (from RefSeq NM_001643.2)
Gencode Transcript: ENST00000367990.7_8
Gencode Gene: ENSG00000158874.12_16
Transcript (Including UTRs)
   Position: hg19 chr1:161,192,082-161,193,418 Size: 1,337 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr1:161,192,195-161,193,191 Size: 997 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 (chr1:161,192,082-161,193,418)mRNA (may differ from genome)Protein (100 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: APOA2_HUMAN
DESCRIPTION: RecName: Full=Apolipoprotein A-II; Short=Apo-AII; Short=ApoA-II; AltName: Full=Apolipoprotein A2; Contains: RecName: Full=Truncated apolipoprotein A-II; AltName: Full=Apolipoprotein A-II(1-76); Flags: Precursor;
FUNCTION: May stabilize HDL (high density lipoprotein) structure by its association with lipids, and affect the HDL metabolism.
SUBUNIT: Homodimer; disulfide-linked. Also forms a disulfide- linked heterodimer with APOD. Interacts with HCV core protein. Interacts with APOA1BP and NDRG1.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Plasma; synthesized in the liver and intestine.
PTM: Met-49 is oxidized to methionine sulfoxide.
PTM: Phosphorylation sites are present in the extracellular medium.
MASS SPECTROMETRY: Mass=17252; Method=Electrospray; Range=24-100; Note=Homodimer, without methionine sulfoxide; Source=PubMed:12576517;
MASS SPECTROMETRY: Mass=17269; Method=Electrospray; Range=24-100; Note=Homodimer, with 1 methionine sulfoxide, oxidation at Met-49; Source=PubMed:12576517;
MASS SPECTROMETRY: Mass=8701.2; Method=MALDI; Range=24-100; Source=PubMed:12562854;
MASS SPECTROMETRY: Mass=8823.4; Method=MALDI; Range=24-100; Note=Cysteinylated ApoA-II; Source=PubMed:12562854;
MASS SPECTROMETRY: Mass=17421.3; Method=MALDI; Range=24-100; Note=Homodimer; Source=PubMed:12562854;
MASS SPECTROMETRY: Mass=17293.4; Method=MALDI; Range=24-100; Note=Heterodimer with truncated apolipoprotein A-II; Source=PubMed:12562854;
MASS SPECTROMETRY: Mass=8578.3; Method=MALDI; Range=24-99; Source=PubMed:12562854;
MASS SPECTROMETRY: Mass=17166.2; Method=MALDI; Range=24-99; Note=Homodimer; Source=PubMed:12562854;
SIMILARITY: Belongs to the apolipoprotein A2 family.
WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=APOA2";

-  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: APOA2
Diseases sorted by gene-association score: apolipoprotein a-ii deficiency* (539), hypercholesterolemia, familial* (410), aapoaii amyloidosis* (350), norum disease (25), fish-eye disease (20), tangier disease (16), hypoalphalipoproteinemia (14), coronary artery disease (13), hyperalphalipoproteinemia (12), artery disease (10), hypertriglyceridemia (9), amyloidosis, familial visceral (9), familial lcat deficiency (9), leukodystrophy, hypomyelinating, 3 (9), lipoprotein glomerulopathy (8), hyperlipidemia, familial combined (7), hereditary amyloidosis (6), arcus senilis (6), hypolipoproteinemia (6), myocardial infarction (1), diabetes mellitus, noninsulin-dependent (1)
* = 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: 2822.58 RPKM in Liver
Total median expression: 2828.76 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 -9.4058-0.162 Picture PostScript Text
3' UTR -15.60113-0.138 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
IPR006801 - ApoA-II

Pfam Domains:
PF04711 - Apolipoprotein A-II (ApoA-II)

SCOP Domains:
47162 - Apolipoprotein
82936 - Apolipoprotein A-II

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1L6L - X-ray 2OU1 - X-ray


ModBase Predicted Comparative 3D Structure on P02652
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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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005319 lipid transporter activity
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0008035 high-density lipoprotein particle binding
GO:0008289 lipid binding
GO:0015485 cholesterol binding
GO:0017127 cholesterol transporter activity
GO:0031072 heat shock protein binding
GO:0031210 phosphatidylcholine binding
GO:0034190 apolipoprotein receptor binding
GO:0042803 protein homodimerization activity
GO:0046982 protein heterodimerization activity
GO:0055102 lipase inhibitor activity
GO:0060228 phosphatidylcholine-sterol O-acyltransferase activator activity
GO:0070653 high-density lipoprotein particle receptor binding

Biological Process:
GO:0001523 retinoid metabolic process
GO:0002526 acute inflammatory response
GO:0002740 negative regulation of cytokine secretion involved in immune response
GO:0006641 triglyceride metabolic process
GO:0006656 phosphatidylcholine biosynthetic process
GO:0006869 lipid transport
GO:0008203 cholesterol metabolic process
GO:0009395 phospholipid catabolic process
GO:0009749 response to glucose
GO:0010873 positive regulation of cholesterol esterification
GO:0010903 negative regulation of very-low-density lipoprotein particle remodeling
GO:0016032 viral process
GO:0018158 protein oxidation
GO:0018206 peptidyl-methionine modification
GO:0019216 regulation of lipid metabolic process
GO:0030300 regulation of intestinal cholesterol absorption
GO:0030301 cholesterol transport
GO:0031100 animal organ regeneration
GO:0031647 regulation of protein stability
GO:0032375 negative regulation of cholesterol transport
GO:0033344 cholesterol efflux
GO:0033700 phospholipid efflux
GO:0034370 triglyceride-rich lipoprotein particle remodeling
GO:0034371 chylomicron remodeling
GO:0034374 low-density lipoprotein particle remodeling
GO:0034375 high-density lipoprotein particle remodeling
GO:0034378 chylomicron assembly
GO:0034380 high-density lipoprotein particle assembly
GO:0034384 high-density lipoprotein particle clearance
GO:0042157 lipoprotein metabolic process
GO:0042493 response to drug
GO:0042632 cholesterol homeostasis
GO:0043085 positive regulation of catalytic activity
GO:0043627 response to estrogen
GO:0043687 post-translational protein modification
GO:0043691 reverse cholesterol transport
GO:0044267 cellular protein metabolic process
GO:0045416 positive regulation of interleukin-8 biosynthetic process
GO:0046340 diacylglycerol catabolic process
GO:0050995 negative regulation of lipid catabolic process
GO:0050996 positive regulation of lipid catabolic process
GO:0051384 response to glucocorticoid
GO:0060192 negative regulation of lipase activity
GO:0060621 negative regulation of cholesterol import
GO:0060695 negative regulation of cholesterol transporter activity

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005769 early endosome
GO:0005788 endoplasmic reticulum lumen
GO:0005829 cytosol
GO:0034361 very-low-density lipoprotein particle
GO:0034364 high-density lipoprotein particle
GO:0034366 spherical high-density lipoprotein particle
GO:0042627 chylomicron
GO:0070062 extracellular exosome
GO:0072562 blood microparticle


-  Descriptions from all associated GenBank mRNAs
  KJ890686 - Synthetic construct Homo sapiens clone ccsbBroadEn_00080 APOA2 gene, encodes complete protein.
JD167432 - Sequence 148456 from Patent EP1572962.
M29882 - Human apolipoprotein A-II mRNA, complete cds.
X00955 - Human mRNA for apolipoprotein AII precursor.
BC005282 - Homo sapiens apolipoprotein A-II, mRNA (cDNA clone MGC:12334 IMAGE:3934476), complete cds.
AB106565 - Homo sapiens APOA2 mRNA for apolipoprotein A-II, complete cds.
JD061654 - Sequence 42678 from Patent EP1572962.
JD023188 - Sequence 4212 from Patent EP1572962.
JD036123 - Sequence 17147 from Patent EP1572962.
JD546996 - Sequence 528020 from Patent EP1572962.
JD269436 - Sequence 250460 from Patent EP1572962.
JD023688 - Sequence 4712 from Patent EP1572962.
AK312034 - Homo sapiens cDNA, FLJ92311, Homo sapiens apolipoprotein A-II (APOA2), mRNA.
BT006786 - Homo sapiens apolipoprotein A-II mRNA, complete cds.
DQ892493 - Synthetic construct clone IMAGE:100005123; FLH186817.01X; RZPDo839A1072D apolipoprotein A-II (APOA2) gene, encodes complete protein.
DQ895705 - Synthetic construct Homo sapiens clone IMAGE:100010165; FLH186813.01L; RZPDo839A1062D apolipoprotein A-II (APOA2) gene, encodes complete protein.
AB590164 - Synthetic construct DNA, clone: pFN21AE1405, Homo sapiens APOA2 gene for apolipoprotein A-II, without stop codon, in Flexi system.
JD031806 - Sequence 12830 from Patent EP1572962.
JD027115 - Sequence 8139 from Patent EP1572962.
JD035046 - Sequence 16070 from Patent EP1572962.
JD212080 - Sequence 193104 from Patent EP1572962.
JD437982 - Sequence 419006 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_pparaPathway - Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha)

Reactome (by CSHL, EBI, and GO)

Protein P02652 (Reactome details) participates in the following event(s):

R-HSA-174741 ApoB-48:TG:PL complex + 100 triacylglycerols + ApoA-I + ApoA-IV => nascent chylomicron
R-HSA-174587 nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular]
R-HSA-174757 chylomicron => TG-depleted chylomicron + 50 long-chain fatty acids + 50 diacylglycerols
R-HSA-174660 nascent chylomicron + spherical HDL:apoC-II:apoC-III:apoE =>spherical HDL + chylomicron
R-HSA-174690 TG-depleted chylomicron + spherical HDL => chylomicron remnant + spherical HDL:apoA-I:apoA-II:apoA-IV:apoC-II:apoC-III
R-HSA-2395784 Nascent CMs transform into mature CMs
R-HSA-2187332 Cytosolic CMs translocate to extracellular region
R-HSA-2395768 LPL hydrolyses TGs from mature CMs
R-HSA-2395764 atREs binds to nascent CM
R-HSA-2404140 NREH hydrolyses atREs to atROL and FAs
R-HSA-2429643 NREH hydrolyses atREs (HSPG:apoE) to atROL and FAs
R-HSA-2423785 CR:atREs binds apoE and HSPG
R-HSA-2424254 LDLR transports extracellular CR:atREs to cytosol
R-HSA-8952289 FAM20C phosphorylates FAM20C substrates
R-HSA-2404131 LRPs transport extracellular CR:atREs:HSPG:apoE to cytosol
R-HSA-8963888 Chylomicron assembly
R-HSA-1989781 PPARA activates gene expression
R-HSA-8963898 Plasma lipoprotein assembly
R-HSA-8963901 Chylomicron remodeling
R-HSA-975634 Retinoid metabolism and transport
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-174824 Plasma lipoprotein assembly, remodeling, and clearance
R-HSA-8963899 Plasma lipoprotein remodeling
R-HSA-2187338 Visual phototransduction
R-HSA-6806667 Metabolism of fat-soluble vitamins
R-HSA-556833 Metabolism of lipids
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275 Post-translational protein phosphorylation
R-HSA-382551 Transport of small molecules
R-HSA-418594 G alpha (i) signalling events
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-1430728 Metabolism
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification
R-HSA-388396 GPCR downstream signalling
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: APOA2_HUMAN, B2R524, ENST00000367990.1, ENST00000367990.2, ENST00000367990.3, ENST00000367990.4, ENST00000367990.5, ENST00000367990.6, NM_001643, P02652, uc318gjh.1, uc318gjh.2
UCSC ID: ENST00000367990.7_8
RefSeq Accession: NM_001643.2
Protein: P02652 (aka APOA2_HUMAN or APA2_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.