Human Gene ABCA2 (uc022bpy.1) Description and Page Index
  Description: Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 2 (ABCA2), transcript variant 1, mRNA.
RefSeq Summary (NM_001606): The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is highly expressed in brain tissue and may play a role in macrophage lipid metabolism and neural development. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr9:139,901,686-139,922,740 Size: 21,055 Total Exon Count: 48 Strand: -
Coding Region
   Position: hg19 chr9:139,902,381-139,917,457 Size: 15,077 Coding Exon Count: 46 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr9:139,901,686-139,922,740)mRNA (may differ from genome)Protein (2436 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ABCA2
CDC HuGE Published Literature: ABCA2
Positive Disease Associations: Alzheimer's disease
Related Studies:
  1. Alzheimer's disease
    Wollmer, M. A. et al. 2006, Ethnicity-dependent genetic association of ABCA2 with sporadic Alzheimer's disease, Am J Med Genet B Neuropsychiatr Genet 2006. [PubMed 16752360]

-  MalaCards Disease Associations
  MalaCards Gene Search: ABCA2
Diseases sorted by gene-association score: acoustic neuroma (8)

-  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: 176.33 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 1171.36 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 -567.831143-0.497 Picture PostScript Text
3' UTR -324.60695-0.467 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
  Pfam Domains:
PF00005 - ABC transporter
PF12698 - ABC-2 family transporter protein
PF13304 - AAA domain, putative AbiEii toxin, Type IV TA system

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like

ModBase Predicted Comparative 3D Structure on Q9BZC7-3
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Descriptions from all associated GenBank mRNAs
  AL162060 - Homo sapiens mRNA; cDNA DKFZp547P193 (from clone DKFZp547P193); partial cds.
AK226112 - Homo sapiens mRNA for ATP-binding cassette, sub-family A, member 2 isoform a variant, clone: hg01099.
BC008755 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 2, mRNA (cDNA clone IMAGE:3344721), partial cds.
AB028985 - Homo sapiens mRNA for KIAA1062 protein, partial cds.
AF178941 - Homo sapiens ATP-binding cassette sub-family A member 2 (ABCA2) mRNA, complete cds.
AB177854 - Homo sapiens mRNA for KIAA1062 splice variant 1.
BC144588 - Homo sapiens cDNA clone IMAGE:9053118.
BC144589 - Homo sapiens cDNA clone IMAGE:9053119, containing frame-shift errors.
JD134786 - Sequence 115810 from Patent EP1572962.
JD526785 - Sequence 507809 from Patent EP1572962.
JD491439 - Sequence 472463 from Patent EP1572962.
JD467376 - Sequence 448400 from Patent EP1572962.
JD477076 - Sequence 458100 from Patent EP1572962.
JD118665 - Sequence 99689 from Patent EP1572962.
AK295489 - Homo sapiens cDNA FLJ61118 complete cds, highly similar to ATP-binding cassette sub-family A member 2.
JD523137 - Sequence 504161 from Patent EP1572962.
AF327657 - Homo sapiens ABC transporter ABCA2 (ABCA2) mRNA, complete cds.
JD108714 - Sequence 89738 from Patent EP1572962.
JD269947 - Sequence 250971 from Patent EP1572962.
JD466417 - Sequence 447441 from Patent EP1572962.
JD115713 - Sequence 96737 from Patent EP1572962.
JD137436 - Sequence 118460 from Patent EP1572962.
JF279960 - Homo sapiens clone ASV8 ABCA2 mRNA, partial sequence, alternatively spliced.
BC172448 - Synthetic construct Homo sapiens clone IMAGE:100069142, MGC:199153 ATP-binding cassette, sub-family A (ABC1), member 2 (ABCA2) mRNA, encodes complete protein.
AB384556 - Synthetic construct DNA, clone: pF1KA1062, Homo sapiens ABCA2 gene for ATP-binding cassette, sub-family A member 2, complete cds, without stop codon, in Flexi system.
U18236 - Human ATP-binding cassette protein (ABCA2) mRNA HHCMH89 clone, partial cds.
AL833967 - Homo sapiens mRNA; cDNA DKFZp761O022 (from clone DKFZp761O022).
BC109244 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 2, mRNA (cDNA clone IMAGE:40017408), complete cds.
U18235 - Human ATP-binding cassette protein (ABC2) mRNA HFBCD04 clone, partial cds.
JF279959 - Homo sapiens clone ASV3 ABCA2 mRNA, partial sequence, alternatively spliced.
BC029282 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 2, mRNA (cDNA clone IMAGE:5179755).
BC064542 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 2, mRNA (cDNA clone IMAGE:5734084), partial cds.
BC090860 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 2, mRNA (cDNA clone IMAGE:6184253), with apparent retained intron.
AK308738 - Homo sapiens cDNA, FLJ98779.
BC072437 - Homo sapiens cDNA clone IMAGE:5756372, **** WARNING: chimeric clone ****.
JD019868 - Sequence 892 from Patent EP1572962.
JD035775 - Sequence 16799 from Patent EP1572962.
JD027906 - Sequence 8930 from Patent EP1572962.
JD025672 - Sequence 6696 from Patent EP1572962.
JD339879 - Sequence 320903 from Patent EP1572962.
JD125159 - Sequence 106183 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa02010 - ABC transporters
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein Q9BZC7 (Reactome details) participates in the following event(s):

R-HSA-1369028 ABCAs mediate lipid efflux
R-HSA-1369052 ABCAs mediate lipid influx
R-HSA-1369062 ABC transporters in lipid homeostasis
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: ABC2, KIAA1062, NM_001606, NP_001597, Q9BZC7-3
UCSC ID: uc022bpy.1
RefSeq Accession: NM_001606
Protein: Q9BZC7-3 CCDS: CCDS43909.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001606.4
exon count: 48CDS single in 3' UTR: no RNA size: 8171
ORF size: 7101CDS single in intron: no Alignment % ID: 99.99
txCdsPredict score: 13851.00frame shift in genome: no % Coverage: 99.79
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.