Human Gene ABCA9 (uc002jhu.3)
  Description: Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 9 (ABCA9), mRNA.
RefSeq Summary (NM_080283): This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters and the encoded protein contains two transmembrane domains and two nucleotide binding folds. 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, and White). This gene is a member of the ABC1 subfamily and is clustered with four other ABC1 family members on chromosome 17q24. Transcriptional expression of this gene is induced during monocyte differentiation into macrophages and is suppressed by cholesterol import. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:66,970,773-67,057,136 Size: 86,364 Total Exon Count: 39 Strand: -
Coding Region
   Position: hg19 chr17:66,972,056-67,047,267 Size: 75,212 Coding Exon Count: 38 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:66,970,773-67,057,136)mRNA (may differ from genome)Protein (1624 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ABCA9_HUMAN
DESCRIPTION: RecName: Full=ATP-binding cassette sub-family A member 9;
FUNCTION: May play a role in monocyte differentiation and lipid homeostasis.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Widely expressed with higher expression in heart.
DEVELOPMENTAL STAGE: Expressed in fetal tissues with higher expression in fetal heart and kidney.
INDUCTION: Up-regulated during monocyte differentiation into macrophages. Down-regulated by cholesterol loading of macrophages.
SIMILARITY: Belongs to the ABC transporter superfamily. ABCA family.
SIMILARITY: Contains 2 ABC transporter domains.
SEQUENCE CAUTION: Sequence=AAH62472.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC11021.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=Q8IUA7";

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ABCA9
CDC HuGE Published Literature: ABCA9
Positive Disease Associations: Stroke
Related Studies:
  1. Stroke
    , , . [PubMed 0]

-  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: 32.27 RPKM in Nerve - Tibial
Total median expression: 319.75 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 -26.10143-0.183 Picture PostScript Text
3' UTR -302.551283-0.236 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
IPR003593 - AAA+_ATPase
IPR026082 - ABC_A
IPR003439 - ABC_transporter-like

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 Q8IUA7
FrontTopSide
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005524 ATP binding
GO:0016887 ATPase activity
GO:0042626 ATPase activity, coupled to transmembrane movement of substances

Biological Process:
GO:0006869 lipid transport
GO:0055085 transmembrane transport

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  CR627382 - Homo sapiens mRNA; cDNA DKFZp686F2450 (from clone DKFZp686F2450).
AK122687 - Homo sapiens cDNA FLJ16148 fis, clone BRAMY2042195, highly similar to Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 8 (ABCA8).
AL833712 - Homo sapiens mRNA; cDNA DKFZp667N069 (from clone DKFZp667N069).
AY028899 - Homo sapiens ATP-binding cassette A9 mRNA, complete cds.
AF423307 - Homo sapiens ATP-binding cassette sub-family A member 9 (ABCA9) mRNA, complete cds.
BC167781 - Synthetic construct Homo sapiens clone IMAGE:100068171, MGC:195788 ATP-binding cassette, sub-family A (ABC1), member 9 (ABCA9) mRNA, encodes complete protein.
JD232122 - Sequence 213146 from Patent EP1572962.
JD283513 - Sequence 264537 from Patent EP1572962.
JD280921 - Sequence 261945 from Patent EP1572962.
JD473635 - Sequence 454659 from Patent EP1572962.
JD535245 - Sequence 516269 from Patent EP1572962.
JD089150 - Sequence 70174 from Patent EP1572962.
JD404233 - Sequence 385257 from Patent EP1572962.
JD190172 - Sequence 171196 from Patent EP1572962.
JD358732 - Sequence 339756 from Patent EP1572962.
JD409542 - Sequence 390566 from Patent EP1572962.
JD465193 - Sequence 446217 from Patent EP1572962.
JD444291 - Sequence 425315 from Patent EP1572962.
JD369251 - Sequence 350275 from Patent EP1572962.
JD182827 - Sequence 163851 from Patent EP1572962.
JD396977 - Sequence 378001 from Patent EP1572962.
JD305445 - Sequence 286469 from Patent EP1572962.
JD274517 - Sequence 255541 from Patent EP1572962.
JD184965 - Sequence 165989 from Patent EP1572962.
JD038295 - Sequence 19319 from Patent EP1572962.
JD085231 - Sequence 66255 from Patent EP1572962.
JD276013 - Sequence 257037 from Patent EP1572962.
JD101213 - Sequence 82237 from Patent EP1572962.
JD320749 - Sequence 301773 from Patent EP1572962.
AK074491 - Homo sapiens cDNA FLJ90010 fis, clone HEMBA1000349, weakly similar to ATP-BINDING CASSETTE TRANSPORTER 1.
AK057068 - Homo sapiens cDNA FLJ32506 fis, clone SMINT1000042, weakly similar to ATP-BINDING CASSETTE, SUB-FAMILY A, MEMBER 3.
BC062472 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 9, mRNA (cDNA clone IMAGE:30407790), complete cds.
HQ258547 - Synthetic construct Homo sapiens clone IMAGE:100072976 Unknown protein gene, complete cds.
KJ902093 - Synthetic construct Homo sapiens clone ccsbBroadEn_11487 ABCA9 gene, encodes complete protein.
JD290137 - Sequence 271161 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein Q8IUA7 (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: ABCA9_HUMAN, NM_080283, NP_525022, Q6P655, Q8IUA7, Q8N2S4, Q8WWZ5, Q96MD8
UCSC ID: uc002jhu.3
RefSeq Accession: NM_080283
Protein: Q8IUA7 (aka ABCA9_HUMAN)
CCDS: CCDS11681.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_080283.3
exon count: 39CDS single in 3' UTR: no RNA size: 6310
ORF size: 4875CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9767.00frame shift in genome: no % Coverage: 99.86
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # 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.