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ABCA1 Gene

protein-coding   GIFtS: 69
GCID: GC09M107543

ATP-Binding Cassette, Sub-Family A (ABC1), Member 1


(Previous symbols: ABC1, HDLDT1)
  See ABCA1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
ATP-Binding Cassette, Sub-Family A (ABC1), Member 11 2     ATP-Binding Cassette Transporter A12
ABC11 2 3 5     membrane-bound2
HDLDT11 2 5     ATP-Binding Cassette 13
Cholesterol Efflux Regulatory Protein2 3     ATP-Binding Cassette Transporter 13
ABC-12 3     EC 2.7.7.88
CERP2 3     EC 2.8.1.88
TGD2 5     EC 3.6.38
Tangier Disease1     EC 3.6.3.418
ATP-Binding Cassette Sub-Family A Member 12     

External Ids:    HGNC: 291   Entrez Gene: 192   Ensembl: ENSG000001650297   OMIM: 6000465   UniProtKB: O954773   

Export aliases for ABCA1 gene to outside databases

Previous GC identifers: GC09M098343 GC09M099286 GC09M101000 GC09M102923 GC09M104622 GC09M106583 GC09M077145


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for ABCA1 Gene:
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. With cholesterol as its substrate, this protein functions as a cholesteral efflux pump
in the cellular lipid removal pathway. Mutations in this gene have been associated with Tangier's disease and
familial high-density lipoprotein deficiency. (provided by RefSeq, Jul 2008)

GeneCards Summary for ABCA1 Gene:
ABCA1 (ATP-binding cassette, sub-family A (ABC1), member 1) is a protein-coding gene. Diseases associated with ABCA1 include familial hdl deficiency, and abca1-associated familial high density lipoprotein deficiency. GO annotations related to this gene include phospholipid binding and cholesterol binding. An important paralog of this gene is ABCA10.

UniProtKB/Swiss-Prot: ABCA1_HUMAN, O95477
Function: cAMP-dependent and sulfonylurea-sensitive anion transporter. Key gatekeeper influencing intracellular
cholesterol transport

Gene Wiki entry for ABCA1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ABCA1 gene promoter:
         CREB   STAT1   Sp1   AP-1   ATF-2   deltaCREB   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidABCA1 promoter sequence
   Search Chromatin IP Primers for ABCA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ABCA1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q31.1   Ensembl cytogenetic band:  9q31.1   HGNC cytogenetic band: 9q31

ABCA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ABCA1 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M107543:  view genomic region     (about GC identifiers)

Start:
107,543,283 bp from pter      End:
107,690,527 bp from pter
Size:
147,245 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ABCA1_HUMAN, O95477 (See protein sequence)
Recommended Name: ATP-binding cassette sub-family A member 1  
Size: 2261 amino acids; 254302 Da
Subunit: Interacts with MEGF10
Sequence caution: Sequence=AAD49849.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=CAA10005.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q5VX33 Q96S56 Q96T85 Q9NQV4 Q9UN06 Q9UN07 Q9UN08 Q9UN09

Explore the universe of human proteins at neXtProt for ABCA1: NX_O95477

Explore proteomics data for ABCA1 at MOPED

Post-translational modifications: 

  • Phosphorylation on Ser-2054 regulates phospholipid efflux1
  • Palmitoylation by DHHC8 is essential for membrane localization1
  • Glycosylation2 at Asn14, Asn98, Asn151, Asn161, Asn196, Asn244, Asn292, Asn337, Asn349, Asn400,
                                 Asn478, Asn489, Asn521, Asn820, Asn1144, Asn1294, Asn1453, Asn1504, Asn1637, Asn2044 (see all 21)
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for ABCA1 (O95477) (see all 5)
     LDEPTAG  LDEPTTG  YVVLTSV  NGAGKTT 


    See ABCA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_005493.2  
    ENSEMBL proteins: 
     ENSP00000363868   ENSP00000416623   ENSP00000363865  
    Reactome Protein details: O95477

    ABCA1 Human Recombinant Protein Products:

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    Search eBioscience for ELISAs for ABCA1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ABCA: ATP binding cassette transporters / subfamily A

    IUPHAR Guide to PHARMACOLOGY protein family classification: ABCA1
    ABCA subfamily

    5 InterPro protein domains:
     IPR003439 ABC_transporter-like
     IPR027417 P-loop_NTPase
     IPR003593 AAA+_ATPase
     IPR026082 ABC_A
     IPR017871 ABC_transporter_CS

    Graphical View of Domain Structure for InterPro Entry O95477

    ProtoNet protein and cluster: O95477

    UniProtKB/Swiss-Prot: ABCA1_HUMAN, O95477
    Domain: Multifunctional polypeptide with two homologous halves, each containing a hydrophobic membrane-anchoring
    domain and an ATP binding cassette (ABC) domain
    Similarity: Belongs to the ABC transporter superfamily. ABCA family
    Similarity: Contains 2 ABC transporter domains


    Find genes that share domains with ABCA1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ABCA1_HUMAN, O95477
    Function: cAMP-dependent and sulfonylurea-sensitive anion transporter. Key gatekeeper influencing intracellular
    cholesterol transport
    Induction: By bacterial lipopolysaccharides (LPS). LPS regulates expression through a liver X receptor (LXR)
    -independent mechanism. Repressed by ZNF202

         Genatlas biochemistry entry for ABCA1:
    ATP binding cassette superfamily,subfamily A,member 1,mouse ABC1 homolog,widely expressed,cholesterol carrying out
    of the cell for uptake into HDL particles

         Enzyme Numbers (IUBMB): EC 3.6.3.412 EC 3.6.32 EC 2.7.7.82 EC 2.8.1.82

         Gene Ontology (GO): Selected molecular function terms (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding ----
    GO:0005515protein binding IPI12084722
    GO:0005524ATP binding IDA11700048
    GO:0005543phospholipid binding IC16702602
    GO:0005548phospholipid transporter activity IDA16702602
         
    Find genes that share ontologies with ABCA1           About GenesLikeMe


    Phenotypes:
         Selected MGI mutant phenotypes (inferred from 7 alleles(MGI details for Abca1) (see all 18):
     cardiovascular system  cellular  digestive/alimentary  embryogenesis  endocrine/exocrine gland 
     growth/size/body  hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system 
     mortality/aging  muscle  nervous system  other  renal/urinary system 

    Find genes that share phenotypes with ABCA1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for ABCA1: Abca1tm2Jp Abca1tm1Blt Abca1tm1Jdm Abca1tm1Wpfl Abca1tm1.1Jp

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ABCA1
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for ABCA1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for ABCA1

    miRNA
    Products:
        
    miRTarBase miRNAs that target ABCA1:
    hsa-mir-26a-5p (MIRT006711), hsa-mir-33b-5p (MIRT003670), hsa-mir-26b-5p (MIRT006713), hsa-mir-27a-3p (MIRT007123), hsa-mir-19a-3p (MIRT007121), hsa-mir-33a-5p (MIRT003672)

    Block miRNA regulation of human, mouse, rat ABCA1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate ABCA1 (see all 113):
    hsa-miR-140-5p hsa-miR-520e hsa-miR-520f hsa-miR-3194-5p hsa-miR-106a hsa-miR-199a-3p hsa-miR-128 hsa-miR-93
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for ABCA1
    Predesigned siRNA for gene silencing in human, mouse, rat ABCA1

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: ABCA1 (NM_005502)
    Sino Biological Human cDNA Clone for ABCA1
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ABCA1_HUMAN, O95477: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    extracellular3
    endoplasmic reticulum2
    endosome2
    golgi apparatus2
    nucleus2
    peroxisome2
    lysosome1
    vacuole1

    Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005794Golgi apparatus IEA--
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane IDA10525055
    GO:0009986cell surface IEA--
    GO:0030139endocytic vesicle IDA14747463

    Find genes that share ontologies with ABCA1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for ABCA1 About   (see all 15)  
    See pathways by source

    SuperPathContained pathways About
    1Fatty acid, triacylglycerol, and ketone body metabolism
    Fatty acid, triacylglycerol, and ketone body metabolism0.65
    PPARA Activates Gene Expression0.63
    Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)0.65
    2Lipoprotein metabolism
    Lipoprotein metabolism0.59
    HDL-mediated lipid transport0.00
    Lipid digestion, mobilization, and transport0.59
    3Folate Metabolism
    Folate Metabolism0.54
    Vitamin B12 Metabolism0.54
    4Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    5Statin Pathway
    Statin Pathway0.73


    Find genes that share SuperPaths with ABCA1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 GeneGo (Thomson Reuters) Pathways for ABCA1
        Cholesterol and Sphingolipids transport / Transport from Golgi and ER to the apical membrane (normal and CF)
    Cholesterol and Sphingolipids transport / Recycling to plasma membrane in lung (normal and CF)

    Selected BioSystems Pathways for ABCA1 (see all 7)
        Statin Pathway
    SREBF and miR33 in cholesterol and lipid homeostasis
    Folate Metabolism
    Selenium Pathway
    Nuclear receptors in lipid metabolism and toxicity


    2 Reactome Pathways for ABCA1
        PPARA activates gene expression
    HDL-mediated lipid transport


    2 Kegg Pathways  (Kegg details for ABCA1):
        ABC transporters
    Fat digestion and absorption

        Pathway & Disease-focused RT2 Profiler PCR Arrays including ABCA1: 
              Atherosclerosis in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              Drug Transporters in human mouse rat
              Alzheimer's Disease in human mouse rat
              Fatty Liver in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for ABCA1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for ABCA1 (O954771, 2, 3 ENSP000003638684) via UniProtKB, MINT, STRING, and/or I2D (see all 71)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SNTB1Q138841, 3, ENSP000003789654EBI-784112,EBI-295843 I2D: score=2 STRING: ENSP00000378965
    TRIM27P143733, ENSP000003664044I2D: score=1 STRING: ENSP00000366404
    ENSG00000215641P143733I2D: score=1 
    ENSG00000229006P143733I2D: score=1 
    ENSG00000234495P143733I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 36):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002790peptide secretion IEA--
    GO:0006497protein lipidation IEA--
    GO:0006911phagocytosis, engulfment IEA--
    GO:0007040lysosome organization IDA15163665
    GO:0007186G-protein coupled receptor signaling pathway IMP16443932

    Find genes that share ontologies with ABCA1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ABCA1

    2 HMDB Compounds for ABCA1    About this table
    CompoundSynonyms CAS #PubMed Ids
    Cholesterol(+)-ent-Cholesterol (see all 39)57-88-5--
    Cyclic AMPCyclic AMP (see all 19)60-92-4--

    3 DrugBank Compounds for ABCA1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Probucol4,4'- (Isopropylidenedithio)bis(2, 6-di-tert-butylphenol) (see all 8)23288-49-5targetinhibitor19075491 20075420 15514211 19458386 19427182 1868500
    GlyburideApo-Glibenclamide (see all 4)10238-21-8targetinhibitor14660039 12426219 15039140 15102890 15905177
    Adenosine triphosphate5'-ATP (see all 8)56-65-5target--16858612 17224860 17135600

    Selected Novoseek inferred chemical compound relationships for ABCA1 gene (see all 81)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cholesterol 88.9 1179 17409096 (8), 18427282 (7), 12700343 (7), 20037141 (7) (see all 99)
    22r-hydroxycholesterol 85.1 21 12401893 (2), 16142410 (1), 17767055 (1), 18427282 (1) (see all 14)
    24(s),25-epoxycholesterol 82.9 6 16901265 (4), 15514210 (1), 17186944 (1)
    sterol 78.6 39 11742879 (6), 16254198 (3), 15358760 (3), 16788211 (2) (see all 22)
    abc2 76.7 4 11270397 (2), 19806386 (1), 9027511 (1)
    lipid 75.6 262 18776170 (6), 19202195 (5), 19151332 (4), 20185793 (4) (see all 99)
    27-hydroxycholesterol 72.6 3 17088262 (2), 16099444 (1)
    cholesterol ester 71.9 12 17652712 (1), 12759900 (1), 18270459 (1), 19644050 (1) (see all 11)
    phospholipid 71.2 91 12738681 (4), 16855366 (4), 14703508 (3), 11309399 (3) (see all 62)
    gw 3965 68.6 1 15145986 (1)

    4 PharmGKB related drug/compound annotations for ABCA1 gene    About this table
    Drug/compound PharmGKB Annotation
    atorvastatinCA  
    fenofibrateCA  
    pravastatinCA  
    simvastatinCA  



    Find genes that share compounds with ABCA1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ABCA1 gene: 
    NM_005502.3  

    Unigene Cluster for ABCA1:

    ATP-binding cassette, sub-family A (ABC1), member 1
    Hs.659274  [show with all ESTs]
    Unigene Representative Sequence: NM_005502
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000374736(uc004bcl.3) ENST00000494467 ENST00000423487 ENST00000374733(uc004bcm.3)

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    hsa-miR-140-5p hsa-miR-520e hsa-miR-520f hsa-miR-3194-5p hsa-miR-106a hsa-miR-199a-3p hsa-miR-128 hsa-miR-93
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    Additional mRNA sequence: 

    AB037924.1 AB055982.1 AB445477.1 AF165281.1 AF258627.1 AF285167.1 AJ012376.1 AK024328.1 
    AK027864.1 BC034824.1 BC146856.1 

    9 DOTS entries:

    DT.414915  DT.75116842  DT.92430391  DT.92054245  DT.97780029  DT.95163274  DT.40194073  DT.40233262 
    DT.91746745 

    Selected AceView cDNA sequences (see all 134):

    BM769397 BF988872 CA976033 AA669024 BM728651 AA328733 AL701341 AA748860 
    AA731742 BC034824 BF891375 BX955241 C01846 BE222116 AA521292 BF438337 
    Z40310 NM_005502 BE857175 BU753834 AA292158 BM153383 Z44377 BM768930 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for ABCA1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
    SP1:                                                                                                                    -                                       
    SP2:                                                                                                                                                            
    SP3:              -                                                                                                                                             
    SP4:                                                                                                                                                            

    ExUns: 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49a ·
    SP1:                                                                                                                                                        -   
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            

    ExUns: 49b ^ 50a · 50b
    SP1:                  
    SP2:                  
    SP3:                  
    SP4:                  


    ECgene alternative splicing isoforms for ABCA1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    ABCA1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    ABCA1 Expression
    About this image


    ABCA1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Neural Tube (Nervous System)    fully expand to see all 4 entries
             Metencephalon
     
     Blood (Cardiovascular System)    fully expand to see all 3 entries
             Mature B-Cells Peripheral Blood
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Midbrain tegmentum
     
     Kidney (Urinary System)
             Ureteric Bud Cells Ureteric Bud
     
     Lateral Plate Mesoderm (Gastrulation Derivatives)
             Hematopoietic Stem Cells Aorta-Gonad-Mesonephros
    ABCA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ABCA1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.659274

    UniProtKB/Swiss-Prot: ABCA1_HUMAN, O95477
    Tissue specificity: Widely expressed, but most abundant in macrophages

        Pathway & Disease-focused RT2 Profiler PCR Arrays including ABCA1: 
              Atherosclerosis in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              Drug Transporters in human mouse rat
              Alzheimer's Disease in human mouse rat
              Fatty Liver in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for ABCA1 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Abca11 , 5 ATP-binding cassette, sub-family A (ABC1), member 11, 5 88.99(n)1
    95.31(a)1
      4 (28.57 cM)5
    113031  NM_013454.31  NP_038482.31 
     530307875 
    chicken
    (Gallus gallus)
    Aves ABCA11 ATP-binding cassette, sub-family A (ABC1), member 1 78.5(n)
    85.8(a)
      373945  NM_204145.2  NP_989476.1 
    lizard
    (Anolis carolinensis)
    Reptilia ABCA16
    ATP-binding cassette, sub-family A (ABC1), member ...
    84(a)
    1 ↔ 1
    2(75535339-75692018)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia abca11 ATP-binding cassette, sub-family A (ABC1), member 1 74.4(n)
    81.5(a)
      100491942  XM_002933982.2  XP_002934028.2 
    zebrafish
    (Danio rerio)
    Actinopterygii abca1b2 ATP-binding cassette, sub-family A (ABC1), member 1B 72.88(n)   321246  57041705 
    worm
    (Caenorhabditis elegans)
    Secernentea abt-21 abt-2 45.87(n)
    34.98(a)
      171782  NM_058548.6  NP_490949.3 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons ABCA11 ABCA1 47.35(n)
    38.55(a)
      818768  NM_180023.3  NP_850354.2 


    ENSEMBL Gene Tree for ABCA1 (if available)
    TreeFam Gene Tree for ABCA1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ABCA1 gene
    ABCA102  ABCA132  ABCA32  ABCA82  ABCA122  ABCA42  ABCA72  ABCA22  
    ABCA92  ABCA62  ABCA52  
    16 SIMAP similar genes for ABCA1 using alignment to 8 protein entries:     ABCA1_HUMAN (see all proteins):
    ABC-1    ABC1    DKFZp547P193    DKFZp434E1030    ABC2    DKFZp781N1972
    ABCA7    ABCA4    ABCA2    DKFZp686K07118    ABCA12    DKFZp313D2411
    ABCA13    ABCA3    ABCG2    ABCA3 variant protein

    Find genes that share paralogs with ABCA1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Polymorphic Variants from UniProtKB/Swiss-Prot
    ABCA1_HUMAN, O95477: Genetic variations in ABCA1 define the high density lipoprotein cholesterol level quantitative trait
    locus 13 (HDLCQ13) [MIM:600046]


    Selected SNPs for ABCA1 (see all 3830)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs289336921,2,,4
    CHigh density lipoprotein deficiency 2 (HDLD2)4 pathogenic1107594247(-) TGGGGA/G/TACAGG 2 D Y mis1 ese30--------
    rs289373131,2,,4
    CHigh density lipoprotein deficiency 1 (HDLD1)4 pathogenic1107597939(-) CCACAA/GTGGAG 2 N S mis1 ese30--------
    rs289373141,2,,4
    CHigh density lipoprotein deficiency 1 (HDLD1)4 pathogenic1107597940(-) GCCACA/CATGGA 2 N H mis1 ese30--------
    rs28535781,2,,4
    CHigh density lipoprotein deficiency 1 (HDLD1)4 pathogenic1107606446(-) CTTGCA/GGGATG 2 Q R mis1 ese31Minor allele frequency- G:0.00NA 2
    rs92825411,2,,4
    C,F,HHigh density lipoprotein deficiency 2 (HDLD2)4 --107633973(-) TACTTC/TGTTCC 2 R C mis1 ese314Minor allele frequency- T:0.00MN NS EA NA EU 6739
    rs1451832031,2,,4
    C,FHigh density lipoprotein deficiency 2 (HDLD2)4 --107659922(+) GAGTCG/AGGTAA 2 /P /L mis11Minor allele frequency- A:0.00NA 4550
    VAR_0625074
    High density lipoprotein deficiency 1 (HDLD1)4--see VAR_0625072 Q H mis40--------
    VAR_0625024
    High density lipoprotein deficiency 1 (HDLD1)4--see VAR_0625022 R Q mis40--------
    VAR_0091554
    High density lipoprotein deficiency 1 (HDLD1)4--see VAR_0091552 N H mis40--------
    VAR_0126274
    High density lipoprotein deficiency 1 (HDLD1)4--see VAR_0126272 A D mis40--------

    HapMap Linkage Disequilibrium report for ABCA1 (107543283 - 107690527 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ABCA1 (see all 24):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2738878CNV Deletion23290073
    esv2738879CNV Deletion23290073
    dgv1366e199CNV Deletion23128226
    nsv6651CNV Insertion18451855
    nsv509315CNV Insertion20534489
    nsv44CNV Insertion15895083
    nsv6650CNV Loss18451855
    nsv6652CNV Loss18451855
    nsv893676CNV Loss21882294
    nsv893674CNV Loss21882294

    Human Gene Mutation Database (HGMD): ABCA1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ABCA1
    DNA2.0 Custom Variant and Variant Library Synthesis for ABCA1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600046   
    OMIM disorders: 205400  604091  143890  
    UniProtKB/Swiss-Prot: ABCA1_HUMAN, O95477
  • High density lipoprotein deficiency 1 (HDLD1) [MIM:205400]: Recessive disorder characterized by absence
    of high density lipoprotein (HDL) cholesterol from plasma, accumulation of cholesteryl esters, premature coronary
    artery disease (CAD), hepatosplenomegaly, recurrent peripheral neuropathy and progressive muscle wasting and
    weakness. Note=The disease is caused by mutations affecting the gene represented in this entry
  • High density lipoprotein deficiency 2 (HDLD2) [MIM:604091]: Inherited as autosomal dominant trait. It is
    characterized by moderately low HDL cholesterol, predilection toward premature coronary artery disease (CAD) and
    a reduction in cellular cholesterol efflux. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • 19 diseases for ABCA1:    
    About MalaCards
    familial hdl deficiency    abca1-associated familial high density lipoprotein deficiency    tangier disease    abca1-related disorders
    lewis-sumner syndrome    coronary artery disease in familial hypercholesterolemia, protection against    hypoalphalipoproteinemia    lysosomal acid lipase deficiency
    cholesteryl ester storage disease    syringomyelia    scott syndrome    chediak-higashi syndrome
    familial hypercholesterolemia    artery disease    hyperalphalipoproteinemia    xeroderma pigmentosum, group c
    hypercholesterolemia    coronary artery disease    atherosclerosis

    5 diseases from the University of Copenhagen DISEASES database for ABCA1:
    Tangier disease     Atherosclerosis     Coronary heart disease     Alzheimer's disease
    Diabetes mellitus

    Find genes that share disorders with ABCA1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for ABCA1 gene (see all 45)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tangier disease 97.4 172 10535983 (6), 12236582 (3), 11855831 (2), 12576507 (2) (see all 99)
    lipoprotein deficiencies 87.1 8 11785958 (2), 11476961 (1), 12706378 (1), 15177564 (1) (see all 6)
    hypoalphalipoproteinemia 81.9 8 11279031 (2), 15767853 (1), 16610615 (1), 17287470 (1) (see all 6)
    atherosclerosis 77.8 108 19201688 (7), 11752403 (5), 20137092 (3), 15528481 (3) (see all 67)
    hyperalphalipoproteinemia 63.7 1 11457883 (1)
    scott syndrome 53.5 2 15790791 (1), 16855366 (1)
    lipoprotein disorder 51.2 1 15019541 (1)
    atherosclerotic plaque 51 11 15961705 (2), 15528463 (2), 18221072 (1), 20137092 (1) (see all 9)
    cardiovascular diseases 50.5 21 15262183 (2), 16183915 (2), 17093293 (1), 16446539 (1) (see all 14)
    coronary artery disease 48.4 26 11086027 (2), 11940086 (2), 18996286 (2), 17412755 (2) (see all 20)

    Genetic Association Database (GAD): ABCA1
    Human Genome Epidemiology (HuGE) Navigator: ABCA1 (163 documents)

    Export disorders for ABCA1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ABCA1 gene, integrated from 10 sources (see all 945):
    (articles sorted by number of sources associating them with ABCA1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Screening for functional sequence variations and mutations in ABCA1. (PubMed id 15262183)1, 2, 4, 9 Probst M.C.... Schmitz G. (Atherosclerosis 2004)
    2. Mutation in ABCA1 predicted risk of ischemic heart disease in the Copenhagen City Heart Study Population. (PubMed id 16226177)1, 2, 4, 9 Frikke-Schmidt R....Tybjaerg-Hansen A. (J. Am. Coll. Cardiol. 2005)
    3. Tangier disease is caused by mutations in the gene encoding ATP- binding cassette transporter 1. (PubMed id 10431238)1, 2, 3, 9 Rust S.... Assmann G. (Nat. Genet. 1999)
    4. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. (PubMed id 15297675)1, 2, 4, 9 Cohen J.C....Hobbs H.H. (Science 2004)
    5. A common variant in the ABCA1 gene is associated with a lower risk for premature coronary heart disease in familial hypercholesterolaemia. (PubMed id 12624133)1, 2, 4, 9 Cenarro A.... Civeira F. (J. Med. Genet. 2003)
    6. ABCA1 gene polymorphisms and their associations with coronary artery disease and plasma lipids in males from three ethnic populations in Singapore. (PubMed id 12709788)1, 2, 4, 9 Tan J.H.... Heng C.K. (Hum. Genet. 2003)
    7. Common genetic variation in ABCA1 is associated with altered lipoprotein levels and a modified risk for coronary artery disease. (PubMed id 11238261)1, 2, 4, 9 Clee S.M....Hayden M.R. (Circulation 2001)
    8. Common variants in the gene encoding ATP-binding cassette transporter 1 in men with low HDL cholesterol levels and coronary heart disease. (PubMed id 11257261)1, 2, 4, 9 Brousseau M.E....Schmitz G. (Atherosclerosis 2001)
    9. The gene encoding ATP-binding cassette transporter 1 is mutated in Tangier disease. (PubMed id 10431237)1, 2, 3, 9 Bodzioch M.... Schmitz G. (Nat. Genet. 1999)
    10. ABCA1 single nucleotide polymorphisms on high-density lipoprotein-cholesterol and overweight: the D.E.S.I.R. study. (PubMed id 17135600)1, 4, 7 Porchay I....Fumeron F. (Obesity (Silver Spring) 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 19 HGNC: 29 AceView: ABCA1 Ensembl:ENSG00000165029 euGenes: HUgn19
    ECgene: ABCA1 Kegg: 19 H-InvDB: ABCA1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for ABCA1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=ABCA1[genesymbol]
    SHMPDhttp://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=ABCA1
    ABCMdbhttp://abcmutations.hegelab.org/proteinDetails?uniprot_id=O95477

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ABCA1 gene:
    Search GeneIP for patents involving ABCA1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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