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ABCA1 (ATP binding cassette subfamily A member 1)

Identity

Other namesABC-1
ABC1
CERP
HDLDT1
TGD
HGNC (Hugo) ABCA1
LocusID (NCBI) 19
Atlas_Id 50442
Location 9q31.1
Location_base_pair Starts at 107543284 and ends at 107690527 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
ABCA1 (9q31.1) / ABCA1 (9q31.1)ABCA1 (9q31.1) / EIF4E (4q23)ABCA1 (9q31.1) / HDHD3 (9q32)
ABCA1 (9q31.1) / HNRNPK (9q21.32)ABCA1 (9q31.1) / KCNMA1 (10q22.3)ABCA1 (9q31.1) / LAS1L (Xq12)
ABCA1 (9q31.1) / ZBTB26 (9q33.2)ABCA1 (9q31.1) / ZBTB6 (9q33.2)RGS3 (9q32) / ABCA1 (9q31.1)
SNRNP200 (2q11.2) / ABCA1 (9q31.1)ABCA1 9q31.1 / HDHD3 9q32ABCA1 9q31.1 / ZBTB26 9q33.2
ABCA1 9q31.1 / ZBTB6 9q33.2RGS3 9q32 / ABCA1 9q31.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)ABCA1   29
Cards
Entrez_Gene (NCBI)ABCA1  19  ATP binding cassette subfamily A member 1
GeneCards (Weizmann)ABCA1
Ensembl hg19 (Hinxton)ENSG00000165029 [Gene_View]  chr9:107543284-107690527 [Contig_View]  ABCA1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000165029 [Gene_View]  chr9:107543284-107690527 [Contig_View]  ABCA1 [Vega]
ICGC DataPortalENSG00000165029
TCGA cBioPortalABCA1
AceView (NCBI)ABCA1
Genatlas (Paris)ABCA1
WikiGenes19
SOURCE (Princeton)ABCA1
Genomic and cartography
GoldenPath hg19 (UCSC)ABCA1  -     chr9:107543284-107690527 -  9q31.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)ABCA1  -     9q31.1   [Description]    (hg38-Dec_2013)
EnsemblABCA1 - 9q31.1 [CytoView hg19]  ABCA1 - 9q31.1 [CytoView hg38]
Mapping of homologs : NCBIABCA1 [Mapview hg19]  ABCA1 [Mapview hg38]
OMIM143890   205400   600046   604091   
Gene and transcription
Genbank (Entrez)AB037924 AB055982 AB208839 AB445477 AF165281
RefSeq transcript (Entrez)NM_005502
RefSeq genomic (Entrez)NC_000009 NC_018920 NG_007981 NT_008470 NW_004929366
Consensus coding sequences : CCDS (NCBI)ABCA1
Cluster EST : UnigeneHs.659274 [ NCBI ]
CGAP (NCI)Hs.659274
Alternative Splicing GalleryENSG00000165029
Gene ExpressionABCA1 [ NCBI-GEO ]   ABCA1 [ EBI - ARRAY_EXPRESS ]   ABCA1 [ SEEK ]   ABCA1 [ MEM ]
Gene Expression Viewer (FireBrowse)ABCA1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)19
GTEX Portal (Tissue expression)ABCA1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO95477 (Uniprot)
NextProtO95477  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO95477
Splice isoforms : SwissVarO95477 (Swissvar)
PhosPhoSitePlusO95477
Domaine pattern : Prosite (Expaxy)ABC_TRANSPORTER_1 (PS00211)    ABC_TRANSPORTER_2 (PS50893)   
Domains : Interpro (EBI)AAA+_ATPase    ABC_A    ABC_transporter-like    ABC_transporter_CS    ABCA1    P-loop_NTPase   
Domain families : Pfam (Sanger)ABC_tran (PF00005)   
Domain families : Pfam (NCBI)pfam00005   
Domain families : Smart (EMBL)AAA (SM00382)  
DMDM Disease mutations19
Blocks (Seattle)ABCA1
SuperfamilyO95477
Human Protein AtlasENSG00000165029
Peptide AtlasO95477
HPRD02501
IPIIPI00293460   IPI00303441   IPI00642100   
Protein Interaction databases
DIP (DOE-UCLA)O95477
IntAct (EBI)O95477
FunCoupENSG00000165029
BioGRIDABCA1
STRING (EMBL)ABCA1
ZODIACABCA1
Ontologies - Pathways
QuickGOO95477
Ontology : AmiGOpeptide secretion  receptor binding  protein binding  ATP binding  phospholipid binding  phospholipid transporter activity  endoplasmic reticulum membrane  Golgi apparatus  plasma membrane  plasma membrane  integral component of plasma membrane  protein lipidation  phagocytosis, engulfment  lysosome organization  G-protein coupled receptor signaling pathway  response to nutrient  cholesterol metabolic process  anion transmembrane transporter activity  external side of plasma membrane  negative regulation of macrophage derived foam cell differentiation  positive regulation of cholesterol efflux  negative regulation of cholesterol storage  cholesterol binding  endosomal transport  cholesterol transporter activity  syntaxin binding  endocytic vesicle  positive regulation of cAMP biosynthetic process  small GTPase binding  intracellular cholesterol transport  regulation of Cdc42 protein signal transduction  cholesterol efflux  cholesterol efflux  phospholipid efflux  phospholipid efflux  apolipoprotein binding  apolipoprotein A-I binding  apolipoprotein A-I receptor activity  high-density lipoprotein particle  high-density lipoprotein particle assembly  response to laminar fluid shear stress  apolipoprotein A-I-mediated signaling pathway  lipoprotein metabolic process  response to drug  ATPase activity, coupled to transmembrane movement of substances  cholesterol homeostasis  reverse cholesterol transport  membrane raft  phospholipid translocation  phagocytic vesicle  perinuclear region of cytoplasm  interleukin-1 beta secretion  ATPase binding  phospholipid homeostasis  response to low-density lipoprotein particle  platelet dense granule organization  cellular response to lipopolysaccharide  cellular response to retinoic acid  cellular response to cholesterol  anion transmembrane transport  
Ontology : EGO-EBIpeptide secretion  receptor binding  protein binding  ATP binding  phospholipid binding  phospholipid transporter activity  endoplasmic reticulum membrane  Golgi apparatus  plasma membrane  plasma membrane  integral component of plasma membrane  protein lipidation  phagocytosis, engulfment  lysosome organization  G-protein coupled receptor signaling pathway  response to nutrient  cholesterol metabolic process  anion transmembrane transporter activity  external side of plasma membrane  negative regulation of macrophage derived foam cell differentiation  positive regulation of cholesterol efflux  negative regulation of cholesterol storage  cholesterol binding  endosomal transport  cholesterol transporter activity  syntaxin binding  endocytic vesicle  positive regulation of cAMP biosynthetic process  small GTPase binding  intracellular cholesterol transport  regulation of Cdc42 protein signal transduction  cholesterol efflux  cholesterol efflux  phospholipid efflux  phospholipid efflux  apolipoprotein binding  apolipoprotein A-I binding  apolipoprotein A-I receptor activity  high-density lipoprotein particle  high-density lipoprotein particle assembly  response to laminar fluid shear stress  apolipoprotein A-I-mediated signaling pathway  lipoprotein metabolic process  response to drug  ATPase activity, coupled to transmembrane movement of substances  cholesterol homeostasis  reverse cholesterol transport  membrane raft  phospholipid translocation  phagocytic vesicle  perinuclear region of cytoplasm  interleukin-1 beta secretion  ATPase binding  phospholipid homeostasis  response to low-density lipoprotein particle  platelet dense granule organization  cellular response to lipopolysaccharide  cellular response to retinoic acid  cellular response to cholesterol  anion transmembrane transport  
Pathways : BIOCARTANuclear Receptors in Lipid Metabolism and Toxicity [Genes]    FXR and LXR Regulation of Cholesterol Metabolism [Genes]   
Pathways : KEGGABC transporters    Fat digestion and absorption   
NDEx Network
Atlas of Cancer Signalling NetworkABCA1
Wikipedia pathwaysABCA1
Orthology - Evolution
OrthoDB19
GeneTree (enSembl)ENSG00000165029
Phylogenetic Trees/Animal Genes : TreeFamABCA1
Homologs : HomoloGeneABCA1
Homology/Alignments : Family Browser (UCSC)ABCA1
Gene fusions - Rearrangements
Fusion: TCGAABCA1 9q31.1 HDHD3 9q32 BRCA
Fusion: TCGAABCA1 9q31.1 ZBTB26 9q33.2 LUSC
Fusion: TCGAABCA1 9q31.1 ZBTB6 9q33.2 LUSC
Fusion: TCGARGS3 9q32 ABCA1 9q31.1 PRAD
Polymorphisms : SNP, variants
NCBI Variation ViewerABCA1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ABCA1
dbVarABCA1
ClinVarABCA1
1000_GenomesABCA1 
Exome Variant ServerABCA1
ExAC (Exome Aggregation Consortium)ABCA1 (select the gene name)
Genetic variants : HAPMAP19
Genomic Variants (DGV)ABCA1 [DGVbeta]
Mutations
ICGC Data PortalABCA1 
TCGA Data PortalABCA1 
Broad Tumor PortalABCA1
OASIS PortalABCA1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICABCA1 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch ABCA1
DgiDB (Drug Gene Interaction Database)ABCA1
DoCM (Curated mutations)ABCA1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ABCA1 (select a term)
intoGenABCA1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)9:107543284-107690527  ENSG00000165029
CONAN: Copy Number AnalysisABCA1 
Mutations and Diseases : HGMDABCA1
OMIM143890    205400    600046    604091   
MedgenABCA1
Genetic Testing Registry ABCA1
NextProtO95477 [Medical]
TSGene19
GENETestsABCA1
Huge Navigator ABCA1 [HugePedia]
snp3D : Map Gene to Disease19
BioCentury BCIQABCA1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD19
Chemical/Pharm GKB GenePA24373
Clinical trialABCA1
Miscellaneous
canSAR (ICR)ABCA1 (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineABCA1
EVEXABCA1
GoPubMedABCA1
iHOPABCA1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sun May 8 18:35:32 CEST 2016

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