ABCA2
ATP binding cassette subfamily A member 2 | ABC2

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]

Developmental clusters: GC2
Biological processes 69 terms
ABC-type transporter activity (GO:0140359)ATP binding (GO:0005524)ATP binding (GO:0005524)ATP binding (GO:0005524)ATP hydrolysis activity (GO:0016887)ATP-binding cassette (ABC) transporter complex (GO:0043190)ATPase-coupled transmembrane transporter activity (GO:0042626)ATPase-coupled transmembrane transporter activity (GO:0042626)central nervous system myelin formation (GO:0032289)central nervous system myelin formation (GO:0032289)ceramide floppase activity (GO:0099038)ceramide translocation (GO:0099040)cholesterol homeostasis (GO:0042632)cytoplasmic vesicle (GO:0031410)endopeptidase regulator activity (GO:0061135)endosome (GO:0005768)endosome membrane (GO:0010008)endosome membrane (GO:0010008)floppase activity (GO:0140328)ganglioside metabolic process (GO:0001573)glycosphingolipid metabolic process (GO:0006687)intracellular membrane-bounded organelle (GO:0043231)intracellular sphingolipid homeostasis (GO:0090156)lipid carrier activity (GO:0005319)lipid metabolic process (GO:0006629)lipid transport (GO:0006869)locomotory behavior (GO:0007626)lysosomal membrane (GO:0005765)lysosomal membrane (GO:0005765)lysosomal membrane (GO:0005765)lysosomal membrane (GO:0005765)lysosome (GO:0005764)membrane (GO:0016020)membrane (GO:0016020)membrane (GO:0016020)membrane (GO:0016020)microtubule organizing center (GO:0005815)negative regulation of cholesterol efflux (GO:0090370)negative regulation of intracellular cholesterol transport (GO:0032384)negative regulation of phospholipid biosynthetic process (GO:0071072)negative regulation of receptor-mediated endocytosis involved in cholesterol transport (GO:1905601)negative regulation of sphingolipid biosynthetic process (GO:0090155)negative regulation of steroid metabolic process (GO:0045939)nucleotide binding (GO:0000166)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)positive regulation of amyloid precursor protein catabolic process (GO:1902993)positive regulation of amyloid precursor protein catabolic process (GO:1902993)positive regulation of amyloid-beta formation (GO:1902004)positive regulation of amyloid-beta formation (GO:1902004)positive regulation of low-density lipoprotein particle receptor catabolic process (GO:0032805)positive regulation of protein metabolic process (GO:0051247)protein binding (GO:0005515)regulation of cholesterol biosynthetic process (GO:0045540)regulation of intracellular cholesterol transport (GO:0032383)regulation of intracellular cholesterol transport (GO:0032383)regulation of post-translational protein modification (GO:1901873)regulation of protein localization to cell periphery (GO:1904375)regulation of protein localization to cell surface (GO:2000008)regulation of steroid metabolic process (GO:0019218)response to cholesterol (GO:0070723)response to steroid hormone (GO:0048545)response to xenobiotic stimulus (GO:0009410)sphingomyelin metabolic process (GO:0006684)sphingosine biosynthetic process (GO:0046512)transmembrane transport (GO:0055085)transmembrane transport (GO:0055085)transport across blood-brain barrier (GO:0150104)
Expression (TPM)
ABCA2 — as a Regulated Gene

TFs regulating ABCA2 0 TFs

Transcription factors with Perturb-seq knockdown data for ABCA2. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = ABCA2 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to ABCA2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ABCA2, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr9:136,727,616–136,729,079 300.1 kb Distal (>10kb) Multiome 1013
chr9:136,762,846–136,763,902 265.1 kb Distal (>10kb) Multiome 271
chr9:136,788,889–136,789,680 239.0 kb Distal (>10kb) Multiome 351
chr9:136,790,433–136,792,285 237.2 kb Distal (>10kb) Multiome HiCAR 864
chr9:136,798,823–136,801,421 226.9 kb Distal (>10kb) Multiome 874
chr9:136,807,251–136,808,764 220.4 kb Distal (>10kb) Multiome 714
chr9:136,842,325–136,842,872 185.8 kb Distal (>10kb) Multiome 492
chr9:136,846,187–136,850,214 178.8 kb Distal (>10kb) Multiome 1074
chr9:136,865,842–136,866,772 161.9 kb Distal (>10kb) Multiome 742
chr9:136,885,976–136,887,547 141.9 kb Distal (>10kb) Multiome 770
chr9:136,943,250–136,945,621 83.6 kb Distal (>10kb) Multiome HiCAR 883
chr9:136,949,631–136,950,846 78.1 kb Distal (>10kb) Multiome HiCAR 776
chr9:136,977,106–136,980,430 49.8 kb Distal (>10kb) Multiome 413
chr9:136,991,827–136,993,248 36.0 kb Distal (>10kb) Multiome 720
chr9:137,022,191–137,022,569 5.7 kb Proximal (<10kb) 346
chr9:137,027,536–137,029,054 29 bp At TSS Multiome 539
chr9:137,029,231–137,029,652 1.3 kb Proximal (<10kb) Multiome 386
chr9:137,035,297–137,035,519 7.0 kb Proximal (<10kb) 402
chr9:137,045,334–137,046,838 18.3 kb Distal (>10kb) Multiome 829
chr9:137,053,352–137,054,892 25.9 kb Distal (>10kb) Multiome 544
chr9:137,067,810–137,068,494 39.8 kb Distal (>10kb) Multiome 492
chr9:137,069,879–137,071,138 42.4 kb Distal (>10kb) Multiome 703
chr9:137,076,758–137,078,723 49.1 kb Distal (>10kb) Multiome 530
chr9:137,085,844–137,087,716 58.6 kb Distal (>10kb) Multiome 890
chr9:137,129,244–137,130,499 101.5 kb Distal (>10kb) Multiome 823
chr9:137,167,984–137,170,155 141.2 kb Distal (>10kb) Multiome 560
chr9:137,188,099–137,189,538 160.4 kb Distal (>10kb) Multiome 954
chr9:137,200,175–137,201,689 172.6 kb Distal (>10kb) Multiome 856
chr9:137,205,371–137,205,975 177.4 kb Distal (>10kb) Multiome 758
chr9:137,221,373–137,224,294 193.6 kb Distal (>10kb) Multiome 843
chr9:137,227,249–137,228,051 199.4 kb Distal (>10kb) Multiome 533
chr9:137,236,161–137,237,143 208.4 kb Distal (>10kb) Multiome 748
chr9:137,239,991–137,242,933 212.7 kb Distal (>10kb) Multiome 1117
chr9:137,243,659–137,245,307 216.0 kb Distal (>10kb) Multiome 471
chr9:137,253,801–137,256,036 227.0 kb Distal (>10kb) Multiome 843
chr9:137,280,593–137,281,861 252.9 kb Distal (>10kb) Multiome 223
chr9:137,294,859–137,296,916 267.2 kb Distal (>10kb) Multiome 501
chr9:137,300,591–137,303,141 274.2 kb Distal (>10kb) Multiome 790
chr9:137,316,104–137,316,916 288.0 kb Distal (>10kb) Multiome 395

Genome Browser

Genomic view of the ABCA2 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr9:136,717,616 – 137,326,916
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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