ATG9A
autophagy related 9A | FLJ22169, APG9L1

Enables phospholipid scramblase activity. Involved in autophagosome assembly. Located in several cellular components, including Golgi apparatus; endosome; and phagophore assembly site. [provided by Alliance of Genome Resources, Jul 2025]

Biological processes 41 terms
Golgi apparatus (GO:0005794)Golgi apparatus (GO:0005794)Golgi membrane (GO:0000139)Golgi membrane (GO:0000139)autophagosome (GO:0005776)autophagosome (GO:0005776)autophagosome assembly (GO:0000045)autophagosome assembly (GO:0000045)autophagosome assembly (GO:0000045)autophagosome membrane (GO:0000421)autophagy (GO:0006914)bone morphogenesis (GO:0060349)bone morphogenesis (GO:0060349)cytoplasm (GO:0005737)endoplasmic reticulum membrane (GO:0005789)endoplasmic reticulum membrane (GO:0005789)endosome (GO:0005768)late endosome (GO:0005770)late endosome membrane (GO:0031902)membrane (GO:0016020)mitochondrial membrane (GO:0031966)mitochondrion (GO:0005739)mitophagy (GO:0000423)phagophore assembly site (GO:0000407)phagophore assembly site (GO:0000407)phagophore assembly site membrane (GO:0034045)phagophore assembly site membrane (GO:0034045)phospholipid scramblase activity (GO:0017128)phospholipid scramblase activity (GO:0017128)piecemeal microautophagy of the nucleus (GO:0034727)plasma membrane phospholipid scrambling (GO:0017121)programmed necrotic cell death (GO:0097300)programmed necrotic cell death (GO:0097300)protein binding (GO:0005515)protein localization to phagophore assembly site (GO:0034497)recycling endosome (GO:0055037)recycling endosome membrane (GO:0055038)recycling endosome membrane (GO:0055038)reticulophagy (GO:0061709)synaptic membrane (GO:0097060)trans-Golgi network (GO:0005802)
Expression (TPM)
ATG9A — as a Regulated Gene

TFs regulating ATG9A 0 TFs

Transcription factors with Perturb-seq knockdown data for ATG9A. 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 = ATG9A 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 ATG9A

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ATG9A, 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
chr2:218,959,145–218,960,352 270.0 kb Distal (>10kb) Multiome 416
chr2:218,962,902–218,964,278 266.3 kb Distal (>10kb) Multiome 768
chr2:218,979,814–218,980,492 249.5 kb Distal (>10kb) Multiome 499
chr2:218,984,382–218,985,013 244.9 kb Distal (>10kb) Multiome 126
chr2:218,992,930–218,994,312 236.0 kb Distal (>10kb) Multiome 265
chr2:218,995,885–218,998,018 233.3 kb Distal (>10kb) Multiome 534
chr2:218,998,611–219,003,562 227.5 kb Distal (>10kb) Multiome 941
chr2:219,057,853–219,058,462 171.4 kb Distal (>10kb) Multiome 469
chr2:219,060,260–219,061,256 168.7 kb Distal (>10kb) Multiome 240
chr2:219,159,910–219,161,297 69.0 kb Distal (>10kb) Multiome 901
chr2:219,176,168–219,177,450 52.7 kb Distal (>10kb) Multiome 999
chr2:219,177,596–219,178,930 51.3 kb Distal (>10kb) Multiome 930
chr2:219,206,194–219,207,456 22.7 kb Distal (>10kb) Multiome 861
chr2:219,217,908–219,219,751 10.6 kb Distal (>10kb) Multiome 1058
chr2:219,228,940–219,230,470 66 bp At TSS Multiome 914
chr2:219,245,074–219,245,804 15.9 kb Distal (>10kb) Multiome 891
chr2:219,252,908–219,254,656 24.4 kb Distal (>10kb) Multiome 808
chr2:219,277,516–219,280,537 49.8 kb Distal (>10kb) Multiome 1073
chr2:219,294,524–219,295,391 65.3 kb Distal (>10kb) Multiome 892
chr2:219,308,224–219,309,089 78.8 kb Distal (>10kb) Multiome 742
chr2:219,386,994–219,389,117 158.7 kb Distal (>10kb) Multiome 911
chr2:219,402,761–219,403,203 173.4 kb Distal (>10kb) Multiome 234
chr2:219,418,154–219,419,089 189.1 kb Distal (>10kb) Multiome 147
chr2:219,433,920–219,435,459 204.6 kb Distal (>10kb) Multiome 315
chr2:219,441,439–219,442,557 212.4 kb Distal (>10kb) Multiome 338
chr2:219,447,946–219,449,531 219.2 kb Distal (>10kb) Multiome 244
chr2:219,476,330–219,477,528 247.2 kb Distal (>10kb) Multiome 373
chr2:219,484,139–219,485,299 255.3 kb Distal (>10kb) Multiome 146
chr2:219,497,658–219,499,313 269.1 kb Distal (>10kb) Multiome 907
chr2:219,506,707–219,507,641 277.5 kb Distal (>10kb) Multiome 205
chr2:219,509,036–219,510,612 280.5 kb Distal (>10kb) Multiome 614
chr2:219,521,083–219,521,760 291.8 kb Distal (>10kb) Multiome 325
chr2:219,522,621–219,523,337 293.4 kb Distal (>10kb) Multiome 201
chr2:219,525,558–219,526,393 296.4 kb Distal (>10kb) Multiome 321

Genome Browser

Genomic view of the ATG9A 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.

chr2:218,949,145 – 219,536,393
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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