ARHGAP39

Rho GTPase activating protein 39 | CrGAP, KIAA1688, Vilse

Predicted to enable GTPase activator activity. Involved in postsynapse organization. Is active in glutamatergic synapse. [provided by Alliance of Genome Resources, Jul 2025]

Member of: DE-12 Developmental clusters: GC6

Biological processes 12 terms

GTPase activator activity (GO:0005096)GTPase activator activity (GO:0005096)cytoplasm (GO:0005737)cytoskeleton (GO:0005856)cytosol (GO:0005829)glutamatergic synapse (GO:0098978)glutamatergic synapse (GO:0098978)nucleus (GO:0005634)postsynapse organization (GO:0099173)postsynapse organization (GO:0099173)regulation of small GTPase mediated signal transduction (GO:0051056)signal transduction (GO:0007165)

Expression (TPM)

TFs regulating ARHGAP39 0 TFs

Transcription factors with Perturb-seq knockdown data for ARHGAP39. 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 = ARHGAP39 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to ARHGAP39

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ARHGAP39, 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.

Element	Dist. to TSS	Link type	TFs
chr8:144,408,968–144,410,189	276.4 kb	Distal (>10kb) Multiome	920
chr8:144,427,691–144,429,571	257.3 kb	Distal (>10kb) Multiome	1000
chr8:144,443,691–144,445,047	241.5 kb	Distal (>10kb) Multiome	743
chr8:144,462,568–144,463,422	222.9 kb	Distal (>10kb) Multiome	548
chr8:144,463,885–144,468,178	220.1 kb	Distal (>10kb) Multiome	910
chr8:144,471,960–144,474,391	213.3 kb	Distal (>10kb) Multiome	482
chr8:144,474,517–144,476,543	210.0 kb	Distal (>10kb) Multiome	321
chr8:144,477,277–144,478,749	207.9 kb	Distal (>10kb) Multiome	679
chr8:144,478,851–144,479,509	206.5 kb	Distal (>10kb) Multiome	392
chr8:144,483,979–144,484,843	201.5 kb	Distal (>10kb) Multiome	125
chr8:144,495,748–144,496,431	189.8 kb	Distal (>10kb) Multiome	131
chr8:144,500,182–144,501,505	184.8 kb	Distal (>10kb) Multiome	484
chr8:144,507,995–144,510,268	177.0 kb	Distal (>10kb) Multiome	1067
chr8:144,517,168–144,518,442	167.9 kb	Distal (>10kb) Multiome	637
chr8:144,521,935–144,523,450	163.3 kb	Distal (>10kb) Multiome	663
chr8:144,524,105–144,525,099	161.2 kb	Distal (>10kb) Multiome	264
chr8:144,526,399–144,529,305	158.8 kb	Distal (>10kb) Multiome	934
chr8:144,529,455–144,530,630	155.7 kb	Distal (>10kb) Multiome	284
chr8:144,580,290–144,581,657	105.1 kb	Distal (>10kb) Multiome	271
chr8:144,672,507–144,672,989	13.0 kb	Distal (>10kb) Multiome	150
chr8:144,684,108–144,686,340	1.4 kb	Proximal (<10kb) Multiome	862
chr8:144,695,713–144,696,123	9.9 kb	Proximal (<10kb)	8
chr8:144,755,078–144,755,956	69.7 kb	Distal (>10kb) Multiome	769
chr8:144,785,987–144,788,592	101.3 kb	Distal (>10kb) Multiome	997
chr8:144,791,751–144,793,221	106.6 kb	Distal (>10kb) Multiome	899
chr8:144,798,389–144,799,501	113.1 kb	Distal (>10kb) Multiome	832
chr8:144,826,059–144,827,981	141.5 kb	Distal (>10kb) Multiome	905
chr8:144,852,614–144,853,614	167.3 kb	Distal (>10kb) Multiome	850
chr8:144,900,754–144,902,675	215.8 kb	Distal (>10kb) Multiome	1021
chr8:144,950,374–144,951,024	264.9 kb	Distal (>10kb) Multiome	695

Genome Browser

Genomic view of the ARHGAP39 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.