This gene encodes a DENN-domain-containing protein that functions as a RAB-activating guanine nucleotide exchange factor (GEF). This protein catalyzes the conversion of GDP to GTP and thereby converts inactive GDP-bound Rab proteins into their active GTP-bound form. The encoded protein is recruited by RAB6 onto Golgi membranes and is therefore referred to as RAB6-interacting protein 1. This protein binds with RAB39 as well. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Mutations in this gene are associated with early infantile epileptic encephalopathy-49. [provided by RefSeq, Feb 2017]
Transcription factors with Perturb-seq knockdown data for DENND5A. 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 = DENND5A 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 |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of DENND5A, 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 |
|---|---|---|---|---|
| chr11:9,003,516–9,004,824 | 261.2 kb | Distal (>10kb) Multiome | 534 | |
| chr11:9,090,882–9,091,926 | 173.9 kb | Distal (>10kb) Multiome | 196 | |
| chr11:9,264,697–9,266,230 | 63 bp | At TSS Multiome | 703 | |
| chr11:9,267,723–9,268,077 | 2.4 kb | Proximal (<10kb) | 21 | |
| chr11:9,313,980–9,315,407 | 49.4 kb | Distal (>10kb) Multiome | 997 | |
| chr11:9,318,649–9,319,624 | 53.9 kb | Distal (>10kb) Multiome | 258 | |
| chr11:9,363,967–9,364,851 | 99.2 kb | Distal (>10kb) Multiome | 1019 | |
| chr11:9,384,450–9,385,531 | 119.3 kb | Distal (>10kb) Multiome | 939 | |
| chr11:9,460,209–9,461,643 | 195.5 kb | Distal (>10kb) Multiome | 1040 |
Genomic view of the DENND5A 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.