This gene encodes a member of the HOMER family of postsynaptic density scaffolding proteins that share a similar domain structure consisting of an N-terminal Enabled/vasodilator-stimulated phosphoprotein homology 1 domain which mediates protein-protein interactions, and a carboxy-terminal coiled-coil domain and two leucine zipper motifs that are involved in self-oligomerization. The encoded protein binds numerous other proteins including group I metabotropic glutamate receptors, inositol 1,4,5-trisphosphate receptors and amyloid precursor proteins and has been implicated in diverse biological functions such as neuronal signaling, T-cell activation and trafficking of amyloid beta peptides. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
Transcription factors with Perturb-seq knockdown data for HOMER3. 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 = HOMER3 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 HOMER3, 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 |
|---|---|---|---|---|
| chr19:18,682,925–18,684,360 | 256.7 kb | Distal (>10kb) Multiome | 701 | |
| chr19:18,785,146–18,785,600 | 155.0 kb | Distal (>10kb) Multiome | 247 | |
| chr19:18,831,386–18,833,070 | 108.5 kb | Distal (>10kb) Multiome | 833 | |
| chr19:18,870,063–18,870,526 | 69.9 kb | Distal (>10kb) Multiome | 148 | |
| chr19:18,895,036–18,896,591 | 44.2 kb | Distal (>10kb) Multiome | 554 | |
| chr19:18,918,971–18,919,972 | 20.8 kb | Distal (>10kb) Multiome | 828 | |
| chr19:18,932,038–18,933,012 | 7.8 kb | Proximal (<10kb) Multiome | 312 | |
| chr19:18,940,031–18,940,411 | 805 bp | At TSS | 351 | |
| chr19:18,940,835–18,941,417 | 921 bp | At TSS Multiome | 336 | |
| chr19:19,017,061–19,017,561 | 76.9 kb | Distal (>10kb) Multiome | 21 | |
| chr19:19,032,820–19,034,059 | 93.3 kb | Distal (>10kb) Multiome | 944 | |
| chr19:19,063,253–19,064,386 | 123.4 kb | Distal (>10kb) Multiome | 781 | |
| chr19:19,105,310–19,106,514 | 165.4 kb | Distal (>10kb) Multiome | 447 | |
| chr19:19,110,429–19,110,857 | 170.3 kb | Distal (>10kb) Multiome | 131 | |
| chr19:19,119,998–19,121,362 | 180.2 kb | Distal (>10kb) Multiome | 304 | |
| chr19:19,138,171–19,138,698 | 198.1 kb | Distal (>10kb) Multiome | 642 | |
| chr19:19,170,055–19,170,692 | 230.0 kb | Distal (>10kb) Multiome | 403 | |
| chr19:19,191,912–19,193,209 | 252.2 kb | Distal (>10kb) Multiome | 939 | |
| chr19:19,202,895–19,203,773 | 263.1 kb | Distal (>10kb) Multiome | 599 | |
| chr19:19,224,938–19,225,553 | 284.9 kb | Distal (>10kb) Multiome | 646 |
Genomic view of the HOMER3 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.