LRFN3

leucine rich repeat and fibronectin type III domain containing 3 | FIGLER1, MGC2656, SALM4

Predicted to be involved in regulation of presynapse assembly; regulation of synaptic membrane adhesion; and synaptic membrane adhesion. Predicted to be located in plasma membrane. Predicted to be active in cell surface; glutamatergic synapse; and synaptic membrane. [provided by Alliance of Genome Resources, Apr 2025]

Biological processes 17 terms

axon (GO:0030424)cell surface (GO:0009986)cell surface (GO:0009986)dendrite (GO:0030425)glutamatergic synapse (GO:0098978)plasma membrane (GO:0005886)plasma membrane (GO:0005886)postsynaptic density membrane (GO:0098839)postsynaptic membrane (GO:0045211)postsynaptic specialization membrane (GO:0099634)presynaptic active zone membrane (GO:0048787)presynaptic active zone membrane (GO:0048787)presynaptic membrane (GO:0042734)regulation of presynapse assembly (GO:1905606)regulation of synaptic membrane adhesion (GO:0099179)synapse (GO:0045202)synaptic membrane adhesion (GO:0099560)

Expression (TPM)

TFs regulating LRFN3 0 TFs

Transcription factors with Perturb-seq knockdown data for LRFN3. 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 = LRFN3 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 LRFN3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of LRFN3, 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
chr19:35,641,602–35,642,192	294.6 kb	Distal (>10kb) Multiome	183
chr19:35,643,064–35,645,730	292.8 kb	Distal (>10kb) Multiome	1010
chr19:35,648,040–35,648,575	288.2 kb	Distal (>10kb) Multiome	599
chr19:35,673,179–35,673,643	263.0 kb	Distal (>10kb) Multiome	311
chr19:35,702,152–35,702,985	233.9 kb	Distal (>10kb) Multiome	662
chr19:35,716,025–35,718,811	218.6 kb	Distal (>10kb) Multiome	1018
chr19:35,740,083–35,741,430	195.6 kb	Distal (>10kb) Multiome	829
chr19:35,744,481–35,746,086	191.1 kb	Distal (>10kb) Multiome	679
chr19:35,748,170–35,749,017	187.9 kb	Distal (>10kb) Multiome	749
chr19:35,757,432–35,758,657	178.3 kb	Distal (>10kb) Multiome	851
chr19:35,767,601–35,768,256	168.4 kb	Distal (>10kb) Multiome	276
chr19:35,775,066–35,776,063	160.9 kb	Distal (>10kb) Multiome	474
chr19:35,784,357–35,785,306	151.6 kb	Distal (>10kb) Multiome	183
chr19:35,860,621–35,861,651	75.1 kb	Distal (>10kb) Multiome	299
chr19:35,868,369–35,868,860	67.9 kb	Distal (>10kb) Multiome	320
chr19:35,869,343–35,870,482	66.4 kb	Distal (>10kb) Multiome	492
chr19:35,899,240–35,900,760	36.7 kb	Distal (>10kb) Multiome	751
chr19:35,931,342–35,932,167	4.7 kb	Proximal (<10kb) Multiome	835
chr19:35,936,083–35,936,704	36 bp	At TSS Multiome	417
chr19:35,986,945–35,987,622	50.9 kb	Distal (>10kb) Multiome	363
chr19:35,994,796–35,995,940	58.8 kb	Distal (>10kb) Multiome	897
chr19:36,008,519–36,009,006	72.4 kb	Distal (>10kb) Multiome	427
chr19:36,013,972–36,014,810	78.0 kb	Distal (>10kb) Multiome	623
chr19:36,032,424–36,033,187	96.5 kb	Distal (>10kb) Multiome	179
chr19:36,053,782–36,055,591	118.1 kb	Distal (>10kb) Multiome	1026
chr19:36,113,981–36,116,196	178.9 kb	Distal (>10kb) Multiome	1052
chr19:36,127,575–36,128,707	191.7 kb	Distal (>10kb) Multiome	942
chr19:36,139,425–36,141,811	204.9 kb	Distal (>10kb) Multiome	1037
chr19:36,160,493–36,161,405	224.5 kb	Distal (>10kb) Multiome	94
chr19:36,214,162–36,215,543	278.5 kb	Distal (>10kb) Multiome	1008

Genome Browser

Genomic view of the LRFN3 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.