SYP

synaptophysin | MRX96

This gene encodes an integral membrane protein of small synaptic vesicles in brain and endocrine cells. The protein also binds cholesterol and is thought to direct targeting of vesicle-associated membrane protein 2 (synaptobrevin) to intracellular compartments. Mutations in this gene are associated with an X-linked form of cognitive disability. [provided by RefSeq, Jul 2017]

Biological processes 35 terms

SH2 domain binding (GO:0042169)Schaffer collateral - CA1 synapse (GO:0098685)cholesterol binding (GO:0015485)endocytosis (GO:0006897)excitatory synapse (GO:0060076)identical protein binding (GO:0042802)membrane (GO:0016020)modulation of chemical synaptic transmission (GO:0050804)neuromuscular junction (GO:0031594)neuron projection (GO:0043005)neuron projection (GO:0043005)neuron projection (GO:0043005)neuron projection terminus (GO:0044306)perinuclear region of cytoplasm (GO:0048471)presynapse (GO:0098793)presynaptic active zone (GO:0048786)presynaptic active zone (GO:0048786)presynaptic membrane (GO:0042734)protein binding (GO:0005515)regulation of long-term neuronal synaptic plasticity (GO:0048169)regulation of long-term neuronal synaptic plasticity (GO:0048169)regulation of neuronal synaptic plasticity (GO:0048168)regulation of opioid receptor signaling pathway (GO:2000474)regulation of short-term neuronal synaptic plasticity (GO:0048172)regulation of short-term neuronal synaptic plasticity (GO:0048172)regulation of synaptic vesicle priming (GO:0010807)synapse (GO:0045202)synaptic vesicle (GO:0008021)synaptic vesicle (GO:0008021)synaptic vesicle maturation (GO:0016188)synaptic vesicle membrane (GO:0030672)synaptic vesicle membrane (GO:0030672)synaptic vesicle membrane (GO:0030672)synaptic vesicle membrane organization (GO:0048499)terminal bouton (GO:0043195)

Expression (TPM)

TFs regulating SYP 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SYP, 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
chrX:48,911,574–48,912,414	288.3 kb	Distal (>10kb) Multiome	671
chrX:48,917,179–48,917,999	282.7 kb	Distal (>10kb) Multiome	468
chrX:48,918,412–48,919,792	281.0 kb	Distal (>10kb) Multiome	693
chrX:48,957,469–48,959,105	241.8 kb	Distal (>10kb) Multiome	722
chrX:49,001,538–49,002,676	197.8 kb	Distal (>10kb) Multiome	540
chrX:49,039,840–49,040,493	160.0 kb	Distal (>10kb) Multiome	436
chrX:49,042,954–49,044,182	156.6 kb	Distal (>10kb) Multiome	664
chrX:49,053,328–49,054,050	146.5 kb	Distal (>10kb) Multiome	403
chrX:49,071,863–49,072,612	128.1 kb	Distal (>10kb) Multiome	107
chrX:49,073,903–49,074,451	126.1 kb	Distal (>10kb) Multiome	464
chrX:49,100,885–49,101,855	98.9 kb	Distal (>10kb) Multiome	562
chrX:49,155,633–49,156,658	44.1 kb	Distal (>10kb) Multiome	524
chrX:49,163,555–49,164,377	36.1 kb	Distal (>10kb) Multiome	485
chrX:49,166,140–49,166,713	33.7 kb	Distal (>10kb) Multiome	416
chrX:49,184,219–49,185,254	15.6 kb	Distal (>10kb) Multiome	389
chrX:49,190,730–49,191,899	9.0 kb	Proximal (<10kb) Multiome	636
chrX:49,199,793–49,200,448	44 bp	At TSS Multiome	806
chrX:49,230,792–49,231,268	30.8 kb	Distal (>10kb) Multiome	221
chrX:49,268,786–49,270,236	69.2 kb	Distal (>10kb) Multiome	603

Genome Browser

Genomic view of the SYP 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.