NFATC4
nuclear factor of activated T cells 4 | NFAT3

This gene encodes a member of the nuclear factor of activated T cells (NFAT) protein family. The encoded protein is part of a DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor stimulation and an inducible nuclear component. NFAT proteins are activated by the calmodulin-dependent phosphatase, calcineurin. The encoded protein plays a role in the inducible expression of cytokine genes in T cells, especially in the induction of interleukin-2 and interleukin-4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

Developmental clusters: GC2
Biological processes 39 terms
DNA binding (GO:0003677)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)calcineurin-NFAT signaling cascade (GO:0033173)chromatin (GO:0000785)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)inflammatory response (GO:0006954)long-term memory (GO:0007616)long-term memory (GO:0007616)long-term synaptic potentiation (GO:0060291)long-term synaptic potentiation (GO:0060291)negative regulation of Wnt signaling pathway (GO:0030178)negative regulation of miRNA transcription (GO:1902894)negative regulation of neuron apoptotic process (GO:0043524)negative regulation of neuron apoptotic process (GO:0043524)negative regulation of transcription by RNA polymerase II (GO:0000122)nuclear speck (GO:0016607)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)sequence-specific double-stranded DNA binding (GO:1990837)transcription cis-regulatory region binding (GO:0000976)transcription cis-regulatory region binding (GO:0000976)transcription regulator complex (GO:0005667)transcription regulator complex (GO:0005667)
Expression (TPM)
NFATC4 — as a Regulated Gene

TFs regulating NFATC4 0 TFs

Transcription factors with Perturb-seq knockdown data for NFATC4. 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 = NFATC4 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to NFATC4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NFATC4, 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
chr14:24,080,914–24,082,038 286.7 kb Distal (>10kb) Multiome 706
chr14:24,093,491–24,095,115 274.0 kb Distal (>10kb) Multiome 990
chr14:24,113,681–24,115,917 253.2 kb Distal (>10kb) Multiome 1166
chr14:24,135,549–24,136,884 232.1 kb Distal (>10kb) Multiome 778
chr14:24,140,526–24,142,331 226.5 kb Distal (>10kb) Multiome 1034
chr14:24,146,204–24,148,108 221.4 kb Distal (>10kb) Multiome 918
chr14:24,160,877–24,161,762 206.9 kb Distal (>10kb) Multiome 970
chr14:24,171,489–24,172,698 196.3 kb Distal (>10kb) Multiome 365
chr14:24,188,229–24,189,111 179.4 kb Distal (>10kb) Multiome 1074
chr14:24,195,072–24,196,365 172.6 kb Distal (>10kb) Multiome 1059
chr14:24,212,871–24,213,884 154.8 kb Distal (>10kb) Multiome 1036
chr14:24,215,523–24,216,241 152.2 kb Distal (>10kb) Multiome 955
chr14:24,231,706–24,233,147 135.6 kb Distal (>10kb) Multiome 1027
chr14:24,241,845–24,243,572 125.6 kb Distal (>10kb) Multiome 1077
chr14:24,270,770–24,271,924 96.7 kb Distal (>10kb) Multiome 1089
chr14:24,299,120–24,300,273 68.4 kb Distal (>10kb) Multiome 892
chr14:24,315,948–24,316,753 51.8 kb Distal (>10kb) Multiome 736
chr14:24,332,251–24,333,127 35.7 kb Distal (>10kb) Multiome 740
chr14:24,365,652–24,366,243 2.4 kb Proximal (<10kb) Multiome 668
chr14:24,366,594–24,369,358 977 bp At TSS Multiome 921
chr14:24,376,512–24,376,811 8.3 kb Proximal (<10kb) 102
chr14:24,388,547–24,389,510 20.8 kb Distal (>10kb) Multiome 161
chr14:24,398,424–24,399,423 30.8 kb Distal (>10kb) Multiome 354
chr14:24,429,597–24,431,070 61.9 kb Distal (>10kb) Multiome HiCAR 903
chr14:24,431,554–24,432,205 63.7 kb Distal (>10kb) Multiome HiCAR 604
chr14:24,441,935–24,443,373 74.4 kb Distal (>10kb) Multiome 1072
chr14:24,481,599–24,482,121 113.6 kb Distal (>10kb) Multiome 593

Genome Browser

Genomic view of the NFATC4 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.

chr14:24,070,914 – 24,492,121
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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