NFATC3
nuclear factor of activated T cells 3 | NFAT4, NFATX, n339260

The product of this gene is a member of the nuclear factors of activated T cells 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 (TCR) stimulation and an inducible nuclear component. Other members of this family participate to form this complex also. The product of this gene plays a role in the regulation of gene expression in T cells and immature thymocytes. Several transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Nov 2010]

Member of: DE-3
Biological processes 36 terms
DN4 thymocyte differentiation (GO:1904157)DNA binding (GO:0003677)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)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 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)calcineurin-NFAT signaling cascade (GO:0033173)chromatin (GO:0000785)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)inflammatory response (GO:0006954)negative regulation of miRNA transcription (GO:1902894)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of vascular associated smooth muscle cell differentiation (GO:1905064)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of artery morphogenesis (GO:1905653)positive regulation of nitric oxide biosynthetic process (GO:0045429)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive thymic T cell selection (GO:0045059)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific double-stranded DNA binding (GO:1990837)transcription regulator complex (GO:0005667)
Expression (TPM)
NFATC3 — as a Regulated Gene

TFs regulating NFATC3 0 TFs

Transcription factors with Perturb-seq knockdown data for NFATC3. 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 = NFATC3 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 NFATC3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NFATC3, 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
chr16:67,806,066–67,807,386 278.6 kb Distal (>10kb) Multiome 914
chr16:67,816,404–67,816,888 268.6 kb Distal (>10kb) Multiome 690
chr16:67,833,426–67,834,269 251.4 kb Distal (>10kb) Multiome 838
chr16:67,841,337–67,843,276 243.2 kb Distal (>10kb) Multiome 927
chr16:67,846,090–67,847,897 238.6 kb Distal (>10kb) Multiome 1025
chr16:67,872,739–67,873,665 212.3 kb Distal (>10kb) Multiome 982
chr16:67,884,566–67,885,097 200.5 kb Distal (>10kb) Multiome 264
chr16:67,892,898–67,893,885 192.1 kb Distal (>10kb) Multiome 867
chr16:67,915,108–67,915,887 169.9 kb Distal (>10kb) Multiome 92
chr16:67,935,189–67,936,596 149.5 kb Distal (>10kb) Multiome 980
chr16:67,963,746–67,964,209 121.4 kb Distal (>10kb) Multiome 161
chr16:67,968,087–67,969,341 116.7 kb Distal (>10kb) Multiome 861
chr16:67,993,130–67,993,736 91.9 kb Distal (>10kb) Multiome 790
chr16:68,019,222–68,020,043 65.9 kb Distal (>10kb) Multiome 108
chr16:68,022,490–68,023,556 62.1 kb Distal (>10kb) Multiome 958
chr16:68,084,205–68,086,133 102 bp At TSS Multiome 1092
chr16:68,235,016–68,238,254 150.8 kb Distal (>10kb) Multiome HiCAR 1055
chr16:68,239,582–68,240,355 154.7 kb Distal (>10kb) Multiome HiCAR 223
chr16:68,244,730–68,245,757 159.9 kb Distal (>10kb) Multiome 803
chr16:68,264,033–68,265,087 179.1 kb Distal (>10kb) Multiome 876
chr16:68,310,451–68,311,505 225.7 kb Distal (>10kb) Multiome 1061
chr16:68,328,654–68,329,423 243.4 kb Distal (>10kb) Multiome 438

Genome Browser

Genomic view of the NFATC3 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.

chr16:67,796,066 – 68,339,423
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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