CNOT3

CCR4-NOT transcription complex subunit 3 | KIAA0691, LENG2, NOT3H, NOT3

Involved in regulation of stem cell population maintenance. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Jul 2025]

Member of: DE-4 Developmental clusters: GC2

Biological processes 24 terms

CCR4-NOT complex (GO:0030014)CCR4-NOT core complex (GO:0030015)CCR4-NOT core complex (GO:0030015)P-body (GO:0000932)P-body (GO:0000932)P-body (GO:0000932)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)determination of left/right symmetry (GO:0007368)determination of left/right symmetry (GO:0007368)mRNA catabolic process (GO:0006402)mRNA catabolic process (GO:0006402)nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)nucleus (GO:0005634)positive regulation of cold-induced thermogenesis (GO:0120162)positive regulation of cold-induced thermogenesis (GO:0120162)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of stem cell population maintenance (GO:2000036)regulation of stem cell population maintenance (GO:2000036)regulation of stem cell population maintenance (GO:2000036)trophectodermal cell differentiation (GO:0001829)

Expression (TPM)

TFs regulating CNOT3 0 TFs

Transcription factors with Perturb-seq knockdown data for CNOT3. 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 = CNOT3 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 CNOT3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CNOT3, 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
chr19:53,865,880–53,866,753	271.5 kb	Distal (>10kb) Multiome	532
chr19:53,866,887–53,869,891	270.1 kb	Distal (>10kb) Multiome	993
chr19:53,878,918–53,880,011	258.2 kb	Distal (>10kb) Multiome	561
chr19:53,881,744–53,882,458	255.6 kb	Distal (>10kb) Multiome	435
chr19:53,889,715–53,890,286	247.7 kb	Distal (>10kb) Multiome	322
chr19:53,898,176–53,899,412	238.8 kb	Distal (>10kb) Multiome	212
chr19:53,907,868–53,908,722	229.5 kb	Distal (>10kb) Multiome	276
chr19:53,941,849–53,943,229	195.3 kb	Distal (>10kb) Multiome	240
chr19:53,957,309–53,957,858	180.2 kb	Distal (>10kb) Multiome	97
chr19:53,977,539–53,979,011	159.3 kb	Distal (>10kb) Multiome	412
chr19:53,979,770–53,982,403	156.5 kb	Distal (>10kb) Multiome	530
chr19:53,982,560–53,983,015	154.9 kb	Distal (>10kb) Multiome	119
chr19:54,095,628–54,096,220	41.8 kb	Distal (>10kb) Multiome	457
chr19:54,102,597–54,103,302	35.0 kb	Distal (>10kb) Multiome	703
chr19:54,114,870–54,116,009	22.2 kb	Distal (>10kb) Multiome	911
chr19:54,136,562–54,138,683	362 bp	At TSS Multiome	751
chr19:54,159,030–54,160,865	22.1 kb	Distal (>10kb) Multiome	793
chr19:54,161,897–54,162,738	24.7 kb	Distal (>10kb) Multiome	233
chr19:54,164,508–54,165,013	27.1 kb	Distal (>10kb) Multiome	183
chr19:54,172,536–54,173,532	35.4 kb	Distal (>10kb) Multiome	397
chr19:54,188,192–54,192,172	52.2 kb	Distal (>10kb) Multiome	979
chr19:54,200,383–54,201,351	63.1 kb	Distal (>10kb) Multiome	891
chr19:54,208,780–54,209,556	71.7 kb	Distal (>10kb) Multiome	358
chr19:54,231,547–54,232,136	94.1 kb	Distal (>10kb) Multiome	471
chr19:54,420,287–54,421,161	283.1 kb	Distal (>10kb) Multiome	334
chr19:54,430,381–54,431,285	293.3 kb	Distal (>10kb) Multiome	240

Genome Browser

Genomic view of the CNOT3 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.