CNOT9
CCR4-NOT transcription complex subunit 9 | CAF40, CT129, RCD1, RCD1+, RQCD1

This gene encodes a member of the highly conserved RCD1 protein family. The encoded protein is a transcriptional cofactor and a core protein of the CCR4-NOT complex. It may be involved in signal transduction as well as retinoic acid-regulated cell differentiation and development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2012]

Member of: DE-6
Biological processes 25 terms
CCR4-NOT complex (GO:0030014)CCR4-NOT complex (GO:0030014)CCR4-NOT core complex (GO:0030015)P-body (GO:0000932)P-body (GO:0000932)P-body (GO:0000932)cytosol (GO:0005829)cytosol (GO:0005829)epidermal growth factor receptor binding (GO:0005154)kinase binding (GO:0019900)mRNA catabolic process (GO:0006402)membrane (GO:0016020)negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)negative regulation of translation (GO:0017148)nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)positive regulation of peptidyl-serine phosphorylation (GO:0033138)protein binding (GO:0005515)protein domain specific binding (GO:0019904)protein homodimerization activity (GO:0042803)protein-containing complex (GO:0032991)sex differentiation (GO:0007548)transcription coactivator activity (GO:0003713)
Expression (TPM)
CNOT9 — as a Regulated Gene

TFs regulating CNOT9 0 TFs

Transcription factors with Perturb-seq knockdown data for CNOT9. 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 = CNOT9 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 CNOT9

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CNOT9, 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
chr2:218,269,385–218,270,929 298.6 kb Distal (>10kb) Multiome 913
chr2:218,290,037–218,290,611 278.6 kb Distal (>10kb) Multiome 264
chr2:218,291,910–218,292,722 276.4 kb Distal (>10kb) Multiome 695
chr2:218,322,154–218,324,454 245.7 kb Distal (>10kb) Multiome 914
chr2:218,367,421–218,368,194 201.1 kb Distal (>10kb) Multiome 450
chr2:218,387,091–218,388,220 181.0 kb Distal (>10kb) Multiome 514
chr2:218,395,568–218,397,399 172.7 kb Distal (>10kb) Multiome 1048
chr2:218,397,484–218,401,433 171.0 kb Distal (>10kb) Multiome 1114
chr2:218,405,424–218,407,478 162.5 kb Distal (>10kb) Multiome 1093
chr2:218,567,787–218,569,400 415 bp At TSS Multiome 1083
chr2:218,569,571–218,569,873 992 bp At TSS 106
chr2:218,658,668–218,660,011 90.7 kb Distal (>10kb) Multiome 870
chr2:218,671,689–218,672,558 103.1 kb Distal (>10kb) Multiome 794
chr2:218,710,272–218,711,420 141.9 kb Distal (>10kb) Multiome 957
chr2:218,781,682–218,782,718 213.2 kb Distal (>10kb) Multiome 674
chr2:218,798,810–218,799,640 230.3 kb Distal (>10kb) Multiome 163
chr2:218,799,866–218,800,388 231.4 kb Distal (>10kb) Multiome 82
chr2:218,860,491–218,861,382 292.1 kb Distal (>10kb) Multiome 241

Genome Browser

Genomic view of the CNOT9 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.

chr2:218,259,385 – 218,871,382
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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