NKRF

NFKB repressing factor | ITBA4, NRF, XTBD3

This gene encodes a transcriptional repressor that interacts with specific negative regulatory elements to mediate transcriptional repression of certain nuclear factor kappa B responsive genes. The protein localizes predominantly to the nucleolus with a small fraction found in the nucleoplasm and cytoplasm. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

Developmental clusters: GC2

Biological processes 15 terms

ATPase activator activity (GO:0001671)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)RNA binding (GO:0003723)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of DNA-templated transcription (GO:0045892)nucleic acid binding (GO:0003676)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)

Expression (TPM)

TFs regulating NKRF 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NKRF, 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:119,399,020–119,399,773	207.0 kb	Distal (>10kb) Multiome	440
chrX:119,468,031–119,469,511	138.1 kb	Distal (>10kb) Multiome	762
chrX:119,573,862–119,575,243	31.9 kb	Distal (>10kb) Multiome	734
chrX:119,605,775–119,606,635	12 bp	At TSS Multiome	518
chrX:119,692,568–119,693,792	86.9 kb	Distal (>10kb) Multiome	595
chrX:119,757,760–119,759,432	151.9 kb	Distal (>10kb) Multiome	507
chrX:119,791,353–119,792,197	185.3 kb	Distal (>10kb) Multiome	699
chrX:119,852,659–119,853,400	246.7 kb	Distal (>10kb) Multiome	612
chrX:119,871,438–119,872,306	265.4 kb	Distal (>10kb) Multiome	720

Genome Browser

Genomic view of the NKRF 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.