NR6A1
nuclear receptor subfamily 6 group A member 1 | CT150, GCNF1, RTR, GCNF

This gene encodes an orphan nuclear receptor which is a member of the nuclear hormone receptor family. Its expression pattern suggests that it may be involved in neurogenesis and germ cell development. The protein can homodimerize and bind DNA, but in vivo targets have not been identified. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2013]

Member of: DE-3 DE-3.2 Developmental clusters: GC6
Biological processes 35 terms
DNA binding (GO:0003677)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 repressor activity (GO:0001217)DNA-binding transcription repressor activity (GO:0001217)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)chromatin (GO:0000785)chromatin (GO:0000785)estrogen response element binding (GO:0034056)gamete generation (GO:0007276)gamete generation (GO:0007276)intracellular receptor signaling pathway (GO:0030522)negative regulation of transcription by RNA polymerase II (GO:0000122)nuclear receptor activity (GO:0004879)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of mesenchymal stem cell differentiation (GO:2000741)positive regulation of mesenchymal stem cell differentiation (GO:2000741)positive regulation of transcription by RNA polymerase II (GO:0045944)protein homodimerization activity (GO:0042803)protein homodimerization activity (GO:0042803)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)sequence-specific double-stranded DNA binding (GO:1990837)transcription regulator complex (GO:0005667)transcription regulator complex (GO:0005667)zinc ion binding (GO:0008270)
Expression (TPM)
NR6A1 — as a Regulated Gene

TFs regulating NR6A1 0 TFs

Transcription factors with Perturb-seq knockdown data for NR6A1. 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 = NR6A1 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 NR6A1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NR6A1, 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
chr9:124,415,161–124,415,813 355.8 kb Distal (>10kb) Multiome 779
chr9:124,419,615–124,420,013 351.6 kb Distal (>10kb) Multiome 266
chr9:124,449,997–124,450,901 320.9 kb Distal (>10kb) Multiome 232
chr9:124,453,124–124,454,077 317.6 kb Distal (>10kb) Multiome 218
chr9:124,477,322–124,478,654 293.3 kb Distal (>10kb) Multiome 223
chr9:124,482,335–124,482,814 288.6 kb Distal (>10kb) Multiome 94
chr9:124,504,291–124,505,297 266.3 kb Distal (>10kb) Multiome 187
chr9:124,593,694–124,594,006 1.8 kb Proximal (<10kb) 163
chr9:124,769,647–124,772,472 170 bp At TSS Multiome 1006
chr9:124,774,457–124,774,680 3.2 kb Proximal (<10kb) 288
chr9:124,776,976–124,778,058 6.1 kb Proximal (<10kb) Multiome 349
chr9:124,779,329–124,780,041 8.4 kb Proximal (<10kb) Multiome 260
chr9:124,810,709–124,811,373 39.7 kb Distal (>10kb) Multiome HiCAR 209
chr9:124,839,680–124,840,329 68.6 kb Distal (>10kb) Multiome HiCAR 218
chr9:124,852,683–124,853,882 81.9 kb Distal (>10kb) Multiome HiCAR 666
chr9:124,855,555–124,856,920 85.0 kb Distal (>10kb) Multiome HiCAR 402
chr9:124,861,378–124,862,662 90.8 kb Distal (>10kb) Multiome HiCAR 947
chr9:124,868,442–124,869,814 97.8 kb Distal (>10kb) Multiome HiCAR 849
chr9:124,940,496–124,941,902 169.8 kb Distal (>10kb) Multiome 979

Genome Browser

Genomic view of the NR6A1 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.

chr9:124,405,161 – 124,951,902
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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