RFX2

regulatory factor X2 | FLJ14226

This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. This protein can bind to cis elements in the promoter of the IL-5 receptor alpha gene. Two transcript variants encoding different isoforms have been described for this gene, and both variants utilize alternative polyadenylation sites. [provided by RefSeq, Jul 2008]

Member of: DE-3 DE-3.20

Biological processes 32 terms

DNA binding (GO:0003677)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 (GO:0003700)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)acrosome assembly (GO:0001675)acrosome assembly (GO:0001675)chromatin (GO:0000785)cilium assembly (GO:0060271)cilium assembly (GO:0060271)cilium assembly (GO:0060271)cytoplasm (GO:0005737)cytoplasm (GO:0005737)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific double-stranded DNA binding (GO:1990837)spermatid development (GO:0007286)spermatid development (GO:0007286)spermatid development (GO:0007286)

Expression (TPM)

TFs regulating RFX2 0 TFs

Transcription factors with Perturb-seq knockdown data for RFX2. 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 = RFX2 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 RFX2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of RFX2, 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
chr19:5,903,474–5,905,358	295.0 kb	Distal (>10kb) Multiome	1027
chr19:5,977,406–5,978,787	221.4 kb	Distal (>10kb) Multiome	1028
chr19:6,110,281–6,110,936	88.9 kb	Distal (>10kb) Multiome	518
chr19:6,199,134–6,200,121	130 bp	At TSS Multiome	769
chr19:6,279,539–6,280,376	80.5 kb	Distal (>10kb) Multiome	761
chr19:6,361,350–6,362,018	162.0 kb	Distal (>10kb) Multiome	803
chr19:6,372,272–6,374,427	173.9 kb	Distal (>10kb) Multiome	925
chr19:6,392,902–6,394,077	193.9 kb	Distal (>10kb) Multiome	767
chr19:6,423,613–6,425,899	225.6 kb	Distal (>10kb) Multiome	956
chr19:6,458,960–6,460,940	260.8 kb	Distal (>10kb) Multiome	859
chr19:6,463,863–6,464,838	264.7 kb	Distal (>10kb) Multiome	526
chr19:6,470,903–6,471,589	271.7 kb	Distal (>10kb) Multiome	26
chr19:6,475,386–6,477,353	277.0 kb	Distal (>10kb) Multiome	419

Genome Browser

Genomic view of the RFX2 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.