RFX5

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regulatory factor X, 5 (influences HLA class II expression)
RFX5

PDB ID : 2KW3
PDB2KW3
HGNCRFX5
Gene CardRFX5
Entrez5993
RefSeqNM_000449
UniProtP48382
UCSCBrowser view
WikipediaRFX5
Protein FamilyWinged helix DNA-binding domain
TypePol II TF
Ensembl Exp.n/a

Function

RFX5 is a member of a family of DNA-binding proteins that share a novel and highly characteristic DNA-binding domain called the RFX motif. It mediates cooperative binding between RFX and NF-Y, recognizes X-boxes, and activates transcription from class II MHC promoters. RFX5 mutations are seen in cases of a severe immunodeficiency syndrome called MHC-II deficiency (also known as bare lymphocyte syndrome (BLS)). These mutations prevent the RFX complex from binding to the X box in MHC-II promoters, resulting in a lack of MHC-II expression.

ENCODE ChIP-seq Datasets

Indicated in the matrix are the numbers of datasets specified by lab and cell line; when the number is greater than 1, multiple ChIP-seq experiments have been performed, some upon treatments. Click the numbers to download the data files on ChIP-seq peaks, alignments, etc.

+/-
Stanford
GM12878 1
H1-hESC 1
HeLa-S3 1
HepG2 1
K562 1


Average Profiles of Modified Histones around the Summit of ChIP-seq Peaks

Average histone modification profiles are shown for the [-2 kb, +2 kb] window around the summits of TF ChIP-seq peaks, separately for peaks that are proximal ([-1kb, +1kb]) to an annotated transcript (dashed lines) start sites and for peaks that are distal (more than 1kb) to all annotated transcripts (solid lines) start sites. Proximal profiles are arranged such that the transcriptional direction of the nearest transcript is toward the right. Histone modification data were generated by the Broad team, using antibodies to pull down modified histones followed by deep sequencing of the genomic DNA associated with the modified histones. Only histone modification data from the same cell line as the TF ChIP-seq data are shown.

Mouse over a curve to reveal its identity. Mouse over a histone modification in the legend to show its curves and gray out other histone modifications in the figures. Click a histone modification in the legend to toggle on/off its curve in all figures. Click the “Proximal” or “Distal” button in the legend to show only the average histone modification profiles anchored around ChIP-seq peaks that are proximal or distal to annotated transcripts.

Average Profiles of Nucleosomes around the Summit of ChIP-seq Peaks

Average nucleosome occupancy profiles are shown for the [-2 kb, +2 kb] window around the summits of TF ChIP-seq peaks, separately for peaks that are proximal to an annotated transcript (red lines) and for peaks that are distal to all annotated transcripts (blue lines), as defined in the previous section. Nucleosome positioning data in GM12878 and K562 were generated by the Stanford team, with micrococcal nuclease digestion of chromatin followed by deep sequencing of mononucleosomal DNA.

Motifs Enriched in the Top 500 ChIP-seq Peaks

The sequences of the top 500 TF ChIP-seq peaks were used to identify enriched motifs de novo, using the MEME-ChIP suite of tools. Five motifs are reported (M1 to M5), with motif name, sequence logo, and number of peaks out of the top 500 peaks that contain a site for the motif. The motifs are then used to scan the entire set of ChIP-seq peaks and the two flanking (control) regions using the FIMO tool, and two quantities are reported for bins of peaks sorted by their ChIP-seq q-values: percentage of the peaks that contain a site for the motif, and the distribution of the distances of the motif site to the summit of the peak.

Select MotifCell Line:   Lab:   Protocol:   Treatment:   Antibody:  

Cell Line:GM12878   Lab:Stanford   Protocol:IgG-mus   Treatment:None   Antibody:RFX5_(200-401-194)   

Binding of Other Transcription Factors or Histone Marks at the RFX5 Peaks

Select HeatmapLab:   Cellline:  

  • Comparison with the RFX5 peaks in GM12878 cells generated by SYDH

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