RPUSD4
RNA pseudouridine synthase D4 | FLJ14494

Enables mitochondrial ribosomal large subunit rRNA binding activity; pseudouridine synthase activity; and tRNA binding activity. Involved in positive regulation of mitochondrial translation and pseudouridine synthesis. Located in mitochondrial matrix; nucleoplasm; and ribonucleoprotein granule. [provided by Alliance of Genome Resources, Jul 2025]

Biological processes 29 terms
RNA binding (GO:0003723)RNA binding (GO:0003723)RNA modification (GO:0009451)cytoplasm (GO:0005737)enzyme-directed rRNA pseudouridine synthesis (GO:0000455)mRNA pseudouridine synthesis (GO:1990481)mitochondrial RNA modification (GO:1900864)mitochondrial matrix (GO:0005759)mitochondrial matrix (GO:0005759)mitochondrial matrix (GO:0005759)mitochondrial matrix (GO:0005759)mitochondrial ribosomal large subunit rRNA binding (GO:1990400)mitochondrial tRNA pseudouridine synthesis (GO:0070902)mitochondrion (GO:0005739)mitochondrion (GO:0005739)nucleus (GO:0005634)positive regulation of mitochondrial translation (GO:0070131)protein binding (GO:0005515)pseudouridine synthase activity (GO:0009982)pseudouridine synthase activity (GO:0009982)pseudouridine synthase activity (GO:0009982)pseudouridine synthase activity (GO:0009982)pseudouridine synthase activity (GO:0009982)pseudouridine synthesis (GO:0001522)rRNA modification (GO:0000154)rRNA pseudouridine synthesis (GO:0031118)ribonucleoprotein granule (GO:0035770)tRNA binding (GO:0000049)tRNA pseudouridine synthase activity (GO:0106029)
Expression (TPM)
RPUSD4 — as a Regulated Gene

TFs regulating RPUSD4 0 TFs

Transcription factors with Perturb-seq knockdown data for RPUSD4. 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 = RPUSD4 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 RPUSD4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of RPUSD4, 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
chr11:125,938,819–125,939,449 272.6 kb Distal (>10kb) Multiome 161
chr11:125,941,709–125,942,323 269.5 kb Distal (>10kb) Multiome 270
chr11:126,061,736–126,063,712 148.6 kb Distal (>10kb) Multiome 802
chr11:126,082,403–126,083,132 128.9 kb Distal (>10kb) Multiome 134
chr11:126,104,267–126,104,892 107.0 kb Distal (>10kb) Multiome 192
chr11:126,159,698–126,160,582 51.5 kb Distal (>10kb) Multiome 281
chr11:126,210,869–126,212,282 17 bp At TSS Multiome 846
chr11:126,268,478–126,269,613 57.4 kb Distal (>10kb) Multiome 828
chr11:126,282,310–126,283,787 71.4 kb Distal (>10kb) Multiome 754
chr11:126,303,694–126,304,639 92.4 kb Distal (>10kb) Multiome 979
chr11:126,345,823–126,346,956 134.7 kb Distal (>10kb) Multiome 446
chr11:126,355,100–126,356,405 144.0 kb Distal (>10kb) Multiome 596
chr11:126,440,475–126,441,596 229.4 kb Distal (>10kb) Multiome 367
chr11:126,480,538–126,481,044 269.2 kb Distal (>10kb) Multiome 487
chr11:126,497,641–126,499,015 286.8 kb Distal (>10kb) Multiome 250
chr11:126,502,215–126,503,760 291.5 kb Distal (>10kb) Multiome 129

Genome Browser

Genomic view of the RPUSD4 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.

chr11:125,928,819 – 126,513,760
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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