RPUSD3

RNA pseudouridine synthase D3 | MGC29784

This gene encodes a protein that functions in the assembly of the mitochondrial ribosome by adding a pseudouridine group to 16S rRNA. Loss of this gene results in causes defects in mitochondrial protein production. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2017]

Biological processes 18 terms

RNA binding (GO:0003723)RNA binding (GO:0003723)RNA modification (GO:0009451)enzyme-directed rRNA pseudouridine synthesis (GO:0000455)mRNA modification (GO:0016556)mRNA pseudouridine synthesis (GO:1990481)mitochondrial matrix (GO:0005759)mitochondrial matrix (GO:0005759)mitochondrial matrix (GO:0005759)mitochondrion (GO:0005739)mitochondrion (GO:0005739)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 synthesis (GO:0001522)ribonucleoprotein granule (GO:0035770)

Expression (TPM)

TFs regulating RPUSD3 0 TFs

Transcription factors with Perturb-seq knockdown data for RPUSD3. 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 = RPUSD3 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 RPUSD3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of RPUSD3, 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
chr3:9,552,048–9,552,879	291.5 kb	Distal (>10kb) Multiome	372
chr3:9,553,391–9,554,161	290.1 kb	Distal (>10kb) Multiome	128
chr3:9,649,068–9,649,746	194.6 kb	Distal (>10kb) Multiome	793
chr3:9,703,572–9,705,701	138.9 kb	Distal (>10kb) Multiome	664
chr3:9,727,013–9,727,518	116.8 kb	Distal (>10kb) Multiome	264
chr3:9,730,724–9,732,470	112.7 kb	Distal (>10kb) Multiome	934
chr3:9,749,252–9,750,525	94.0 kb	Distal (>10kb) Multiome	873
chr3:9,769,503–9,770,124	74.1 kb	Distal (>10kb) Multiome	504
chr3:9,792,176–9,793,536	51.2 kb	Distal (>10kb) Multiome	915
chr3:9,809,609–9,810,744	33.9 kb	Distal (>10kb) Multiome	437
chr3:9,843,116–9,844,397	11 bp	At TSS Multiome	787
chr3:9,862,465–9,863,231	18.8 kb	Distal (>10kb) Multiome	581
chr3:9,890,247–9,891,058	46.6 kb	Distal (>10kb) Multiome	969
chr3:9,902,504–9,903,128	58.8 kb	Distal (>10kb) Multiome HiCAR	396
chr3:9,914,983–9,916,160	71.3 kb	Distal (>10kb) Multiome	668
chr3:9,916,644–9,917,412	73.1 kb	Distal (>10kb) Multiome	519
chr3:9,932,470–9,934,327	88.8 kb	Distal (>10kb) Multiome	1035
chr3:9,946,152–9,947,739	102.6 kb	Distal (>10kb) Multiome	898
chr3:9,951,898–9,952,503	108.3 kb	Distal (>10kb) Multiome	484
chr3:9,986,547–9,987,409	142.9 kb	Distal (>10kb) Multiome	907
chr3:10,008,678–10,009,458	165.1 kb	Distal (>10kb) Multiome	240
chr3:10,010,580–10,011,700	167.2 kb	Distal (>10kb) Multiome	540
chr3:10,025,904–10,026,762	182.4 kb	Distal (>10kb) Multiome	871
chr3:10,115,394–10,116,145	271.7 kb	Distal (>10kb) Multiome	809
chr3:10,141,441–10,142,425	297.8 kb	Distal (>10kb) Multiome	894

Genome Browser

Genomic view of the RPUSD3 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.