CDK5RAP3
CDK5 regulatory subunit associated protein 3 | C53, FLJ13660, HSF-27, IC53, LZAP, MST016, OK/SW-cl.114

This gene encodes a protein that has been reported to function in signaling pathways governing transcriptional regulation and cell cycle progression. It may play a role in tumorigenesis and metastasis. A pseudogene of this gene is located on the long arm of chromosome 20. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]

Member of: DE-1 Developmental clusters: GC6
Biological processes 61 terms
MDM2/MDM4 family protein binding (GO:0097371)NF-kappaB binding (GO:0051059)apoptotic nuclear changes (GO:0030262)brain development (GO:0007420)cell population proliferation (GO:0008283)centrosome (GO:0005813)centrosome (GO:0005813)cyclin binding (GO:0030332)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoskeleton (GO:0005856)cytosol (GO:0005829)definitive erythrocyte differentiation (GO:0060318)definitive erythrocyte differentiation (GO:0060318)endomembrane system (GO:0012505)endoplasmic reticulum membrane (GO:0005789)endoplasmic reticulum membrane (GO:0005789)endoplasmic reticulum unfolded protein response (GO:0030968)endoplasmic reticulum unfolded protein response (GO:0030968)liver development (GO:0001889)liver development (GO:0001889)membrane (GO:0016020)microtubule (GO:0005874)mitogen-activated protein kinase binding (GO:0051019)mitotic G2 DNA damage checkpoint signaling (GO:0007095)mitotic G2/M transition checkpoint (GO:0044818)negative regulation of MAP kinase activity (GO:0043407)negative regulation of protein catabolic process (GO:0042177)negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)negative regulation of protein phosphorylation (GO:0001933)negative regulation of protein serine/threonine kinase activity (GO:0071901)nucleolus (GO:0005730)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of protein localization to nucleus (GO:1900182)positive regulation of protein ubiquitination (GO:0031398)positive regulation of reticulophagy (GO:0140501)positive regulation of reticulophagy (GO:0140501)positive regulation of signal transduction by p53 class mediator (GO:1901798)positive regulation of ubiquitin-dependent protein catabolic process (GO:2000060)protein binding (GO:0005515)protein kinase binding (GO:0019901)protein kinase binding (GO:0019901)protein ufmylation (GO:0071569)protein ufmylation (GO:0071569)protein ufmylation (GO:0071569)protein ufmylation (GO:0071569)protein-containing complex (GO:0032991)regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)regulation of mitotic cell cycle (GO:0007346)regulation of neuron differentiation (GO:0045664)regulation of phosphatase activity (GO:0010921)rescue of stalled cytosolic ribosome (GO:0072344)rescue of stalled cytosolic ribosome (GO:0072344)response to endoplasmic reticulum stress (GO:0034976)response to endoplasmic reticulum stress (GO:0034976)ribosome disassembly (GO:0032790)ubiquitin-like ligase-substrate adaptor activity (GO:1990756)ubiquitin-like ligase-substrate adaptor activity (GO:1990756)ubiquitin-like protein ligase binding (GO:0044389)ubiquitin-like protein ligase binding (GO:0044389)
Expression (TPM)
CDK5RAP3 — as a Regulated Gene

TFs regulating CDK5RAP3 0 TFs

Transcription factors with Perturb-seq knockdown data for CDK5RAP3. 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 = CDK5RAP3 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 CDK5RAP3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CDK5RAP3, 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
chr17:47,693,705–47,695,210 276.6 kb Distal (>10kb) Multiome 619
chr17:47,733,002–47,733,810 237.8 kb Distal (>10kb) Multiome 366
chr17:47,789,633–47,790,336 181.0 kb Distal (>10kb) Multiome 395
chr17:47,831,256–47,831,955 139.5 kb Distal (>10kb) Multiome 856
chr17:47,840,790–47,841,702 129.8 kb Distal (>10kb) Multiome HiCAR 833
chr17:47,847,253–47,848,429 123.3 kb Distal (>10kb) Multiome HiCAR 193
chr17:47,850,617–47,851,614 119.9 kb Distal (>10kb) Multiome 694
chr17:47,895,361–47,896,955 74.9 kb Distal (>10kb) Multiome 1031
chr17:47,902,020–47,902,508 68.9 kb Distal (>10kb) Multiome 101
chr17:47,941,283–47,941,880 29.5 kb Distal (>10kb) Multiome 958
chr17:47,970,487–47,971,547 88 bp At TSS Multiome 1061
chr17:47,978,447–47,978,644 7.4 kb Proximal (<10kb) 177
chr17:48,023,351–48,024,470 52.6 kb Distal (>10kb) Multiome 591
chr17:48,024,599–48,025,777 54.2 kb Distal (>10kb) Multiome 759
chr17:48,026,284–48,026,933 55.6 kb Distal (>10kb) Multiome 543
chr17:48,047,576–48,049,198 77.2 kb Distal (>10kb) Multiome 1134
chr17:48,053,836–48,055,155 83.5 kb Distal (>10kb) Multiome 327
chr17:48,055,581–48,056,000 84.9 kb Distal (>10kb) Multiome 337
chr17:48,100,593–48,101,963 130.4 kb Distal (>10kb) Multiome 974
chr17:48,107,198–48,108,007 136.6 kb Distal (>10kb) Multiome 841
chr17:48,160,363–48,161,134 189.7 kb Distal (>10kb) Multiome 299

Genome Browser

Genomic view of the CDK5RAP3 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.

chr17:47,683,705 – 48,171,134
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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