CDK5
cyclin dependent kinase 5 | PSSALRE

This gene encodes a proline-directed serine/threonine kinase that is a member of the cyclin-dependent kinase family of proteins. Unlike other members of the family, the protein encoded by this gene does not directly control cell cycle regulation. Instead the protein, which is predominantly expressed at high levels in mammalian postmitotic central nervous system neurons, functions in diverse processes such as synaptic plasticity and neuronal migration through phosphorylation of proteins required for cytoskeletal organization, endocytosis and exocytosis, and apoptosis. In humans, an allelic variant of the gene that results in undetectable levels of the protein has been associated with lethal autosomal recessive lissencephaly-7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]

Member of: DE-1
Biological processes 98 terms
ATP binding (GO:0005524)ErbB-2 class receptor binding (GO:0005176)ErbB-2 class receptor binding (GO:0005176)ErbB-3 class receptor binding (GO:0043125)ErbB-3 class receptor binding (GO:0043125)Hsp90 protein binding (GO:0051879)acetylcholine receptor activator activity (GO:0030549)acetylcholine receptor activator activity (GO:0030549)actin cytoskeleton organization (GO:0030036)axon (GO:0030424)axon (GO:0030424)axon extension (GO:0048675)axonogenesis (GO:0007409)axonogenesis (GO:0007409)cellular response to amyloid-beta (GO:1904646)chemical synaptic transmission (GO:0007268)cyclin-dependent protein kinase holoenzyme complex (GO:0000307)cyclin-dependent protein serine/threonine kinase activity (GO:0004693)cyclin-dependent protein serine/threonine kinase activity (GO:0004693)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)dendrite (GO:0030425)establishment of localization in cell (GO:0051649)filopodium (GO:0030175)growth cone (GO:0030426)growth cone (GO:0030426)ionotropic glutamate receptor binding (GO:0035255)kinase activity (GO:0016301)lamellipodium (GO:0030027)membrane (GO:0016020)microtubule (GO:0005874)microtubule binding (GO:0008017)microtubule cytoskeleton organization (GO:0000226)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903234)negative regulation of proteolysis (GO:0045861)neuromuscular junction (GO:0031594)neuron apoptotic process (GO:0051402)neuron apoptotic process (GO:0051402)neuron differentiation (GO:0030182)neuron differentiation (GO:0030182)neuron migration (GO:0001764)neuron projection (GO:0043005)neuron projection development (GO:0031175)neuron projection development (GO:0031175)neuronal cell body (GO:0043025)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)oligodendrocyte differentiation (GO:0048709)p53 binding (GO:0002039)perikaryon (GO:0043204)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of neuron apoptotic process (GO:0043525)positive regulation of presynaptic cytosolic calcium concentration (GO:0099533)postsynaptic density (GO:0014069)postsynaptic density (GO:0014069)presynapse (GO:0098793)protein binding (GO:0005515)protein kinase 5 complex (GO:0016533)protein kinase activity (GO:0004672)protein kinase activity (GO:0004672)protein serine kinase activity (GO:0106310)protein serine/threonine kinase activity (GO:0004674)protein serine/threonine kinase activity (GO:0004674)protein serine/threonine kinase activity (GO:0004674)protein serine/threonine kinase activity (GO:0004674)protein serine/threonine kinase activity (GO:0004674)regulation of apoptotic process (GO:0042981)regulation of cell cycle (GO:0051726)regulation of cell cycle (GO:0051726)regulation of cell cycle phase transition (GO:1901987)regulation of dendritic spine morphogenesis (GO:0061001)regulation of dendritic spine morphogenesis (GO:0061001)regulation of macroautophagy (GO:0016241)regulation of protein localization to plasma membrane (GO:1903076)regulation of protein localization to plasma membrane (GO:1903076)regulation of synaptic plasticity (GO:0048167)regulation of synaptic plasticity (GO:0048167)regulation of synaptic transmission, glutamatergic (GO:0051966)regulation of synaptic transmission, glutamatergic (GO:0051966)regulation of synaptic vesicle recycling (GO:1903421)signaling receptor inhibitor activity (GO:0030547)signaling receptor inhibitor activity (GO:0030547)synapse (GO:0045202)synapse assembly (GO:0007416)synaptic vesicle endocytosis (GO:0048488)synaptic vesicle exocytosis (GO:0016079)synaptic vesicle transport (GO:0048489)tau protein binding (GO:0048156)tau-protein kinase activity (GO:0050321)tau-protein kinase activity (GO:0050321)
Expression (TPM)
CDK5 — as a Regulated Gene

TFs regulating CDK5 0 TFs

Transcription factors with Perturb-seq knockdown data for CDK5. 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 = CDK5 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 CDK5

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CDK5, 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
chr7:150,876,795–150,877,753 180.8 kb Distal (>10kb) Multiome 396
chr7:150,973,967–150,975,352 83.1 kb Distal (>10kb) Multiome 572
chr7:150,977,414–150,979,693 79.5 kb Distal (>10kb) Multiome 629
chr7:150,988,543–150,989,168 69.1 kb Distal (>10kb) Multiome 348
chr7:151,007,679–151,009,192 49.2 kb Distal (>10kb) Multiome 693
chr7:151,012,895–151,014,461 44.0 kb Distal (>10kb) Multiome 414
chr7:151,017,863–151,019,302 39.5 kb Distal (>10kb) Multiome 677
chr7:151,026,724–151,029,117 29.4 kb Distal (>10kb) Multiome 1003
chr7:151,050,894–151,051,476 6.6 kb Proximal (<10kb) Multiome 289
chr7:151,056,786–151,057,165 731 bp At TSS 130
chr7:151,057,294–151,063,500 1.8 kb Proximal (<10kb) Multiome 1138
chr7:151,080,217–151,081,897 23.0 kb Distal (>10kb) Multiome 909
chr7:151,083,053–151,083,998 25.6 kb Distal (>10kb) Multiome 581
chr7:151,085,505–151,086,758 28.3 kb Distal (>10kb) Multiome 774
chr7:151,110,933–151,111,501 53.3 kb Distal (>10kb) Multiome 365
chr7:151,114,416–151,115,951 57.6 kb Distal (>10kb) Multiome 279
chr7:151,123,775–151,124,402 66.2 kb Distal (>10kb) Multiome 399
chr7:151,125,352–151,126,446 68.0 kb Distal (>10kb) Multiome 283
chr7:151,166,900–151,168,657 110.4 kb Distal (>10kb) Multiome 533
chr7:151,172,589–151,173,067 114.9 kb Distal (>10kb) Multiome 592
chr7:151,226,743–151,227,948 169.5 kb Distal (>10kb) Multiome 820
chr7:151,232,039–151,233,087 174.6 kb Distal (>10kb) Multiome 692
chr7:151,244,849–151,245,940 187.7 kb Distal (>10kb) Multiome 325
chr7:151,247,809–151,249,951 190.9 kb Distal (>10kb) Multiome 522
chr7:151,251,506–151,252,414 194.0 kb Distal (>10kb) Multiome 448
chr7:151,259,810–151,260,360 202.2 kb Distal (>10kb) Multiome 135
chr7:151,275,718–151,276,602 218.4 kb Distal (>10kb) Multiome 99
chr7:151,276,919–151,277,487 219.3 kb Distal (>10kb) Multiome 367
chr7:151,303,363–151,304,005 245.7 kb Distal (>10kb) Multiome 458
chr7:151,306,906–151,307,424 249.2 kb Distal (>10kb) Multiome 60
chr7:151,341,187–151,342,118 283.8 kb Distal (>10kb) Multiome 757

Genome Browser

Genomic view of the CDK5 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.

chr7:150,866,795 – 151,352,118
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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