CALM3

calmodulin 3 | PHKD, PHKD3

This gene encodes a member of a family of proteins that binds calcium and functions as a enzymatic co-factor. Activity of this protein is important in the regulation of the cell cycle and cytokinesis. Multiple alternatively spliced transcript variants have been observed at this gene. [provided by RefSeq, Aug 2016]

Member of: DE-1 DE-1.36 Developmental clusters: GC6

Biological processes 93 terms

G protein-coupled receptor signaling pathway (GO:0007186)Schaffer collateral - CA1 synapse (GO:0098685)adenylate cyclase activator activity (GO:0010856)adenylate cyclase activator activity (GO:0010856)adenylate cyclase binding (GO:0008179)calcineurin-mediated signaling (GO:0097720)calcineurin-mediated signaling (GO:0097720)calcineurin-mediated signaling (GO:0097720)calcium channel complex (GO:0034704)calcium channel complex (GO:0034704)calcium channel regulator activity (GO:0005246)calcium channel regulator activity (GO:0005246)calcium ion binding (GO:0005509)calcium ion binding (GO:0005509)calcium ion binding (GO:0005509)calcium-dependent protein binding (GO:0048306)calyx of Held (GO:0044305)catalytic complex (GO:1902494)centrosome (GO:0005813)centrosome (GO:0005813)centrosome (GO:0005813)chromatin (GO:0000785)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)detection of calcium ion (GO:0005513)detection of calcium ion (GO:0005513)detection of calcium ion (GO:0005513)growth cone (GO:0030426)long-term synaptic potentiation (GO:0060291)long-term synaptic potentiation (GO:0060291)membrane (GO:0016020)mitochondrial membrane (GO:0031966)myelin sheath (GO:0043209)myelin sheath (GO:0043209)negative regulation of calcium ion export across plasma membrane (GO:1905913)negative regulation of high voltage-gated calcium channel activity (GO:1901842)nitric-oxide synthase binding (GO:0050998)nitric-oxide synthase regulator activity (GO:0030235)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)phosphatidylinositol 3-kinase binding (GO:0043548)plasma membrane (GO:0005886)postsynaptic cytosol (GO:0099524)presynaptic cytosol (GO:0099523)presynaptic endocytosis (GO:0140238)protein binding (GO:0005515)protein domain specific binding (GO:0019904)protein kinase binding (GO:0019901)protein kinase binding (GO:0019901)protein phosphatase activator activity (GO:0072542)protein phosphatase activator activity (GO:0072542)protein serine/threonine kinase activator activity (GO:0043539)protein serine/threonine kinase activator activity (GO:0043539)protein serine/threonine kinase activator activity (GO:0043539)protein-containing complex (GO:0032991)regulation of cardiac muscle cell action potential (GO:0098901)regulation of cardiac muscle contraction (GO:0055117)regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)regulation of cytokinesis (GO:0032465)regulation of cytokinesis (GO:0032465)regulation of heart rate (GO:0002027)regulation of heart rate (GO:0002027)regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)regulation of synaptic vesicle endocytosis (GO:1900242)regulation of synaptic vesicle exocytosis (GO:2000300)response to amphetamine (GO:0001975)response to calcium ion (GO:0051592)response to corticosterone (GO:0051412)sarcomere (GO:0030017)sarcomere (GO:0030017)sperm midpiece (GO:0097225)spindle (GO:0005819)spindle microtubule (GO:0005876)spindle microtubule (GO:0005876)spindle pole (GO:0000922)spindle pole (GO:0000922)substantia nigra development (GO:0021762)synaptic vesicle membrane (GO:0030672)titin binding (GO:0031432)titin binding (GO:0031432)transmembrane transporter binding (GO:0044325)transmembrane transporter binding (GO:0044325)transporter inhibitor activity (GO:0141110)type 3 metabotropic glutamate receptor binding (GO:0031800)vesicle (GO:0031982)vesicle (GO:0031982)voltage-gated potassium channel complex (GO:0008076)

Expression (TPM)

TFs regulating CALM3 0 TFs

Transcription factors with Perturb-seq knockdown data for CALM3. 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 = CALM3 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 CALM3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CALM3, 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
chr19:46,300,632–46,301,183	300.2 kb	Distal (>10kb) Multiome	282
chr19:46,303,439–46,304,504	297.1 kb	Distal (>10kb) Multiome	300
chr19:46,346,454–46,347,599	254.2 kb	Distal (>10kb) Multiome	835
chr19:46,373,466–46,374,149	227.5 kb	Distal (>10kb) Multiome	293
chr19:46,413,092–46,414,029	187.6 kb	Distal (>10kb) Multiome	530
chr19:46,416,168–46,416,925	184.7 kb	Distal (>10kb) Multiome	522
chr19:46,426,339–46,427,101	174.5 kb	Distal (>10kb) Multiome	220
chr19:46,471,149–46,471,898	129.7 kb	Distal (>10kb) Multiome	339
chr19:46,495,489–46,496,206	105.4 kb	Distal (>10kb) Multiome	177
chr19:46,587,845–46,588,467	13.1 kb	Distal (>10kb) Multiome	21
chr19:46,600,411–46,601,577	257 bp	At TSS Multiome	1006
chr19:46,633,826–46,635,061	33.1 kb	Distal (>10kb) Multiome	365
chr19:46,638,437–46,639,929	37.8 kb	Distal (>10kb) Multiome	741
chr19:46,659,987–46,662,280	60.1 kb	Distal (>10kb) Multiome	691
chr19:46,696,773–46,698,048	96.2 kb	Distal (>10kb) Multiome	408
chr19:46,713,710–46,714,718	112.8 kb	Distal (>10kb) Multiome	566
chr19:46,716,676–46,717,696	115.9 kb	Distal (>10kb) Multiome	487
chr19:46,745,601–46,746,962	145.1 kb	Distal (>10kb) Multiome	561
chr19:46,787,215–46,789,013	187.4 kb	Distal (>10kb) Multiome	944
chr19:46,850,211–46,851,336	249.6 kb	Distal (>10kb) Multiome	946
chr19:46,855,920–46,856,711	255.0 kb	Distal (>10kb) Multiome	610
chr19:46,859,815–46,861,611	259.1 kb	Distal (>10kb) Multiome	1061

Genome Browser

Genomic view of the CALM3 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.