CC2D1A

coiled-coil and C2 domain containing 1A | Aki-1, FLJ20241, Freud-1, Lgd2, MRT3, TAPE

This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5'-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities of the protein are inhibited by calcium. A mutation in this gene results in a nonsyndromic form of cognitive disability (MRT3). [provided by RefSeq, Jul 2017]

Biological processes 17 terms

DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)cadherin binding (GO:0045296)centrosome (GO:0005813)cytoplasm (GO:0005737)cytosol (GO:0005829)extracellular exosome (GO:0070062)membrane (GO:0016020)negative regulation of snRNA transcription by RNA polymerase II (GO:1905381)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of canonical NF-kappaB signal transduction (GO:0043123)protein binding (GO:0005515)regulation of transcription by RNA polymerase II (GO:0006357)

Expression (TPM)

TFs regulating CC2D1A 0 TFs

Transcription factors with Perturb-seq knockdown data for CC2D1A. 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 = CC2D1A 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 CC2D1A

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CC2D1A, 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
chr19:13,747,559–13,748,233	158.5 kb	Distal (>10kb) Multiome	785
chr19:13,774,293–13,775,050	131.8 kb	Distal (>10kb) Multiome	904
chr19:13,794,728–13,795,999	111.0 kb	Distal (>10kb) Multiome	763
chr19:13,817,290–13,818,525	88.3 kb	Distal (>10kb) Multiome	368
chr19:13,833,328–13,834,074	72.6 kb	Distal (>10kb) Multiome	638
chr19:13,841,592–13,843,282	63.4 kb	Distal (>10kb) Multiome	600
chr19:13,846,368–13,848,126	58.6 kb	Distal (>10kb) Multiome	1040
chr19:13,850,226–13,850,701	55.7 kb	Distal (>10kb) Multiome	516
chr19:13,861,855–13,862,533	43.9 kb	Distal (>10kb) Multiome	655
chr19:13,872,706–13,873,325	33.2 kb	Distal (>10kb) Multiome	254
chr19:13,879,942–13,880,779	26.0 kb	Distal (>10kb) Multiome	780
chr19:13,905,895–13,906,734	117 bp	At TSS Multiome	835
chr19:13,951,898–13,953,117	46.1 kb	Distal (>10kb) Multiome	667
chr19:13,962,408–13,964,055	57.5 kb	Distal (>10kb) Multiome	166
chr19:13,978,193–13,979,385	72.3 kb	Distal (>10kb) Multiome	238
chr19:14,005,474–14,007,363	100.2 kb	Distal (>10kb) Multiome	1098
chr19:14,031,574–14,032,483	125.9 kb	Distal (>10kb) Multiome	726
chr19:14,057,383–14,057,841	151.4 kb	Distal (>10kb) Multiome	244
chr19:14,071,936–14,072,417	166.0 kb	Distal (>10kb) Multiome HiCAR	676
chr19:14,072,991–14,073,911	167.4 kb	Distal (>10kb) Multiome HiCAR	589
chr19:14,081,022–14,082,024	175.2 kb	Distal (>10kb) Multiome	806
chr19:14,089,535–14,092,049	184.7 kb	Distal (>10kb) Multiome	766
chr19:14,117,519–14,118,617	211.7 kb	Distal (>10kb) Multiome	734
chr19:14,136,079–14,137,770	230.6 kb	Distal (>10kb) Multiome	978

Genome Browser

Genomic view of the CC2D1A 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.