ZC3H4

zinc finger CCCH-type containing 4 | KIAA1064, C19orf7

This gene encodes a member of a family of CCCH (C-x8-C-x5-C-x3-H type) zinc finger domain-containing proteins. These zinc finger domains, which coordinate zinc finger binding and are characterized by three cysteine residues and one histidine residue, are nucleic acid-binding. Other family members are known to function in post-transcriptional regulation. [provided by RefSeq, Aug 2011]

Member of: DE-2

Biological processes 24 terms

DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA binding (GO:0003723)chromatin binding (GO:0003682)chromosome (GO:0005694)cytosol (GO:0005829)lncRNA catabolic process (GO:0110064)lncRNA catabolic process (GO:0110064)metal ion binding (GO:0046872)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of DNA-templated transcription, elongation (GO:0032785)negative regulation of DNA-templated transcription, elongation (GO:0032785)negative regulation of DNA-templated transcription, elongation (GO:0032785)negative regulation of lncRNA transcription (GO:0140744)negative regulation of lncRNA transcription (GO:0140744)negative regulation of transcription by RNA polymerase II (GO:0000122)nuclear RNA surveillance (GO:0071027)nuclear RNA surveillance (GO:0071027)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)promoter-specific chromatin binding (GO:1990841)protein binding (GO:0005515)

Expression (TPM)

TFs regulating ZC3H4 0 TFs

Transcription factors with Perturb-seq knockdown data for ZC3H4. 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 = ZC3H4 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 ZC3H4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ZC3H4, 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
chr19:46,850,211–46,851,336	261.4 kb	Distal (>10kb) Multiome	946
chr19:46,855,920–46,856,711	256.0 kb	Distal (>10kb) Multiome	610
chr19:46,859,815–46,861,611	251.9 kb	Distal (>10kb) Multiome	1061
chr19:47,019,502–47,020,076	92.5 kb	Distal (>10kb) Multiome	188
chr19:47,035,599–47,036,293	76.2 kb	Distal (>10kb) Multiome	627
chr19:47,047,837–47,048,980	64.3 kb	Distal (>10kb) Multiome	760
chr19:47,058,561–47,059,308	53.3 kb	Distal (>10kb) Multiome	357
chr19:47,111,821–47,113,936	53 bp	At TSS Multiome	1117
chr19:47,130,439–47,131,651	18.6 kb	Distal (>10kb) Multiome	908
chr19:47,157,325–47,158,494	45.3 kb	Distal (>10kb) Multiome	271
chr19:47,196,586–47,197,452	84.6 kb	Distal (>10kb) Multiome	94
chr19:47,225,386–47,231,990	115.6 kb	Distal (>10kb) Multiome	1389
chr19:47,240,827–47,241,572	129.0 kb	Distal (>10kb) Multiome	616
chr19:47,242,713–47,243,645	130.9 kb	Distal (>10kb) Multiome	568
chr19:47,243,835–47,244,896	132.1 kb	Distal (>10kb) Multiome	1001
chr19:47,256,041–47,258,057	144.9 kb	Distal (>10kb) Multiome	907
chr19:47,272,778–47,275,890	161.2 kb	Distal (>10kb) Multiome	931
chr19:47,348,695–47,349,758	237.0 kb	Distal (>10kb) Multiome	766
chr19:47,406,825–47,407,408	295.1 kb	Distal (>10kb) Multiome	333

Genome Browser

Genomic view of the ZC3H4 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.