SNAPC4

small nuclear RNA activating complex polypeptide 4 | FLJ13451, PTFalpha, SNAP190

This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]

Member of: DE-5 DE-5.12 Developmental clusters: GC6

Biological processes 18 terms

DNA binding (GO:0003677)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II general transcription initiation factor activity (GO:0016251)RNA polymerase III general transcription initiation factor activity (GO:0000995)RNA polymerase III type 3 promoter sequence-specific DNA binding (GO:0001006)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)snRNA transcription by RNA polymerase II (GO:0042795)snRNA transcription by RNA polymerase II (GO:0042795)snRNA transcription by RNA polymerase II (GO:0042795)snRNA transcription by RNA polymerase III (GO:0042796)snRNA transcription by RNA polymerase III (GO:0042796)snRNA transcription by RNA polymerase III (GO:0042796)snRNA-activating protein complex (GO:0019185)snRNA-activating protein complex (GO:0019185)

Expression (TPM)

TFs regulating SNAPC4 0 TFs

Transcription factors with Perturb-seq knockdown data for SNAPC4. 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 = SNAPC4 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 SNAPC4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SNAPC4, 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
chr9:136,109,321–136,110,010	290.5 kb	Distal (>10kb) Multiome	643
chr9:136,117,952–136,119,826	281.3 kb	Distal (>10kb) Multiome	931
chr9:136,132,442–136,133,645	267.0 kb	Distal (>10kb) Multiome	343
chr9:136,245,219–136,246,310	154.3 kb	Distal (>10kb) Multiome	608
chr9:136,267,002–136,267,928	132.8 kb	Distal (>10kb) Multiome	459
chr9:136,327,140–136,327,919	72.6 kb	Distal (>10kb) Multiome	310
chr9:136,342,464–136,343,245	57.3 kb	Distal (>10kb) Multiome	326
chr9:136,362,899–136,364,677	36.8 kb	Distal (>10kb) Multiome	969
chr9:136,399,639–136,400,642	77 bp	At TSS Multiome	776
chr9:136,410,307–136,410,943	10.4 kb	Distal (>10kb) Multiome	740
chr9:136,438,826–136,440,227	39.7 kb	Distal (>10kb) Multiome	608
chr9:136,482,405–136,485,297	83.2 kb	Distal (>10kb) Multiome	938
chr9:136,545,392–136,547,129	146.0 kb	Distal (>10kb) Multiome	710
chr9:136,572,053–136,572,865	172.2 kb	Distal (>10kb) Multiome	239
chr9:136,587,135–136,588,835	188.2 kb	Distal (>10kb) Multiome	453
chr9:136,626,479–136,627,366	226.8 kb	Distal (>10kb) Multiome	451
chr9:136,665,223–136,666,507	265.7 kb	Distal (>10kb) Multiome	409
chr9:136,686,875–136,688,079	287.3 kb	Distal (>10kb) Multiome	610

Genome Browser

Genomic view of the SNAPC4 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.