GSC

goosecoid homeobox | GSC1

This gene encodes a member of the bicoid subfamily of the paired (PRD) homeobox family of proteins. The encoded protein acts as a transcription factor and may be autoregulatory. A similar protein in mice plays a role in craniofacial and rib cage development during embryogenesis. [provided by RefSeq, Jul 2008]

Member of: DE-4 DE-4.1 Developmental clusters: GC2

Biological processes 25 terms

DNA binding (GO:0003677)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)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)RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629)RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629)animal organ development (GO:0048513)chromatin (GO:0000785)gastrulation (GO:0007369)middle ear morphogenesis (GO:0042474)middle ear morphogenesis (GO:0042474)negative regulation of transcription by RNA polymerase II (GO:0000122)neural crest cell fate specification (GO:0014036)nuclear speck (GO:0016607)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific double-stranded DNA binding (GO:1990837)tissue development (GO:0009888)transcription regulator complex (GO:0005667)

Expression (TPM)

TFs regulating GSC 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of GSC, 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
chr14:94,486,142–94,486,886	283.6 kb	Distal (>10kb) Multiome	437
chr14:94,689,361–94,690,123	80.4 kb	Distal (>10kb) Multiome	366
chr14:94,762,880–94,765,691	6.5 kb	Proximal (<10kb) Multiome	156
chr14:94,769,514–94,771,036	207 bp	At TSS Multiome	463
chr14:94,771,191–94,771,577	1.1 kb	Proximal (<10kb)	62
chr14:94,771,685–94,772,421	1.6 kb	Proximal (<10kb)	38
chr14:94,772,857–94,773,397	2.7 kb	Proximal (<10kb)	72
chr14:94,773,854–94,774,248	3.7 kb	Proximal (<10kb)	56
chr14:94,774,975–94,776,127	5.4 kb	Proximal (<10kb) Multiome	178
chr14:94,776,794–94,777,527	7.1 kb	Proximal (<10kb) Multiome	56
chr14:94,780,572–94,781,427	10.9 kb	Distal (>10kb) Multiome	92
chr14:94,795,994–94,796,839	26.3 kb	Distal (>10kb) Multiome	94
chr14:94,893,323–94,894,201	123.5 kb	Distal (>10kb) Multiome	189

Genome Browser

Genomic view of the GSC 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.