HMCES

5-hydroxymethylcytosine binding, ES cell specific | DC12, SRAPD1, C3orf37

Enables DNA-(abasic site) binding activity; protein-DNA covalent cross-linking activity; and single-stranded DNA binding activity. Involved in interstrand cross-link repair; protein-DNA covalent cross-linking repair; and somatic hypermutation of immunoglobulin genes. Is active in replication fork. [provided by Alliance of Genome Resources, Jul 2025]

Biological processes 27 terms

DNA damage response (GO:0006974)DNA damage response (GO:0006974)DNA repair (GO:0006281)DNA-(abasic site) binding (GO:0140431)DNA-(abasic site) binding (GO:0140431)DNA-(apurinic or apyrimidinic site) endonuclease activity (GO:0003906)chromosome (GO:0005694)double-strand break repair via alternative nonhomologous end joining (GO:0097681)double-strand break repair via alternative nonhomologous end joining (GO:0097681)interstrand cross-link repair (GO:0036297)interstrand cross-link repair (GO:0036297)positive regulation of isotype switching (GO:0045830)positive regulation of isotype switching (GO:0045830)protein binding (GO:0005515)protein-DNA covalent cross-linking activity (GO:0160129)protein-DNA covalent cross-linking activity (GO:0160129)protein-DNA covalent cross-linking repair (GO:0106300)protein-DNA covalent cross-linking repair (GO:0106300)protein-DNA covalent cross-linking repair (GO:0106300)replication fork (GO:0005657)replication fork (GO:0005657)single-stranded DNA binding (GO:0003697)single-stranded DNA binding (GO:0003697)single-stranded DNA binding (GO:0003697)somatic hypermutation of immunoglobulin genes (GO:0016446)somatic hypermutation of immunoglobulin genes (GO:0016446)somatic hypermutation of immunoglobulin genes (GO:0016446)

Expression (TPM)

TFs regulating HMCES 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HMCES, 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
chr3:128,993,367–128,994,455	284.8 kb	Distal (>10kb) Multiome	344
chr3:129,027,026–129,027,525	251.6 kb	Distal (>10kb) Multiome	589
chr3:129,045,697–129,046,752	232.3 kb	Distal (>10kb) Multiome	170
chr3:129,120,244–129,122,947	156.8 kb	Distal (>10kb) Multiome	767
chr3:129,160,815–129,162,244	117.5 kb	Distal (>10kb) Multiome	917
chr3:129,183,284–129,184,525	94.9 kb	Distal (>10kb) Multiome	966
chr3:129,249,227–129,250,064	29.3 kb	Distal (>10kb) Multiome	767
chr3:129,278,315–129,279,976	14 bp	At TSS Multiome	767
chr3:129,305,525–129,306,095	27.0 kb	Distal (>10kb) Multiome	342
chr3:129,314,154–129,316,995	36.1 kb	Distal (>10kb) Multiome	949
chr3:129,343,720–129,344,497	65.2 kb	Distal (>10kb) Multiome	346
chr3:129,344,512–129,344,822	65.8 kb	Distal (>10kb) Multiome	58
chr3:129,359,825–129,360,642	81.6 kb	Distal (>10kb) Multiome	65
chr3:129,399,193–129,399,868	120.8 kb	Distal (>10kb) Multiome	625
chr3:129,428,173–129,429,050	149.8 kb	Distal (>10kb) Multiome	504
chr3:129,439,426–129,440,695	161.3 kb	Distal (>10kb) Multiome	875
chr3:129,534,465–129,535,515	256.0 kb	Distal (>10kb) Multiome	397

Genome Browser

Genomic view of the HMCES 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.