H3C2
H3 clustered histone 2 | H3/l, H3FL, HIST1H3B

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H3 family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]

Member of: DE-6 DE-6.13
Biological processes 31 terms
DNA binding (GO:0003677)cadherin binding (GO:0045296)chromatin organization (GO:0006325)chromosome (GO:0005694)epigenetic regulation of gene expression (GO:0040029)extracellular exosome (GO:0070062)extracellular exosome (GO:0070062)extracellular region (GO:0005576)heterochromatin formation (GO:0031507)membrane (GO:0016020)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleosomal DNA binding (GO:0031492)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome assembly (GO:0006334)nucleosome assembly (GO:0006334)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)protein binding (GO:0005515)protein heterodimerization activity (GO:0046982)protein-containing complex (GO:0032991)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)telomere organization (GO:0032200)
Expression (TPM)
H3C2 — as a Regulated Gene

TFs regulating H3C2 0 TFs

Transcription factors with Perturb-seq knockdown data for H3C2. 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 = H3C2 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to H3C2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H3C2, 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.

Accessibility Element Dist. to TSS Link type TFs
chr6:25,882,032–25,882,516 149.8 kb Distal (>10kb) Multiome 165
chr6:25,992,391–25,993,479 39.4 kb Distal (>10kb) Multiome 1012
chr6:26,020,104–26,022,401 11.7 kb Distal (>10kb) Multiome 920
chr6:26,025,866–26,027,859 5.8 kb Proximal (<10kb) Multiome 1194
chr6:26,028,726–26,029,288 2.8 kb Proximal (<10kb) 225
chr6:26,031,341–26,032,990 63 bp At TSS Multiome 1083
chr6:26,033,113–26,034,309 1.6 kb Proximal (<10kb) Multiome 800
chr6:26,054,926–26,057,287 23.2 kb Distal (>10kb) Multiome 1174
chr6:26,087,383–26,088,017 55.6 kb Distal (>10kb) Multiome 572
chr6:26,103,452–26,105,109 71.8 kb Distal (>10kb) Multiome 1169
chr6:26,122,481–26,124,909 90.9 kb Distal (>10kb) Multiome 1216
chr6:26,125,788–26,126,592 94.1 kb Distal (>10kb) Multiome 670
chr6:26,156,184–26,158,744 126.0 kb Distal (>10kb) Multiome 1310
chr6:26,171,798–26,172,499 139.9 kb Distal (>10kb) Multiome 580
chr6:26,183,128–26,184,377 151.6 kb Distal (>10kb) Multiome 311
chr6:26,187,874–26,189,538 157.0 kb Distal (>10kb) Multiome 1053
chr6:26,196,695–26,197,676 165.2 kb Distal (>10kb) Multiome 842
chr6:26,198,203–26,200,197 167.3 kb Distal (>10kb) Multiome 939
chr6:26,203,791–26,205,119 172.4 kb Distal (>10kb) Multiome 1071
chr6:26,214,872–26,218,468 184.8 kb Distal (>10kb) Multiome 1096
chr6:26,223,716–26,224,480 191.9 kb Distal (>10kb) Multiome 507
chr6:26,224,856–26,226,566 193.1 kb Distal (>10kb) Multiome 451
chr6:26,239,944–26,240,920 208.3 kb Distal (>10kb) Multiome 375
chr6:26,249,682–26,251,138 218.2 kb Distal (>10kb) Multiome 731
chr6:26,251,339–26,252,079 219.6 kb Distal (>10kb) Multiome 445
chr6:26,270,815–26,273,967 240.8 kb Distal (>10kb) Multiome 742
chr6:26,285,011–26,286,121 253.5 kb Distal (>10kb) Multiome 1121
chr6:26,304,972–26,305,585 273.3 kb Distal (>10kb) Multiome 586
chr6:26,312,505–26,313,475 280.9 kb Distal (>10kb) Multiome 896
chr6:26,322,092–26,323,232 290.6 kb Distal (>10kb) Multiome 811
chr6:26,327,476–26,328,318 296.0 kb Distal (>10kb) Multiome 716
chr6:27,809,816–27,810,576 1778.0 kb Distal (>10kb) Multiome HiCAR 914
chr6:27,813,688–27,816,146 1782.9 kb Distal (>10kb) Multiome HiCAR 564
chr6:27,836,792–27,839,128 1806.3 kb Distal (>10kb) Multiome HiCAR 1131
chr6:27,865,093–27,868,152 1835.5 kb Distal (>10kb) Multiome HiCAR 744

Genome Browser

Genomic view of the H3C2 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.

chr6:25,872,032 – 27,878,152
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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