H3C12
H3 clustered histone 12 | H3/j, H3FJ, HIST1H3J

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order 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 but instead contain a palindromic termination element. This gene is found in the small histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]

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)
H3C12 — as a Regulated Gene

TFs regulating H3C12 0 TFs

Transcription factors with Perturb-seq knockdown data for H3C12. 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 = H3C12 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 H3C12

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H3C12, 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
chr6:26,020,104–26,022,401 1872.7 kb Distal (>10kb) Multiome HiCAR 920
chr6:26,025,866–26,027,859 1866.8 kb Distal (>10kb) Multiome HiCAR 1194
chr6:26,183,128–26,184,377 1709.4 kb Distal (>10kb) Multiome HiCAR 311
chr6:26,187,874–26,189,538 1704.0 kb Distal (>10kb) Multiome HiCAR 1053
chr6:26,223,716–26,224,480 1669.1 kb Distal (>10kb) Multiome HiCAR 507
chr6:26,224,856–26,226,566 1667.9 kb Distal (>10kb) Multiome HiCAR 451
chr6:26,239,944–26,240,920 1652.8 kb Distal (>10kb) Multiome HiCAR 375
chr6:26,249,682–26,251,138 1642.8 kb Distal (>10kb) Multiome HiCAR 731
chr6:26,270,815–26,273,967 1620.2 kb Distal (>10kb) Multiome HiCAR 742
chr6:26,285,011–26,286,121 1607.5 kb Distal (>10kb) Multiome HiCAR 1121
chr6:27,131,467–27,132,107 761.4 kb Distal (>10kb) Multiome HiCAR 580
chr6:27,132,200–27,134,276 760.2 kb Distal (>10kb) Multiome HiCAR 975
chr6:27,139,091–27,140,128 753.7 kb Distal (>10kb) Multiome HiCAR 662
chr6:27,145,480–27,148,111 746.1 kb Distal (>10kb) Multiome HiCAR 951
chr6:27,177,493–27,178,620 715.1 kb Distal (>10kb) Multiome HiCAR 685
chr6:27,188,443–27,189,128 704.3 kb Distal (>10kb) Multiome HiCAR 398
chr6:27,592,359–27,593,376 300.2 kb Distal (>10kb) Multiome 844
chr6:27,602,046–27,602,794 290.6 kb Distal (>10kb) Multiome 469
chr6:27,605,356–27,606,138 287.3 kb Distal (>10kb) Multiome 562
chr6:27,630,675–27,631,795 261.9 kb Distal (>10kb) Multiome 827
chr6:27,650,587–27,651,063 242.2 kb Distal (>10kb) Multiome 541
chr6:27,668,541–27,669,069 224.4 kb Distal (>10kb) Multiome 577
chr6:27,671,980–27,673,036 220.7 kb Distal (>10kb) Multiome 845
chr6:27,684,282–27,684,819 208.5 kb Distal (>10kb) Multiome 652
chr6:27,687,268–27,688,540 205.4 kb Distal (>10kb) Multiome 972
chr6:27,752,061–27,752,956 140.8 kb Distal (>10kb) Multiome 499
chr6:27,753,073–27,753,588 139.8 kb Distal (>10kb) Multiome 758
chr6:27,762,370–27,762,921 130.5 kb Distal (>10kb) Multiome 65
chr6:27,772,302–27,773,105 120.4 kb Distal (>10kb) Multiome 784
chr6:27,791,232–27,791,741 101.7 kb Distal (>10kb) Multiome 564
chr6:27,791,916–27,792,609 100.7 kb Distal (>10kb) Multiome HiCAR 728
chr6:27,806,645–27,808,975 85.1 kb Distal (>10kb) Multiome HiCAR 963
chr6:27,809,816–27,810,576 83.0 kb Distal (>10kb) Multiome HiCAR 914
chr6:27,813,688–27,816,146 78.2 kb Distal (>10kb) Multiome HiCAR 564
chr6:27,836,792–27,839,128 54.6 kb Distal (>10kb) Multiome HiCAR 1131
chr6:27,865,093–27,868,152 27.8 kb Distal (>10kb) Multiome 744
chr6:27,870,957–27,872,527 20.9 kb Distal (>10kb) Multiome 426
chr6:27,872,808–27,873,995 19.5 kb Distal (>10kb) Multiome 372
chr6:27,889,436–27,895,972 164 bp At TSS Multiome 1215
chr6:27,902,407–27,902,678 9.3 kb Proximal (<10kb) 562
chr6:27,902,800–27,903,766 9.9 kb Proximal (<10kb) Multiome 891
chr6:28,079,998–28,081,441 187.1 kb Distal (>10kb) Multiome 1054
chr6:28,104,510–28,105,291 211.7 kb Distal (>10kb) Multiome 927
chr6:28,136,684–28,137,470 243.9 kb Distal (>10kb) Multiome 1035
chr6:28,141,479–28,142,195 248.7 kb Distal (>10kb) Multiome 1010
chr6:28,171,036–28,171,660 278.3 kb Distal (>10kb) Multiome 67

Genome Browser

Genomic view of the H3C12 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.

chr6:26,010,104 – 28,181,660
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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