H2BC11
H2B clustered histone 11 | H2B/r, H2BFR, HIST1H2BJ

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 H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the histone microcluster on chromosome 6p21.33. [provided by RefSeq, Aug 2015]

Developmental clusters: GC4
Biological processes 37 terms
DNA binding (GO:0003677)DNA binding (GO:0003677)DNA binding (GO:0003677)antibacterial humoral response (GO:0019731)antibacterial humoral response (GO:0019731)antimicrobial humoral immune response mediated by antimicrobial peptide (GO:0061844)antimicrobial humoral immune response mediated by antimicrobial peptide (GO:0061844)chromatin organization (GO:0006325)chromatin organization (GO:0006325)chromosome (GO:0005694)defense response to Gram-negative bacterium (GO:0050829)defense response to Gram-positive bacterium (GO:0050830)extracellular region (GO:0005576)extracellular region (GO:0005576)innate immune response in mucosa (GO:0002227)innate immune response in mucosa (GO:0002227)killing of cells of another organism (GO:0031640)lipopolysaccharide binding (GO:0001530)negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome assembly (GO:0006334)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)plasma membrane (GO:0005886)protein binding (GO:0005515)protein heterodimerization activity (GO:0046982)protein localization to CENP-A containing chromatin (GO:0061644)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)
Expression (TPM)
H2BC11 — as a Regulated Gene

TFs regulating H2BC11 0 TFs

Transcription factors with Perturb-seq knockdown data for H2BC11. 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 = H2BC11 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 H2BC11

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H2BC11, 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
chr6:26,122,481–26,124,909 1009.9 kb Distal (>10kb) Multiome HiCAR 1216
chr6:26,156,184–26,158,744 974.8 kb Distal (>10kb) Multiome HiCAR 1310
chr6:26,183,128–26,184,377 949.1 kb Distal (>10kb) Multiome HiCAR 311
chr6:26,187,874–26,189,538 943.7 kb Distal (>10kb) Multiome HiCAR 1053
chr6:26,196,695–26,197,676 935.6 kb Distal (>10kb) Multiome HiCAR 842
chr6:26,198,203–26,200,197 933.4 kb Distal (>10kb) Multiome HiCAR 939
chr6:26,203,791–26,205,119 928.3 kb Distal (>10kb) Multiome HiCAR 1071
chr6:26,223,716–26,224,480 908.8 kb Distal (>10kb) Multiome HiCAR 507
chr6:26,224,856–26,226,566 907.6 kb Distal (>10kb) Multiome HiCAR 451
chr6:26,239,944–26,240,920 892.5 kb Distal (>10kb) Multiome HiCAR 375
chr6:26,249,682–26,251,138 882.4 kb Distal (>10kb) Multiome HiCAR 731
chr6:26,251,339–26,252,079 881.1 kb Distal (>10kb) Multiome HiCAR 445
chr6:26,285,011–26,286,121 847.2 kb Distal (>10kb) Multiome HiCAR 1121
chr6:26,956,244–26,957,132 176.4 kb Distal (>10kb) Multiome 399
chr6:27,019,699–27,020,456 112.6 kb Distal (>10kb) Multiome 707
chr6:27,091,728–27,092,257 40.9 kb Distal (>10kb) Multiome 610
chr6:27,127,127–27,127,379 5.4 kb Proximal (<10kb) 547
chr6:27,131,467–27,132,107 687 bp At TSS 580
chr6:27,132,200–27,134,276 101 bp At TSS Multiome 975
chr6:27,139,091–27,140,128 6.5 kb Proximal (<10kb) Multiome 662
chr6:27,145,480–27,148,111 14.2 kb Distal (>10kb) Multiome 951
chr6:27,177,493–27,178,620 45.2 kb Distal (>10kb) Multiome 685
chr6:27,188,443–27,189,128 56.0 kb Distal (>10kb) Multiome 398
chr6:27,214,739–27,215,257 82.3 kb Distal (>10kb) Multiome 338
chr6:27,230,181–27,230,668 97.7 kb Distal (>10kb) Multiome 624
chr6:27,250,707–27,252,203 118.9 kb Distal (>10kb) Multiome 736
chr6:27,279,529–27,280,388 147.5 kb Distal (>10kb) Multiome 560
chr6:27,290,574–27,291,026 157.9 kb Distal (>10kb) Multiome 324
chr6:27,332,775–27,333,421 200.4 kb Distal (>10kb) Multiome 657
chr6:27,374,472–27,375,425 242.4 kb Distal (>10kb) Multiome 488
chr6:27,388,369–27,389,372 256.0 kb Distal (>10kb) Multiome 997
chr6:27,791,232–27,791,741 658.6 kb Distal (>10kb) Multiome HiCAR 564
chr6:27,806,645–27,808,975 675.2 kb Distal (>10kb) Multiome HiCAR 963
chr6:27,809,816–27,810,576 677.3 kb Distal (>10kb) Multiome HiCAR 914
chr6:27,813,688–27,816,146 682.2 kb Distal (>10kb) Multiome HiCAR 564
chr6:27,889,436–27,895,972 758.1 kb Distal (>10kb) Multiome HiCAR 1215

Genome Browser

Genomic view of the H2BC11 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.

chr6:26,112,481 – 27,905,972
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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