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LOC111413029 BRD4-independent group 4 enhancer GRCh37_chr16:71605697-71606896 [ Homo sapiens (human) ]

Gene ID: 111413029, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111413029
Gene description
BRD4-independent group 4 enhancer GRCh37_chr16:71605697-71606896
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells, where it was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. Two overlapping subregions were also validated as functional enhancers by high-throughput massively parallel reporter assays (MPRAs) in HepG2 liver carcinoma cells, where each subregion contains overlapping motifs for the FOXA and HNF1 activators, and mutation of either motif results in reduced enhancer activity. [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (71571794..71573046)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77388987..77390239)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (71606800..71606949)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903710 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:71599339-71599870 Neighboring gene RNA, U6 small nuclear 1061, pseudogene Neighboring gene TAT antisense RNA 1 Neighboring gene tyrosine aminotransferase Neighboring gene uncharacterized LOC105371334 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7682 Neighboring gene MARVEL domain containing 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:71671387-71671938 Neighboring gene uncharacterized LOC124903711

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, Free PMC Article
  3. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • FOXA activator MPRA enhancer 166
  • FOXA and HNF1 motif-containing MPRA enhancers 32 and 166
  • HNF1 activator MPRA enhancer 32
  • massively parallel reporter assay enhancers 32 and 166

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_055860.3 

    Range
    101..1353
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    71571794..71573046
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    77388987..77390239
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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