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LOC126862529 BRD4-independent group 4 enhancer GRCh37_chr17:28443345-28444544 [ Homo sapiens (human) ]

Gene ID: 126862529, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862529
Gene description
BRD4-independent group 4 enhancer GRCh37_chr17:28443345-28444544
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) 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. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 liver carcinoma cells. This locus also includes four accessible chromatin subregions, three of which were validated as enhancers and one as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (30116327..30117526)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (31060887..31062086)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene EF-hand calcium binding domain 5 Neighboring gene RNY4 pseudogene 13 Neighboring gene syntaxin 18 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8392 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:28432062-28432163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28468415-28468916 Neighboring gene microRNA 3184 Neighboring gene microRNA 423 Neighboring gene nuclear speckle splicing regulatory protein 1 Neighboring gene uncharacterized LOC124903970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28549461-28549976 Neighboring gene solute carrier family 6 member 4 Neighboring gene MPRA-validated peak2787 silencer Neighboring gene serotonin transporter intronic VNTR enhancer Neighboring gene solute carrier family 6 member 4 gene promoter Neighboring gene uncharacterized LOC105371720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28565347-28566247 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:28575475-28576674 Neighboring gene bleomycin hydrolase

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 identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 11988
  • ATAC-STARR-seq lymphoblastoid active region 11989
  • ATAC-STARR-seq lymphoblastoid active region 11990
  • ATAC-STARR-seq lymphoblastoid silent region 8393
  • ReSE screen-validated silencer GRCh37_chr17:28443659-28444260

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_087026.1 

    Range
    101..1300
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    30116327..30117526
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    31060887..31062086
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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