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LOC126806588 BRD4-independent group 4 enhancer GRCh37_chr3:3079797-3080996 [ Homo sapiens (human) ]

Gene ID: 126806588, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806588
Gene description
BRD4-independent group 4 enhancer GRCh37_chr3:3079797-3080996
Gene type
biological region
Feature type(s)
regulatory: enhancer
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. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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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See LOC126806588 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (3038113..3039312)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (3032428..3033627)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene contactin 4 Neighboring gene uncharacterized LOC105376926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19340 Neighboring gene MPRA-validated peak4526 silencer Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 pseudogene 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69430 Neighboring gene CNTN4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19343 Neighboring gene interleukin 5 receptor subunit alpha

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. 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 19341

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_082908.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    3038113..3039312
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    3032428..3033627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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