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LOC126807405 BRD4-independent group 4 enhancer GRCh37_chr5:59063568-59064767 [ Homo sapiens (human) ]

Gene ID: 126807405, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807405
Gene description
BRD4-independent group 4 enhancer GRCh37_chr5:59063568-59064767
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (59767742..59769142)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (60585975..60587375)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 4D Neighboring gene uncharacterized LOC107986347 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:58858724-58859374 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:59004928-59005660 Neighboring gene Sharpr-MPRA regulatory region 14831 Neighboring gene MPRA-validated peak5261 silencer Neighboring gene uncharacterized LOC105378988 Neighboring gene NANOG hESC enhancer GRCh37_chr5:59096304-59096834 Neighboring gene microRNA 582 Neighboring gene uncharacterized LOC107986350 Neighboring gene NANOG hESC enhancer GRCh37_chr5:59165165-59165666

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:59064453-59064968

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_083719.2 

    Range
    101..1501
    Download
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    59767742..59769142
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    60585975..60587375
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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