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LOC126862154 MED14-independent group 3 enhancer GRCh37_chr15:63448416-63449615 [ Homo sapiens (human) ]

Gene ID: 126862154, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862154
Gene description
MED14-independent group 3 enhancer GRCh37_chr15:63448416-63449615
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 (MPRA). In HCT116 colorectal carcinoma cells, a subregion was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive and primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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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Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (63156217..63157600)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (60960998..60962381)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6510 Neighboring gene lactamase beta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6511 Neighboring gene ribosomal protein S27 like Neighboring gene uncharacterized LOC101928972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63485907-63486407 Neighboring gene RAB8B, member RAS oncogene family Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:63502826-63503391

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
  3. 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

  • ATAC-STARR-seq lymphoblastoid active region 9525
  • ATAC-STARR-seq lymphoblastoid active region 9526
  • H3K27ac hESC enhancer GRCh37_chr15:63449195-63449768

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_086652.3 

    Range
    101..1484
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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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    63156217..63157600
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    60960998..60962381
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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