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LOC126861762 MED14-independent group 3 enhancer GRCh37_chr13:45008784-45009983 [ Homo sapiens (human) ]

Gene ID: 126861762, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126861762
Gene description
MED14-independent group 3 enhancer GRCh37_chr13:45008784-45009983
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 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. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to 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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See LOC126861762 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (44434648..44435847)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (43654408..43655607)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (45008784..45009983)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene stress associated endoplasmic reticulum protein family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:44991723-44992251 Neighboring gene tumor suppressor candidate 8 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:44999732-44999924 Neighboring gene uncharacterized LOC124903167 Neighboring gene TSC22 domain family member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:45026151-45026652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:45026653-45027152 Neighboring gene NANOG hESC enhancer GRCh37_chr13:45090824-45091325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5309 Neighboring gene TSC22D1 antisense RNA 1

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 5305

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_086260.1 

    Range
    101..1300
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    44434648..44435847
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    43654408..43655607
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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