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LOC126806393 MED14-independent group 3 enhancer GRCh37_chr2:163175227-163176426 [ Homo sapiens (human) ]

Gene ID: 126806393, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806393
Gene description
MED14-independent group 3 enhancer GRCh37_chr2:163175227-163176426
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 an enhancer that was validated 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 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]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is regulatory element in the vicinity of coronavirus related gene(s).
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Genomic context

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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (162318599..162319916)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (162775266..162776583)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929532 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_54994 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_55025 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_55061 Neighboring gene uncharacterized LOC105373724 Neighboring gene fibroblast activation protein alpha Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_55125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12062 Neighboring gene interferon induced with helicase C domain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16718 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_55234 Neighboring gene grancalcin Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_55244 Neighboring gene potassium voltage-gated channel subfamily H member 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16719 Neighboring gene uncharacterized LOC124906084 Neighboring gene RNA, 5S ribosomal pseudogene 109 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_55297 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:163568111-163568632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16722 Neighboring gene Sharpr-MPRA regulatory region 9339 Neighboring gene KCNH7 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 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 16717

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_082713.2 

    Range
    101..1418
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    162318599..162319916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    162775266..162776583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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