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LOC126653337 MED14-independent group 3 enhancer GRCh37_chr21:30568347-30569546 [ Homo sapiens (human) ]

Gene ID: 126653337, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126653337
Gene description
MED14-independent group 3 enhancer GRCh37_chr21:30568347-30569546
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 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]
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Genomic context

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Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (29196026..29197225)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (27562284..27563483)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene MAP3K7 C-terminal like Neighboring gene NANOG hESC enhancer GRCh37_chr21:30506062-30506608 Neighboring gene ribosomal protein L12 pseudogene 9 Neighboring gene Sharpr-MPRA regulatory region 14833 Neighboring gene uncharacterized LOC105372767 Neighboring gene small nucleolar RNA U3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18341 Neighboring gene long intergenic non-protein coding RNA 189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18343 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18347 Neighboring gene uncharacterized LOC124905007

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 18342

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_081830.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    29196026..29197225
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791813.1 Reference GRCh38.p14 PATCHES

    Range
    289917..291116
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    27562284..27563483
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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