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LOC121099714 MED14-independent group 3 enhancer GRCh37_chr5:173204773-173205972 [ Homo sapiens (human) ]

Gene ID: 121099714, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121099714
Gene description
MED14-independent group 3 enhancer GRCh37_chr5:173204773-173205972
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion 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. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 23:Low, low signal proximal to active elements). 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:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (173777770..173779065)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (174318145..174319440)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (173205729..173206023)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984118 Neighboring gene long intergenic non-protein coding RNA 1484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173147588-173148088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173148089-173148589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23663 Neighboring gene uncharacterized LOC124901138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173198292-173199282 Neighboring gene uncharacterized LOC107986482 Neighboring gene NFE2L2 motif-containing MPRA enhancer 276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23666 Neighboring gene long intergenic non-protein coding RNA 1485 Neighboring gene Sharpr-MPRA regulatory region 2476 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23667 Neighboring gene Sharpr-MPRA regulatory region 12964 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4558 Neighboring gene Sharpr-MPRA regulatory region 12084 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4561 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4562 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:173301919-173302077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173317123-173317624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173317625-173318124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23671 Neighboring gene Sharpr-MPRA regulatory region 4386 Neighboring gene cytoplasmic polyadenylation element binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:173368663-173369301

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  3. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23664
  • Sharpr-MPRA regulatory region 6355

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_074194.3 

    Range
    101..1396
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    173777770..173779065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    174318145..174319440
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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