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LOC111413048 NFE2L2 motif-containing MPRA enhancer 199 [ Homo sapiens (human) ]

Gene ID: 111413048, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111413048
Gene description
NFE2L2 motif-containing MPRA enhancer 199
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as a functional enhancer by high-throughput massively parallel reporter assays (MPRAs) in liver carcinoma HepG2 cells. That subregion contains a conserved motif for the NFE2L2 activator, and mutation of the motif results in reduced enhancer activity. Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. 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:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (128517807..128518627)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (131821975..131822795)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (129438962..129439106)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene La ribonucleoprotein 1B Neighboring gene FOSL1 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr4:129186588-129187089 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:129197563-129197760 Neighboring gene Sharpr-MPRA regulatory region 13521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15683 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15684 Neighboring gene Sharpr-MPRA regulatory region 12082 Neighboring gene progesterone receptor membrane component 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129242766-129243328 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129271007-129271585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:129271620-129272158 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129283869-129284407 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:129308825-129310024 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73985 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73994 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129337187-129337688 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129337689-129338188 Neighboring gene long intergenic non-protein coding RNA 2615 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:129390695-129391894 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129456135-129456788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129456789-129457442 Neighboring gene uncharacterized LOC101927259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21891 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129487118-129487618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129487619-129488119 Neighboring gene uncharacterized LOC124900778

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. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, Free PMC Article
  3. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  4. 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
  5. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 21889
  • H3K27ac hESC enhancer GRCh37_chr4:129439021-129439782
  • NFE2L2 activator MPRA enhancer 199
  • massively parallel reporter assay enhancer 199

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_055878.2 

    Range
    101..921
    Download
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    128517807..128518627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    131821975..131822795
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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