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LOC111591503 HNF1 motif-containing MPRA enhancer 277 [ Homo sapiens (human) ]

Gene ID: 111591503, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111591503
Gene description
HNF1 motif-containing MPRA enhancer 277
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, 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 identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. It was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. A subregion was also predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project, and was validated as a functional enhancer by MPRAs in HepG2 liver carcinoma cells. That enhancer contains a motif for the HNF1 activator, and mutation of the motif results in reduced enhancer activity. [provided by RefSeq, Apr 2023]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77390282..77390482)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71599661..71599861)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (77856627..77856771)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77787600-77788461 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:77795945-77797144 Neighboring gene glutathione S-transferase zeta 1 Neighboring gene transmembrane p24 trafficking protein family member 8 Neighboring gene ATP binding cassette subfamily G member 2 (Junior blood group) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8800 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:77846838-77847018 Neighboring gene sterile alpha motif domain containing 15 Neighboring gene NADP dependent oxidoreductase domain containing 1 Neighboring gene VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77923742-77924264

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, 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

  • HNF1 activator MPRA enhancer 277
  • MPRA-validated peak2207 silencer
  • massively parallel reporter assay enhancer 277

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_056094.2 

    Range
    101..301
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    77390282..77390482
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71599661..71599861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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