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LOC111828504 Sharpr-MPRA regulatory regions 872 and 4511 [ Homo sapiens (human) ]

Gene ID: 111828504, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111828504
Gene description
Sharpr-MPRA regulatory regions 872 and 4511
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin), with weaker activation in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). An adjacent and partially overlapping subregion was also validated as a functional repressive element by Sharpr-MPRA in both HepG2 cells (group: HepG2 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers) and K562 cells (group: K562 Repressive non-DNase unmatched - State 5:Enh). [provided by RefSeq, Aug 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (244341427..244341981)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (243757765..243758319)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (244504729..244505283)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373261 Neighboring gene uncharacterized LOC105373260 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:244364602-244365102 Neighboring gene uncharacterized LOC105373262 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:244402369-244403568 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:244436364-244436590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2837 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:244486677-244487635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2839 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:244517816-244518334 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:244524996-244525821 Neighboring gene sperm microtubule inner protein 3 Neighboring gene TGFB induced factor homeobox 2 pseudogene 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. 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

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

  • Sharpr-MPRA regulatory region 4511
  • Sharpr-MPRA regulatory region 872

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_056232.2 

    Range
    101..655
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    244341427..244341981
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    243757765..243758319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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