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LOC121331295 Sharpr-MPRA regulatory region 858 [ Homo sapiens (human) ]

Gene ID: 121331295, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121331295
Gene description
Sharpr-MPRA regulatory region 858
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC121331295 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (26265933..26266496)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (26541827..26542390)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (26123449..26123743)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379336 Neighboring gene MPRA-validated peak6960 silencer Neighboring gene RNA, 5S ribosomal pseudogene 258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:26008986-26009594 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:26035468-26035634 Neighboring gene MPRA-validated peak6961 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19037 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:26087585-26088201 Neighboring gene matrix metallopeptidase 12 (macrophage elastase) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19038 Neighboring gene protein phosphatase 2 regulatory subunit Balpha Neighboring gene Sharpr-MPRA regulatory region 13890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:26192157-26192656 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:26239047-26240246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27126 Neighboring gene SDA1 domain containing 1 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
  2. 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

  • H3K4me1 hESC enhancer GRCh37_chr8:26123513-26124012

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_074319.2 

    Range
    101..664
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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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    26265933..26266496
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    26541827..26542390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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