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LOC125387245 Sharpr-MPRA regulatory region 1881 [ Homo sapiens (human) ]

Gene ID: 125387245, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125387245
Gene description
Sharpr-MPRA regulatory region 1881
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element 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 Repressive 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 LOC125387245 in Genome Data Viewer
Location:
20p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (23475672..23476505)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (23535207..23536040)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (23456309..23457142)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 479 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:23372358-23372897 Neighboring gene NSF attachment protein beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:23406421-23407128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:23423063-23423642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12732 Neighboring gene cystatin like 1 Neighboring gene cystatin 11 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:23453588-23454206 Neighboring gene cystatin 12, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:23471218-23471718 Neighboring gene cystatin 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17642 Neighboring gene cystatin 13, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:23513598-23514559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:23515257-23515934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:23515935-23516610

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:23456315-23457142

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_080922.2 

    Range
    101..934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    23475672..23476505
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    23535207..23536040
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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