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LOC123480924 Sharpr-MPRA regulatory region 10032 [ Homo sapiens (human) ]

Gene ID: 123480924, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123480924
Gene description
Sharpr-MPRA regulatory region 10032
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 includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and 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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). 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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See LOC123480924 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (122827494..122828273)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (126131593..126132372)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (123748649..123749428)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Bardet-Biedl syndrome 12 Neighboring gene DNA damage regulated autophagy modulator 1 pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr4.2649 Neighboring gene Sharpr-MPRA regulatory region 2230 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:123705471-123706466 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:123707239-123708438 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123709565-123710492 Neighboring gene Sharpr-MPRA regulatory region 4773 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:123719262-123720461 Neighboring gene FGF2 promoter region Neighboring gene ribosomal protein L34 pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21877 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:123749417-123749942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:123767626-123768139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:123768140-123768652 Neighboring gene fibroblast growth factor 2 Neighboring gene ribosomal protein S26 pseudogene 23 Neighboring gene uncharacterized LOC124900773

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article
  3. 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 21878
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123748891-123749416

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_077618.3 

    Range
    101..880
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    122827494..122828273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    126131593..126132372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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