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LOC123987612 Sharpr-MPRA regulatory region 14576 [ Homo sapiens (human) ]

Gene ID: 123987612, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123987612
Gene description
Sharpr-MPRA regulatory region 14576
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). 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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Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (6428559..6428942)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (6183064..6183446)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (6286169..6286463)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377797 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103459 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:6170563-6171762 Neighboring gene NANOG hESC enhancer GRCh37_chr8:6189146-6189652 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:6247558-6248757 Neighboring gene MPRA-validated peak6892 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26946 Neighboring gene MCPH1 divergent transcript Neighboring gene microcephalin 1 Neighboring gene adenylate kinase isoenzyme 6-like Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:6385720-6386919 Neighboring gene angiopoietin 2 Neighboring gene Sharpr-MPRA regulatory region 12768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:6419583-6420108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6420109-6420635

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 26947

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_078485.2 

    Range
    101..484
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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
    6428559..6428942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791785.1 Reference GRCh38.p14 PATCHES

    Range
    364037..364420
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    6183064..6183446
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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