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LOC112543463 Sharpr-MPRA regulatory region 8704 [ Homo sapiens (human) ]

Gene ID: 112543463, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112543463
Gene description
Sharpr-MPRA regulatory region 8704
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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating 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:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (17579896..17580234)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (17714520..17714858)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (17690749..17691043)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene PGLS divergent transcript Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17621962-17622618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10350 Neighboring gene Sharpr-MPRA regulatory region 7913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17623276-17623931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14278 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17641583-17642201 Neighboring gene 6-phosphogluconolactonase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10353 Neighboring gene niban apoptosis regulator 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10355 Neighboring gene collagen beta(1-O)galactosyltransferase 1 Neighboring gene ribosomal protein L21 pseudogene 130 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17709342-17709923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17715726-17716630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17716631-17717535 Neighboring gene unc-13 homolog A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17797343-17798304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17798305-17799265

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 14279

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_057404.2 

    Range
    101..439
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    17579896..17580234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    17714520..17714858
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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