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LOC113845786 Sharpr-MPRA regulatory region 4463 [ Homo sapiens (human) ]

Gene ID: 113845786, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113845786
Gene description
Sharpr-MPRA regulatory region 4463
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. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). It also displayed weak repressive activity by Sharpr-MRPA in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (119809086..119809380)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (118184210..118184504)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (118943049..118943343)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29897 Neighboring gene sosondowah ankyrin repeat domain family member D Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:118902711-118903910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29899 Neighboring gene uncharacterized LOC107985694 Neighboring gene small nucleolar RNA, H/ACA box 69 Neighboring gene ribosomal protein L39 Neighboring gene UPF3B regulator of nonsense mediated mRNA decay Neighboring gene UPF3B, regulator of nonsense mediated mRNA decay pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29902 Neighboring gene ring finger protein 113A

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  2. 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

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)

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_063190.1 

    Range
    101..395
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    119809086..119809380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    118184210..118184504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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