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LOC123956217 Sharpr-MPRA regulatory region 5263 [ Homo sapiens (human) ]

Gene ID: 123956217, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956217
Gene description
Sharpr-MPRA regulatory region 5263
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element 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 Repressive DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956217 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (124783355..124783649)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (126100708..126101002)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (124423409..124423703)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 102, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:124371425-124371925 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:124372079-124372580 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:124374223-124374759 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:124397814 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18589 Neighboring gene G protein-coupled receptor 37 Neighboring gene Sharpr-MPRA regulatory region 10744 Neighboring gene long intergenic non-protein coding RNA 3043 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:124449868 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:124472442-124472991 Neighboring gene protection of telomeres 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:124533191-124533332 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:124542275 Neighboring gene Sharpr-MPRA regulatory region 5954 Neighboring gene POT1 antisense RNA 1 Neighboring gene eukaryotic translation elongation factor 1 gamma pseudogene 1

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

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_078411.1 

    Range
    101..395
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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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    124783355..124783649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    126100708..126101002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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