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LOC123480937 Sharpr-MPRA regulatory region 15425 [ Homo sapiens (human) ]

Gene ID: 123480937, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123480937
Gene description
Sharpr-MPRA regulatory region 15425
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (153750177..153750471)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (157074618..157074912)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (154671329..154671623)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15767 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74840 Neighboring gene uncharacterized LOC105377499 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74848 Neighboring gene toll like receptor 2 Neighboring gene ring finger protein 175 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154710463-154711164 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154711165-154711866 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74856/74857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:154713271-154713972 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74859 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74875 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74882 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74898 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74905 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74906 Neighboring gene uncharacterized LOC101927947 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74908 Neighboring gene secreted frizzled related protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:154802179-154802342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22072 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:154855107-154855606 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:154871827-154872023 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:154908563-154909762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154944484-154945005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:154945006-154945526 Neighboring gene Sharpr-MPRA regulatory region 8445 Neighboring gene MPRA-validated peak5134 silencer Neighboring gene dachsous cadherin-related 2

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_077631.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    153750177..153750471
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    157074618..157074912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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