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LOC124174281 Sharpr-MPRA regulatory region 233 [ Homo sapiens (human) ]

Gene ID: 124174281, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124174281
Gene description
Sharpr-MPRA regulatory region 233
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (76673654..76673948)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (77102816..77103110)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (77585889..77586183)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1111 Neighboring gene uncharacterized LOC107986952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27544 Neighboring gene ZFHX4 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr8:77553488-77553989 Neighboring gene mitochondrial ribosomal protein L9 pseudogene 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:77585153-77585653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19304 Neighboring gene VISTA enhancer hs1318 Neighboring gene zinc finger homeobox 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:77676670-77677613 Neighboring gene VISTA enhancer hs774 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19305 Neighboring gene VISTA enhancer hs1681 Neighboring gene microRNA 3149

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_078580.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    76673654..76673948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    77102816..77103110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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