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LOC123464487 Sharpr-MPRA regulatory region 6572 [ Homo sapiens (human) ]

Gene ID: 123464487, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123464487
Gene description
Sharpr-MPRA regulatory region 6572
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123464487 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (191376800..191377094)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (194185867..194186161)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (191094589..191094883)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene OSTN antisense RNA 1 Neighboring gene osteocrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20990 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:191019724-191020249 Neighboring gene urotensin 2B Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:191046750-191047351 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:191047352-191047952 Neighboring gene coiled-coil domain containing 50 Neighboring gene PYDC2 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67093 Neighboring gene pyrin domain containing 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:191217087-191217641 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:191217642-191218195 Neighboring gene uncharacterized LOC124909472

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_077472.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    191376800..191377094
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    194185867..194186161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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