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LOC123000068 Sharpr-MPRA regulatory region 14829 [ Homo sapiens (human) ]

Gene ID: 123000068, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123000068
Gene description
Sharpr-MPRA regulatory region 14829
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 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC123000068 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (65915554..65915848)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (65959571..65959865)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (65901229..65901523)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 1 Neighboring gene uncharacterized LOC107986018 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:65747629-65748266 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:65776724-65776896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:65854323-65854824 Neighboring gene ribosomal protein L17 pseudogene 17 Neighboring gene MAGI1 intronic transcript 1 Neighboring gene Sharpr-MPRA regulatory region 7664 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:65887567-65888467 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:65888468-65889367 Neighboring gene MAGI1 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:65949459-65950658 Neighboring gene uncharacterized LOC124900543 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:65985258-65985772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:65985773-65986287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:65995041-65995541 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:65996456-65997048 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66021123-66021952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66021953-66022780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66022781-66023608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14503 Neighboring gene uncharacterized LOC105377128

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_077251.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    65915554..65915848
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    65959571..65959865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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