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LOC123464471 Sharpr-MPRA regulatory region 13352 [ Homo sapiens (human) ]

Gene ID: 123464471, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123464471
Gene description
Sharpr-MPRA regulatory region 13352
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 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:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (184777801..184778095)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (187593618..187593912)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (184495589..184495883)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184458434-184458952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184463957-184464458 Neighboring gene uncharacterized LOC105374253 Neighboring gene long intergenic non-protein coding RNA 2069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184498897-184499397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184508256-184508756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14970 Neighboring gene VPS8 subunit of CORVET complex Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20916 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:184624367-184625028 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:184625029-184625689 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:184629832-184630395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184787208-184787708 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:184788784-184788991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184792904-184793404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184797955-184798456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184798457-184798956 Neighboring gene Sharpr-MPRA regulatory region 10617 Neighboring gene chromosome 3 open reading frame 70 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14972

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_077457.1 

    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
    184777801..184778095
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    187593618..187593912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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