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LOC123256952 Sharpr-MPRA regulatory region 12572 [ Homo sapiens (human) ]

Gene ID: 123256952, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123256952
Gene description
Sharpr-MPRA regulatory region 12572
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC123256952 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 (179289301..179289595)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (182093137..182093431)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (179007089..179007383)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA25 Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14913 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:178905170-178905394 Neighboring gene potassium calcium-activated channel subfamily M regulatory beta subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:178980593-178981094 Neighboring gene LRR binding FLII interacting protein 1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:179008749-179009491 Neighboring gene CRISPRi-validated cis-regulatory element chr3.5052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20865 Neighboring gene zinc finger protein 639 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:179065206-179065735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20866 Neighboring gene mitofusin 1

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_077370.1 

    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
    179289301..179289595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    182093137..182093431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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