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LOC123192019 Sharpr-MPRA regulatory region 7583 [ Homo sapiens (human) ]

Gene ID: 123192019, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123192019
Gene description
Sharpr-MPRA regulatory region 7583
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 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC123192019 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 (151211041..151211335)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (153962098..153962392)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (150928829..150929123)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene mediator complex subunit 12L Neighboring gene RNA, 5S ribosomal pseudogene 145 Neighboring gene G protein-coupled receptor 171 Neighboring gene purinergic receptor P2Y14 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:150959259-150959858 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:150959859-150960456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20700 Neighboring gene Sharpr-MPRA regulatory region 3159 Neighboring gene SET pseudogene 11 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:151033994-151035193 Neighboring gene G protein-coupled receptor 87

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_077335.1 

    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
    151211041..151211335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    153962098..153962392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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