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LOC124819399 Sharpr-MPRA regulatory region 4252 [ Homo sapiens (human) ]

Gene ID: 124819399, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124819399
Gene description
Sharpr-MPRA regulatory region 4252
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110499124..110499418)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110476821..110477115)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903016 Neighboring gene family with sequence similarity 216 member A Neighboring gene uncharacterized LOC124903015 Neighboring gene small nucleolar RNA SNORD50 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7006 Neighboring gene VPS29 retromer complex component Neighboring gene ReSE screen-validated silencer GRCh37_chr12:110953094-110953337 Neighboring gene RAD9 checkpoint clamp component B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978258-110978758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978759-110979259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7008 Neighboring gene protein phosphatase targeting COQ7 Neighboring gene HNF4 motif-containing MPRA enhancer 250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7013 Neighboring gene tectonic family member 1 Neighboring gene RNA, 7SL, cytoplasmic 387, pseudogene

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

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_079816.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    110499124..110499418
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    110476821..110477115
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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