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LOC124849284 Sharpr-MPRA regulatory region 14372 [ Homo sapiens (human) ]

Gene ID: 124849284, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124849284
Gene description
Sharpr-MPRA regulatory region 14372
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [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 (130776624..130776918)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (130815058..130815353)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene piwi like RNA-mediated gene silencing 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25849 Neighboring gene RIMS binding protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:130931901-130932400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:130935063-130935689 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:130938232-130938396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:130947695-130948194 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:130954155-130954656 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:130954657-130955156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:130956221-130956721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7343 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:130966855-130967455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:130988941-130989441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:130988440-130988940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:130998885-130999583 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25887 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:131047373-131048572 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25901 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:131092324-131092520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131097951-131098545 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:131118450-131118967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131145339-131145838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131188343-131189087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131212975-131213518 Neighboring gene uncharacterized LOC105370080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131246445-131247250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7345 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:131271649-131272370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:131272371-131273092 Neighboring gene Sharpr-MPRA regulatory region 967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:131290439-131291361 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:131296228-131296411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7347 Neighboring gene uncharacterized LOC124903117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5092 Neighboring gene Sharpr-MPRA regulatory region 8535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:131335999-131336907 Neighboring gene uncharacterized LOC124903053 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:131337941-131338691 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:131338692-131339442 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:131339443-131340192 Neighboring gene syntaxin 2

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_079859.1 

    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
    130776624..130776918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    130815058..130815353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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