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LOC124153149 Sharpr-MPRA regulatory region 10821 [ Homo sapiens (human) ]

Gene ID: 124153149, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124153149
Gene description
Sharpr-MPRA regulatory region 10821
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 matched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124153149 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38754331..38754625)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (39031363..39031657)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (38611849..38612143)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ring finger protein 5 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19131 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38508629-38509230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38508026-38508628 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:38546721-38547014 Neighboring gene uncharacterized LOC124901936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38558842-38559342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38577151-38577672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38591927-38592426 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38593007-38593506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19135 Neighboring gene transforming acidic coiled-coil containing protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19136 Neighboring gene Sharpr-MPRA regulatory region 13542 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:38654374-38654912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27262 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:38664233-38664424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38692400-38693183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27263 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38718798-38719298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38719299-38719799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38721554-38722054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38722055-38722555 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:38724712-38725911 Neighboring gene uncharacterized LOC124901937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27266 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38771665-38772346 Neighboring gene pleckstrin homology domain containing A2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38793869-38794549 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38794550-38795229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27271 Neighboring gene Sharpr-MPRA regulatory region 15086 Neighboring gene HtrA serine peptidase 4

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_078537.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    38754331..38754625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    39031363..39031657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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