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LOC121853042 Sharpr-MPRA regulatory region 8708 [ Homo sapiens (human) ]

Gene ID: 121853042, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853042
Gene description
Sharpr-MPRA regulatory region 8708
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (36124001..36124305)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (36583785..36584089)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (36520049..36520343)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene RNA binding fox-1 homolog 2 Neighboring gene ribosomal protein L41 pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:36278945-36279446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36312425-36313104 Neighboring gene NADH:ubiquinone oxidoreductase subunit A9 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13660 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:36431275-36432018 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:36448074-36449273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36481448-36482174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36513157-36513657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36512656-36513156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36528024-36528524 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:36530251-36531450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36537001-36537502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36537503-36538002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36552799-36553402 Neighboring gene NANOG hESC enhancer GRCh37_chr22:36557722-36558295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18916 Neighboring gene apolipoprotein L3 Neighboring gene MT-CO1 pseudogene 20

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 13661

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_076150.2 

    Range
    101..405
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    36124001..36124305
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    36583785..36584089
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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