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LOC121627966 Sharpr-MPRA regulatory region 12561 [ Homo sapiens (human) ]

Gene ID: 121627966, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627966
Gene description
Sharpr-MPRA regulatory region 12561
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. It 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - 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:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (40997016..40997310)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (40399055..40399349)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (40856269..40856563)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:40767632-40768831 Neighboring gene ribosomal protein L32 pseudogene 36 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:40809037-40809720 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:40809721-40810402 Neighboring gene ribosomal protein S2 pseudogene 55 Neighboring gene Sharpr-MPRA regulatory region 13807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20771 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:40944771-40945308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20772 Neighboring gene chloride intracellular channel 4 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:40973903-40974035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29553 Neighboring gene ubiquitin specific peptidase 9 X-linked Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:40991170-40991670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:41070375-41071092

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 20769

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_075446.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    40997016..40997310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    40399055..40399349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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