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LOC112533653 Sharpr-MPRA regulatory region 5901 [ Homo sapiens (human) ]

Gene ID: 112533653, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112533653
Gene description
Sharpr-MPRA regulatory region 5901
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 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 non-DNase unmatched - State 1:Tss). 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:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (58083148..58083508)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (58957149..58957509)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (56160509..56160803)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12457 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:56082218-56083417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12459 Neighboring gene serine and arginine rich splicing factor 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:56084242-56084960 Neighboring gene uncharacterized LOC105371840 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:56129666-56130865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56152348-56152941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8758 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8760 Neighboring gene DYNLL2 divergent transcript Neighboring gene dynein light chain LC8-type 2 Neighboring gene Sharpr-MPRA regulatory region 5260 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:56219338-56219838 Neighboring gene olfactory receptor family 4 subfamily D member 1 Neighboring gene msh homeobox 2 pseudogene 1 Neighboring gene olfactory receptor family 4 subfamily D member 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
  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 8757

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_056924.2 

    Range
    101..461
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    58083148..58083508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    58957149..58957509
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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