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LOC112533669 Sharpr-MPRA regulatory region 3986 [ Homo sapiens (human) ]

Gene ID: 112533669, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112533669
Gene description
Sharpr-MPRA regulatory region 3986
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. The major subregion includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. Another subregion was validated as an 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 non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 1:Tss). This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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 (75046436..75047335)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (75937868..75938767)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73043009..73043303)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8952 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73031872-73032031 Neighboring gene tRNA-Arg (anticodon TCG) 3-1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73037362-73037932 Neighboring gene potassium channel tetramerization domain containing 2 Neighboring gene RNA, 7SL, cytoplasmic 573, pseudogene Neighboring gene ATP synthase peripheral stalk subunit d Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12732 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73074528-73075727 Neighboring gene tripartite motif containing 80, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089299-73089872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089873-73090445 Neighboring gene solute carrier family 16 member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73100784-73101284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73101285-73101785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8955 Neighboring gene armadillo repeat containing 7

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
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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 active region 12731
  • ATAC-STARR-seq lymphoblastoid silent region 8953
  • H3K27ac hESC enhancer GRCh37_chr17:73042539-73043124

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_057342.3 

    Range
    101..1000
    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
    75046436..75047335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    75937868..75938767
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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