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LOC112533652 Sharpr-MPRA regulatory region 7909 [ Homo sapiens (human) ]

Gene ID: 112533652, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112533652
Gene description
Sharpr-MPRA regulatory region 7909
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 unmatched - State 1:Tss). This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate 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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See LOC112533652 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (56960888..56961182)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (57838528..57838822)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (55038249..55038543)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene tripartite motif containing 25 Neighboring gene microRNA 3614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12419 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:54990878-54991548 Neighboring gene MPRA-validated peak2907 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:55002389-55002923 Neighboring gene ribosomal protein S15a pseudogene Neighboring gene coilin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8742 Neighboring gene uncharacterized LOC105371836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8743 Neighboring gene serine carboxypeptidase 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:55087342-55087971 Neighboring gene Sharpr-MPRA regulatory region 8860 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55094302-55095128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55095129-55095953 Neighboring gene MPRA-validated peak2908 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55123409-55124336 Neighboring gene ring finger protein 126 pseudogene 1

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 active region 12421
  • ATAC-STARR-seq lymphoblastoid active region 12422

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_056923.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    56960888..56961182
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    57838528..57838822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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