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LOC112533671 Sharpr-MPRA regulatory region 12010 [ Homo sapiens (human) ]

Gene ID: 112533671, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112533671
Gene description
Sharpr-MPRA regulatory region 12010
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 DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). 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 (75516308..75516766)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76409674..76410132)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73512389..73512683)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene transmembrane protein 94 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12766 Neighboring gene microRNA 6785 Neighboring gene CASK interacting protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73510728-73511294 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8971 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73521300-73521484 Neighboring gene tRNA splicing endonuclease subunit 54 Neighboring gene LLGL scribble cell polarity complex component 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73537609-73538426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73540787-73541589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73548510-73549090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73553000-73553936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73553937-73554872 Neighboring gene Sharpr-MPRA regulatory region 3602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12769 Neighboring gene Sharpr-MPRA regulatory region 12965 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73583697-73584530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73584531-73585362 Neighboring gene myosin XVB

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 8970

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_057344.2 

    Range
    101..559
    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
    75516308..75516766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    76409674..76410132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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