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LOC111822952 Sharpr-MPRA regulatory regions 8228 and 8679 [ Homo sapiens (human) ]

Gene ID: 111822952, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111822952
Gene description
Sharpr-MPRA regulatory regions 8228 and 8679
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 contains two overlapping sub-regions, where one sub-region was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). It also showed weak enhancer activity in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss). The other sub-region displayed weak repressive activity by Sharpr-MPRA in both HepG2 cells (group: HepG2 Repressive non-DNase unmatched - State 1:Tss) and K562 cells (group: K562 Repressive non-DNase unmatched - State 1:Tss). [provided by RefSeq, Jan 2018]
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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 (58338028..58338582)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (59205908..59206462)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (56415389..56415943)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene TSPOAP1, SUPT4H1 and RNF43 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56412683-56413183 Neighboring gene MIR142 host genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:56413329-56413870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12477 Neighboring gene microRNA 142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12480 Neighboring gene microRNA 4736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12481 Neighboring gene SPT4 homolog, DSIF elongation factor subunit Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8768 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:56430343-56430878 Neighboring gene ring finger protein 43 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12482 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:56471542-56472741 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:56475825-56476680

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

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

  • Sharpr-MPRA regulatory region 8228
  • Sharpr-MPRA regulatory region 8679

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_056222.1 

    Range
    101..655
    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
    58338028..58338582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    59205908..59206462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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