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LOC121099708 Sharpr-MPRA regulatory region 10017 [ Homo sapiens (human) ]

Gene ID: 121099708, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121099708
Gene description
Sharpr-MPRA regulatory region 10017
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 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 matched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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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See LOC121099708 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149357806..149358100)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (149892621..149892915)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (148737369..148737663)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene actin filament associated protein 1 like 1 Neighboring gene uncharacterized LOC124901103 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:148724745-148725370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:148725371-148725994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148726519-148727019 Neighboring gene GRPEL2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16496 Neighboring gene GrpE like 2, mitochondrial Neighboring gene Sharpr-MPRA regulatory region 12528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148746417-148747281 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148747282-148748145 Neighboring gene prenylcysteine oxidase 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148759103-148759637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148759990-148760702 Neighboring gene uncharacterized LOC101927046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148762129-148762840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148764726-148765226 Neighboring gene interleukin 17B Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148784456-148785046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148786897-148787897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148790014-148790554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148790555-148791094 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82102 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82107 Neighboring gene VISTA enhancer hs1752 Neighboring gene cardiac mesoderm enhancer-associated non-coding RNA Neighboring gene microRNA 143

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 16494
  • ATAC-STARR-seq lymphoblastoid silent region 16495

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_074188.1 

    Range
    101..395
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    149357806..149358100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    149892621..149892915
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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