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LOC121853006 Sharpr-MPRA regulatory region 2194 [ Homo sapiens (human) ]

Gene ID: 121853006, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853006
Gene description
Sharpr-MPRA regulatory region 2194
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This region also displayed repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive 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:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (43666909..43667319)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45400108..45400518)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42295549..42295843)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904906 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42285347-42285942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17905 Neighboring gene ribosomal protein L27a pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17906 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42306550-42307240 Neighboring gene MYB proto-oncogene like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17908 Neighboring gene MPRA-validated peak4221 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17909 Neighboring gene uncharacterized LOC101927200 Neighboring gene gametocyte specific factor 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42374309-42375128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42394850-42395350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42395351-42395851 Neighboring gene RNA, U6 small nuclear 639, pseudogene

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 12929

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_076114.2 

    Range
    101..511
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    43666909..43667319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    45400108..45400518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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