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LOC121587533 Sharpr-MPRA regulatory region 12181 [ Homo sapiens (human) ]

Gene ID: 121587533, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587533
Gene description
Sharpr-MPRA regulatory region 12181
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. 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 non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its 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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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (19130865..19131161)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (19061706..19062002)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (19142189..19142483)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19117151-19118009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7242 Neighboring gene ITPRIP like 2 Neighboring gene uncharacterized LOC124903657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7243 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19179399-19180146 Neighboring gene uncharacterized LOC124903658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19195968-19196784 Neighboring gene synaptotagmin 17 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:19204058-19204226 Neighboring gene C-type lectin domain containing 19A

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 active region 10528

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_074820.2 

    Range
    101..397
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    19130865..19131161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    19061706..19062002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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