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LOC123038195 Sharpr-MPRA regulatory region 4576 [ Homo sapiens (human) ]

Gene ID: 123038195, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123038195
Gene description
Sharpr-MPRA regulatory region 4576
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without 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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See LOC123038195 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (142022412..142022721)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (144769740..144770049)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (141741269..141741563)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATPase Na+/K+ transporting subunit beta 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:141623266-141623766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:141623767-141624267 Neighboring gene RNA, U6 small nuclear 509, pseudogene Neighboring gene uncharacterized LOC124909442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:141656589-141657435 Neighboring gene transcription factor Dp-2 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:141719615-141719808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14783 Neighboring gene NANOG hESC enhancer GRCh37_chr3:141747218-141747719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20640 Neighboring gene ribosomal protein L19 pseudogene 6 Neighboring gene RNA, U6 small nuclear 425, 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 active region 20639

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_077326.2 

    Range
    101..410
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    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    142022412..142022721
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    144769740..144770049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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