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LOC124625878 Sharpr-MPRA regulatory region 3814 [ Homo sapiens (human) ]

Gene ID: 124625878, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625878
Gene description
Sharpr-MPRA regulatory region 3814
Gene type
biological region
Feature type(s)
regulatory: 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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). 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:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (1630369..1630677)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (1626743..1627051)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5803 Neighboring gene F-box and leucine rich repeat protein 14 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:1697008-1697667 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1701701-1702304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1715019-1715538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1714497-1715018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5808 Neighboring gene Wnt family member 5B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1755758-1756258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1756259-1756759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4118 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5809 Neighboring gene microRNA 3649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5811 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:1800052-1800630 Neighboring gene SDA1 domain containing 1 pseudogene Neighboring gene adiponectin receptor 2

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 4117

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_079478.2 

    Range
    101..409
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    1630369..1630677
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    1626743..1627051
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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