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LOC123002328 Sharpr-MPRA regulatory region 5857 [ Homo sapiens (human) ]

Gene ID: 123002328, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123002328
Gene description
Sharpr-MPRA regulatory region 5857
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. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 24:Quies). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC123002328 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 (108386202..108386496)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (111105993..111106287)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (108105049..108105343)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr3:107941185-107941478 Neighboring gene uncharacterized LOC124909405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14596 Neighboring gene HHLA2 member of B7 family Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 17 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:108095636-108096835 Neighboring gene uncharacterized LOC124900545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20221 Neighboring gene myosin heavy chain 15 Neighboring gene uncharacterized LOC124909406 Neighboring gene ribosomal protein L13 pseudogene 8

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

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)

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_077285.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    108386202..108386496
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    111105993..111106287
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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