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LOC123775383 Sharpr-MPRA regulatory region 14578 [ Homo sapiens (human) ]

Gene ID: 123775383, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123775383
Gene description
Sharpr-MPRA regulatory region 14578
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (89927810..89928104)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (91139499..91139793)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (90637529..90637823)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:90596851-90597424 Neighboring gene MPRA-validated peak5956 silencer Neighboring gene G protein pathway suppressor 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:90620440-90621084 Neighboring gene gap junction protein alpha 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:90644322-90644822 Neighboring gene BTB domain and CNC homolog 2 Neighboring gene RN7SK pseudogene 110 Neighboring gene Sharpr-MPRA regulatory region 1684 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90866227 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:90866333-90867532 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90883525 Neighboring gene uncharacterized LOC105377890 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:90894000-90895199

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_078151.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    89927810..89928104
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017363815.1 Reference GRCh38.p14 PATCHES

    Range
    125498..125792
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    91139499..91139793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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