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LOC123620061 Sharpr-MPRA regulatory region 5392 [ Homo sapiens (human) ]

Gene ID: 123620061, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123620061
Gene description
Sharpr-MPRA regulatory region 5392
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 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123620061 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (16071798..16072092)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15944001..15944295)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (16072029..16072323)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374949 Neighboring gene Sharpr-MPRA regulatory region 8871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24095 Neighboring gene Sharpr-MPRA regulatory region 12955 Neighboring gene long intergenic non-protein coding RNA 2543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16954 Neighboring gene CRISPRi-validated cis-regulatory element chr6.836 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:16064773-16065514 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:16065515-16066255 Neighboring gene MDH1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24096 Neighboring gene myosin regulatory light chain interacting protein Neighboring gene microRNA 4639

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_077943.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    16071798..16072092
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15944001..15944295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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