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LOC123924897 Sharpr-MPRA regulatory region 1711 [ Homo sapiens (human) ]

Gene ID: 123924897, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123924897
Gene description
Sharpr-MPRA regulatory region 1711
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123924897 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (5869098..5869392)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (5986849..5987143)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (5908729..5909023)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ring finger protein 216 Neighboring gene microRNA 6874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5775501-5776002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5776003-5776502 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5871051-5871551 Neighboring gene zinc finger protein 815, pseudogene Neighboring gene RNA, 7SL, cytoplasmic 556, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25613 Neighboring gene oncomodulin Neighboring gene nonconserved acetylation island sequence 61 enhancer Neighboring gene CCZ1 homolog, vacuolar protein trafficking and biogenesis associated Neighboring gene radial spoke head 10 homolog B

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_078289.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    5869098..5869392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    5986849..5987143
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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