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LOC123464490 Sharpr-MPRA regulatory region 5455 [ Homo sapiens (human) ]

Gene ID: 123464490, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123464490
Gene description
Sharpr-MPRA regulatory region 5455
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123464490 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 (193781220..193781514)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (196477859..196478153)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (193499009..193499303)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21007 Neighboring gene RNA, 7SL, cytoplasmic 447, pseudogene Neighboring gene uncharacterized LOC105374282 Neighboring gene VISTA enhancer hs1563 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15010 Neighboring gene uncharacterized LOC105374283 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:193509438-193510095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193513397-193513898 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:193530149-193531058 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:193532881-193533792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193536592-193537220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193537221-193537848 Neighboring gene uncharacterized LOC105374284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21010

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_077475.1 

    Range
    101..395
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    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
    193781220..193781514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    196477859..196478153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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