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LOC123493216 Sharpr-MPRA regulatory region 13510 [ Homo sapiens (human) ]

Gene ID: 123493216, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123493216
Gene description
Sharpr-MPRA regulatory region 13510
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 DNase matched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123493216 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (150337817..150338111)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (153661667..153661961)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (151258969..151259263)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1230, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14262 Neighboring gene VISTA enhancer hs1614 Neighboring gene doublecortin like kinase 2 Neighboring gene RNA, U7 small nuclear 194 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:151209299-151209799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22014 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:151287541-151288222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:151288223-151288903 Neighboring gene LPS responsive beige-like anchor protein Neighboring gene nei like DNA glycosylase 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 5429 Neighboring gene uncharacterized LOC729558

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_077640.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    150337817..150338111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    153661667..153661961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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