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LOC123575625 Sharpr-MPRA regulatory region 11389 [ Homo sapiens (human) ]

Gene ID: 123575625, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575625
Gene description
Sharpr-MPRA regulatory region 11389
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 unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123575625 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (174951146..174951440)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (175494419..175494713)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (174378149..174378443)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377742 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:174270439-174271000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:174328123-174328624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:174328625-174329124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174344229-174344968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174344969-174345708 Neighboring gene long intergenic non-protein coding RNA 1951 Neighboring gene NIFK pseudogene 2 Neighboring gene uncharacterized LOC107986484 Neighboring gene Sharpr-MPRA regulatory region 3886 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:174550039-174551238 Neighboring gene Sharpr-MPRA regulatory region 8865 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:174697681-174698880 Neighboring gene ADP ribosylation factor like GTPase 2 binding protein pseudogene 6

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_077884.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    174951146..174951440
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    175494419..175494713
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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