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LOC123575627 Sharpr-MPRA regulatory region 8396 [ Homo sapiens (human) ]

Gene ID: 123575627, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575627
Gene description
Sharpr-MPRA regulatory region 8396
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123575627 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 (175604166..175604460)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (176147945..176148239)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (175031169..175031463)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16644 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr5:174905945-174906540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174911541-174912114 Neighboring gene sideroflexin 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:174943953-174945152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174960972-174961510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174967065-174967566 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:174974284-174975206 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:174988020-174988638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175023214-175023754 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:175044235-175044430 Neighboring gene RN7SK pseudogene 148 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:175065813-175066006 Neighboring gene NANOG hESC enhancer GRCh37_chr5:175076996-175077520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:175090952-175091530 Neighboring gene histamine receptor H2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:175113560-175114280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:175114281-175115000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175115001-175115720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175115721-175116440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175117667-175118168 Neighboring gene uncharacterized LOC105377743 Neighboring gene Sharpr-MPRA regulatory region 12912

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_077886.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    175604166..175604460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    176147945..176148239
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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