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LOC123566733 Sharpr-MPRA regulatory region 8612 [ Homo sapiens (human) ]

Gene ID: 123566733, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123566733
Gene description
Sharpr-MPRA regulatory region 8612
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 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141846104..141846398)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (142372057..142372351)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (141225669..141225963)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141137138-141137707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141137708-141138276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141138277-141138846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141141594-141142094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141166068-141166568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141166569-141167069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141174703-141175204 Neighboring gene uncharacterized LOC107986454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141191515-141192163 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141195215-141196206 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:141196207-141197197 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141202604-141203104 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141204908-141205596 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141218303-141219041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141226341-141227162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141227919-141228475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23313 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141229034-141229590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141243287-141243787 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:141244239-141244418 Neighboring gene protocadherin 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141252448-141253170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141256273-141256957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141257224-141257973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141262003-141262885 Neighboring gene glycine cleavage system protein H (aminomethyl carrier) pseudogene

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_077839.1 

    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
    141846104..141846398
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    142372057..142372351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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