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LOC123575618 Sharpr-MPRA regulatory region 3838 [ Homo sapiens (human) ]

Gene ID: 123575618, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575618
Gene description
Sharpr-MPRA regulatory region 3838
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 DNase matched - State 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr). [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 (172550906..172551200)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (173090786..173091080)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (171977909..171978203)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171762901-171763762 Neighboring gene SH3 and PX domains 2B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:171788418-171789617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23637 Neighboring gene MPRA-validated peak5578 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171839705-171840206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171845006-171845982 Neighboring gene Sharpr-MPRA regulatory region 10478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171858257-171858757 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:171859347-171859604 Neighboring gene Sharpr-MPRA regulatory region 6627 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171880495-171881016 Neighboring gene uncharacterized LOC105377727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171906087-171906708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171906709-171907328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171911421-171911922 Neighboring gene uncharacterized LOC107984004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23638 Neighboring gene long intergenic non-protein coding RNA 1944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172002783-172003530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172011659-172012159 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:172022507-172023006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172023946-172024868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172029510-172030088 Neighboring gene uncharacterized LOC105377729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172043624-172044540

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_077877.1 

    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
    172550906..172551200
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    173090786..173091080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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