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LOC123256950 Sharpr-MPRA regulatory region 5391 [ Homo sapiens (human) ]

Gene ID: 123256950, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123256950
Gene description
Sharpr-MPRA regulatory region 5391
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. A subregion was validated as a functional repressive element by Sharpr-MPRA (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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). An overlapping subregion was identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 cells. [provided by RefSeq, Apr 2023]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (177652847..177653255)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (180455808..180456216)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (177370749..177371043)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 578 Neighboring gene uncharacterized LOC124906306 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:177301340-177301507 Neighboring gene MPRA-validated peak4935 silencer Neighboring gene MPRA-validated peak4936 silencer Neighboring gene Sharpr-MPRA regulatory region 14869 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:177324712-177324912 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:177327959-177328599 Neighboring gene small nucleolar RNA SNORA18 Neighboring gene NANOG hESC enhancer GRCh37_chr3:177383662-177384200 Neighboring gene fibroblast growth factor receptor 3 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177543728-177544228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:177544229-177544729 Neighboring gene long intergenic non-protein coding RNA 2015

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article
  2. 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)

General gene information

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Other Names

  • MPRA-validated peak4940 silencer

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_077368.2 

    Range
    101..509
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    177652847..177653255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    180455808..180456216
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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