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LOC123038185 Sharpr-MPRA regulatory region 14374 [ Homo sapiens (human) ]

Gene ID: 123038185, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123038185
Gene description
Sharpr-MPRA regulatory region 14374
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Oct 2021]
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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 (133945085..133945379)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (136690246..136690540)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (133663929..133664223)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SRP receptor subunit beta Neighboring gene ReSE screen-validated silencer GRCh37_chr3:133554421-133554601 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:133558716-133559216 Neighboring gene RAB6B, member RAS oncogene family Neighboring gene NANOG hESC enhancer GRCh37_chr3:133573718-133574219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:133576178-133576792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:133661421-133662009 Neighboring gene chromosome 3 putative open reading frame 36 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:133667965-133668933 Neighboring gene solute carrier organic anion transporter family member 2A1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:133674467-133674998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:133674999-133675528 Neighboring gene Sharpr-MPRA regulatory region 8475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:133748764-133749264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:133774934-133775740 Neighboring gene uncharacterized LOC105374117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:133784850-133785350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:133786727-133787227 Neighboring gene long intergenic non-protein coding RNA 2000

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_077316.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    133945085..133945379
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    136690246..136690540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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