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LOC123038182 Sharpr-MPRA regulatory region 7150 [ Homo sapiens (human) ]

Gene ID: 123038182, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123038182
Gene description
Sharpr-MPRA regulatory region 7150
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC123038182 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (131819685..131819979)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (134563502..134563796)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (131538529..131538823)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:131221451-131222137 Neighboring gene uncharacterized LOC105374114 Neighboring gene mitochondrial ribosomal protein L3 Neighboring gene BCL2 like 12 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14738 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:131287110-131287684 Neighboring gene copine 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20534 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:131515358-131515894 Neighboring gene uncharacterized LOC105374113 Neighboring gene NANOG hESC enhancer GRCh37_chr3:131633036-131633560 Neighboring gene NANOG hESC enhancer GRCh37_chr3:131716699-131717322 Neighboring gene uncharacterized LOC124906288 Neighboring gene microRNA 5704

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_077313.1 

    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
    131819685..131819979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    134563502..134563796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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