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LOC123230406 Sharpr-MPRA regulatory region 14309 [ Homo sapiens (human) ]

Gene ID: 123230406, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123230406
Gene description
Sharpr-MPRA regulatory region 14309
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 (160180482..160180776)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (162955079..162955373)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (159898269..159898563)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene IL12A antisense RNA 1 Neighboring gene uncharacterized LOC124906252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:159756960-159757562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159794247-159794746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159815928-159816428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159816429-159816929 Neighboring gene Sharpr-MPRA regulatory region 6612 Neighboring gene bromodomain containing 7 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:159896251-159896847 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:159896848-159897443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14854 Neighboring gene TRIM59-IFT80 readthrough (NMD candidate) Neighboring gene chromosome 3 open reading frame 80 Neighboring gene intraflagellar transport 80 Neighboring gene ribosomal protein L35a pseudogene 10

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_077348.1 

    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
    160180482..160180776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    162955079..162955373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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