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LOC124153138 Sharpr-MPRA regulatory region 541 [ Homo sapiens (human) ]

Gene ID: 124153138, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124153138
Gene description
Sharpr-MPRA regulatory region 541
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 non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (30405153..30405447)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (30684931..30685225)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (30262669..30262963)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene tubulin beta pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:30241844-30242514 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:30242515-30243186 Neighboring gene RBPMS antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:30251401-30252099 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:30252799-30253496 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:30254895-30255593 Neighboring gene RNA binding protein, mRNA processing factor Neighboring gene heart enhancer 24 Neighboring gene uncharacterized LOC112268025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:30284105-30284606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:30284607-30285106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:30295211-30295746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:30303831-30304359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:30304360-30304887 Neighboring gene Sharpr-MPRA regulatory region 3907 Neighboring gene NANOG hESC enhancer GRCh37_chr8:30310384-30310885 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:30318783-30319578 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:30333285-30333476 Neighboring gene uncharacterized LOC124901929

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_078526.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    30405153..30405447
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    30684931..30685225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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