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LOC121967053 Sharpr-MPRA regulatory region 1516 [ Homo sapiens (human) ]

Gene ID: 121967053, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121967053
Gene description
Sharpr-MPRA regulatory region 1516
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121967053 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (5415689..5415983)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (4938086..4938380)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (5475749..5476043)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2782 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:5178470-5179138 Neighboring gene uncharacterized LOC105376682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5203113-5203613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5217254-5217754 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5285469-5286066 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5286067-5286664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5371655-5372156 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:5408560-5409759 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:5448514-5449713 Neighboring gene uncharacterized LOC124904590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5487427-5487926 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:5489955-5491154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5510651-5511489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5511490-5512327 Neighboring gene uncharacterized LOC107984911

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_076193.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    5415689..5415983
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    4938086..4938380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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