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LOC113939987 Sharpr-MPRA regulatory region 11409 [ Homo sapiens (human) ]

Gene ID: 113939987, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939987
Gene description
Sharpr-MPRA regulatory region 11409
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 DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jan 2019]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (229430762..229431056)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (228809463..228809757)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (229566509..229566803)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 180, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229542759-229543724 Neighboring gene uncharacterized LOC124904541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229550455-229550955 Neighboring gene RN7SK pseudogene 276 Neighboring gene NANOG hESC enhancer GRCh37_chr1:229552218-229552719 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:229553351-229554106 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:229554107-229554860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229566843-229567462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229567463-229568084 Neighboring gene Sharpr-MPRA regulatory region 2214 Neighboring gene MPRA-validated peak754 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1929 Neighboring gene NANOG hESC enhancer GRCh37_chr1:229576278-229576818 Neighboring gene actin alpha 1, skeletal muscle Neighboring gene Sharpr-MPRA regulatory region 12306 Neighboring gene nucleoporin 133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2703

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_063766.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    229430762..229431056
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    228809463..228809757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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