U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123924893 Sharpr-MPRA regulatory region 9979 [ Homo sapiens (human) ]

Gene ID: 123924893, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123924893
Gene description
Sharpr-MPRA regulatory region 9979
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 histone modification. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC123924893 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (4630755..4631932)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (4747920..4749095)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (4671269..4671563)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375133 Neighboring gene MPRA-validated peak6348 silencer Neighboring gene endogenous retrovirus group K member 6 Env polyprotein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4643917-4644418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17897 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:4704492-4704666 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:4720927-4721427 Neighboring gene Sharpr-MPRA regulatory region 11841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4722783-4723310 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4739232-4739732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4742083-4742842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4744443-4745084 Neighboring gene forkhead box K1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4745727-4746368 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4746369-4747010 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4747011-4747652 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4747653-4748294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4748937-4749577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4750899-4751431 Neighboring gene uncharacterized LOC124901581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4763724-4764310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25560

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • NANOG-H3K4me1 hESC enhancer GRCh37_chr7:4670386-4671364

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_078285.2 

    Range
    101..1278
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    4630755..4631932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    4747920..4749095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases