U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    LOC123477731 MED14-independent group 3 enhancer GRCh37_chr4:40311945-40313144 [ Homo sapiens (human) ]

    Gene ID: 123477731, updated on 10-Oct-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC123477731
    Gene description
    MED14-independent group 3 enhancer GRCh37_chr4:40311945-40313144
    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 STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells, where it was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both are marked by the H3K27ac histone modification and one is additionally associated with the NANOG transcription factor. Another subregion was validated as a functional 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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Oct 2022]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC123477731 in Genome Data Viewer
    Location:
    4p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (40309292..40311127)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (40282971..40284806)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (40311309..40311603)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900183 Neighboring gene NEDD4 binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40140819-40141412 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40149211-40149992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21473 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21480 Neighboring gene ras homolog family member H Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21481 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40239787-40240778 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:40252200-40253399 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40259652-40260430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40270986-40271804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40271805-40272621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40318591-40319429 Neighboring gene long intergenic non-protein coding RNA 2265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21489 Neighboring gene cholinergic receptor nicotinic alpha 9 subunit Neighboring gene RNA, U7 small nuclear 74 pseudogene

    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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
    2. 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
    3. 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

    • H3K27ac hESC enhancer GRCh37_chr4:40312015-40312653
    • NANOG-H3K27ac hESC enhancer GRCh37_chr4:40311376-40312014
    • Sharpr-MPRA regulatory region 8605

    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_077534.2 

      Range
      101..1936
      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      40309292..40311127
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      40282971..40284806
      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