U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC121832791 CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:45882374-45883573 [ Homo sapiens (human) ]

    Gene ID: 121832791, updated on 10-Oct-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC121832791
    Gene description
    CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:45882374-45883573
    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. A 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 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 15:Elon, transcription elongation, stronger H3K36me3, more exonic). The same subregion also displayed repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 15:Elon). [provided by RefSeq, Aug 2022]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC121832791 in Genome Data Viewer
    Location:
    11p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (45860823..45862252)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46016760..46018189)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45883509..45883803)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45792675-45793176 Neighboring gene long intergenic non-protein coding RNA 2716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4666 Neighboring gene solute carrier family 35 member C1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4669 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45869217-45869738 Neighboring gene Sharpr-MPRA regulatory region 9087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4671 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:45880664-45881863 Neighboring gene cryptochrome circadian regulator 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45887051-45887552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3290 Neighboring gene mitogen-activated protein kinase 8 interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45917073-45917944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45917945-45918814 Neighboring gene uncharacterized LOC124902668 Neighboring gene Sharpr-MPRA regulatory region 31 Neighboring gene Sharpr-MPRA regulatory region 10000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45927125-45927626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45927627-45928126 Neighboring gene Frey regulator of sperm-oocyte fusion 1

    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

    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

    • Sharpr-MPRA regulatory region 13574

    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_075881.2 

      Range
      101..1530
      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      45860823..45862252
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      46016760..46018189
      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