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LOC121587532 BRD4-independent group 4 enhancer GRCh37_chr16:15972689-15973888 [ Homo sapiens (human) ]

Gene ID: 121587532, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587532
Gene description
BRD4-independent group 4 enhancer GRCh37_chr16:15972689-15973888
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. A 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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (15878832..15880031)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (15883771..15884970)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15973329..15973623)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene myosin heavy chain 11 Neighboring gene uncharacterized LOC124903651 Neighboring gene Sharpr-MPRA regulatory region 5546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15901002-15901817 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15929109-15929286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15951931-15952432 Neighboring gene RNA, U6 small nuclear 213, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:15993095-15994294 Neighboring gene uncharacterized LOC107984869 Neighboring gene centrosomal protein 20 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:16018443-16018944 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:16036240-16036407 Neighboring gene ribosomal protein L15 pseudogene 20 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:16052042-16052542 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:16052543-16053043 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:16064032-16064671 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:16064672-16065310 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:16065311-16065950 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:16082729-16083392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:16084152-16084684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:16085217-16085748 Neighboring gene ATP binding cassette subfamily C member 1 (ABCC1 blood group) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:16085749-16086280 Neighboring gene Sharpr-MPRA regulatory region 4662 Neighboring gene Sharpr-MPRA regulatory region 7660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:16168601-16169318 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:16169319-16170035 Neighboring gene ribosomal protein L17 pseudogene 40

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. 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

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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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 12091

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_074819.2 

    Range
    101..1300
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    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    15878832..15880031
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1536827..1538026
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    15883771..15884970
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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