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LOC126806833 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:144156282-144157481 [ Homo sapiens (human) ]

Gene ID: 126806833, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806833
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:144156282-144157481
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 region was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. A subregion was also validated as an enhancer by ChIP-STARR-seq in naive and primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC126806833 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (144437440..144438639)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (147183970..147185169)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:143690552-143691132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20663 Neighboring gene divergent protein kinase domain 2A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20665 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:143856144-143856657 Neighboring gene uncharacterized LOC105374140 Neighboring gene RNA, 5S ribosomal pseudogene 144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20670 Neighboring gene uncharacterized LOC124909444 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:144578047-144578587 Neighboring gene uncharacterized LOC105374141

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 20671
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:144156543-144157174

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_083153.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    144437440..144438639
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    147183970..147185169
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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