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LOC124421486 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:10680716-10681915 [ Homo sapiens (human) ]

Gene ID: 124421486, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124421486
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:10680716-10681915
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. 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 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 a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (10659169..10660368)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (10744038..10745237)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (10680969..10681263)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:10532526-10533436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4437 Neighboring gene ring finger protein 141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4438 Neighboring gene IRAG1 antisense RNA 1 Neighboring gene lymphatic vessel endothelial hyaluronan receptor 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:10615146-10616345 Neighboring gene inositol 1,4,5-triphosphate receptor associated 1 Neighboring gene Sharpr-MPRA regulatory regions 8950 and 14430 Neighboring gene MPRA-validated peak1195 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4441 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:10678394-10679593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10696121-10696708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10697483-10697984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4444 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10772162-10772662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4447 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:10785333-10786532 Neighboring gene CTR9 homolog, Paf1/RNA polymerase II complex component Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:10813405-10813954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:10813955-10814504 Neighboring gene eukaryotic translation initiation factor 4 gamma 2 Neighboring gene small nucleolar RNA, C/D box 97

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 9334

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_079175.2 

    Range
    101..1300
    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
    10659169..10660368
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    10744038..10745237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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