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LOC126861716 BRD4-independent group 4 enhancer GRCh37_chr13:27909191-27910390 [ Homo sapiens (human) ]

Gene ID: 126861716, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126861716
Gene description
BRD4-independent group 4 enhancer GRCh37_chr13:27909191-27910390
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC126861716 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (27335054..27336759)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (26555816..26557521)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (27909191..27910896)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 Neighboring gene small nucleolar RNA, H/ACA box 27 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:27844429-27844929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5199 Neighboring gene RAS like family 11 member A Neighboring gene RNA, U6 small nuclear 70, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:27936491-27936992 Neighboring gene uncharacterized LOC105370126 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:27947836-27949035

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. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr13:27910205-27910896

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_086214.2 

    Range
    101..1806
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    27335054..27336759
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    26555816..26557521
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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