LOC108254679 BRD4-independent group 4 enhancer GRCh37_chr1:145455010-145456209 [Homo sapiens (human)] - Gene

Summary

Gene symbol: LOC108254679
Gene description: BRD4-independent group 4 enhancer GRCh37_chr1:145455010-145456209
Gene type: biological region
Feature type(s): misc_feature: CAGE_cluster
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 element is located in the intergenic region between the POLR3GL [polymerase (RNA) III subunit G like] and TXNIP (thioredoxin interacting protein) genes. A subregion was validated as an 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 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 defined as a low expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE), and was validated as an enhancer by reporter assays in both HeLa and HepG2 cells. Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes three accessible chromatin subregions that were validated as enhancers based on their 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

Location:: 1q21.1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (145978502..145980074)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (145095326..145096898)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (145455010..145456582, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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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

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General gene information

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Other Names

ATAC-STARR-seq lymphoblastoid active region 1623
ATAC-STARR-seq lymphoblastoid active region 1624
ATAC-STARR-seq lymphoblastoid active region 1625
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:145455817-145456582
POLR3GL-TXNIP intergenic CAGE-defined low expression enhancer
POLR3GL-TXNIP interval low CAGE FANTOM5 enhancer

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.