LOC111828517 Sharpr-MPRA regulatory regions 1971 and 3941 [Homo sapiens (human)] - Gene

Summary

Gene symbol: LOC111828517
Gene description: Sharpr-MPRA regulatory regions 1971 and 3941
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, which overlaps the promoter and 5' region of the RAB28 (RAB28, member RAS oncogene family) gene on chromosome 4, was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. This region also contains two overlapping subregions, one of which was validated as an enhancer 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 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss). The other subregion displayed weak repressive activity by Sharpr-MPRA in K562 cells (group: K562 Repressive DNase matched - State 1:Tss). This locus also includes three accessible chromatin subregions, two of which were validated as silencers and one as an enhancer based on their ability to repress or 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:: 4p

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (13483872..13485222)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (13463555..13464905)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (13485496..13486846)

Chromosome 4 - NC_000004.12 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

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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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General gene information

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Other Names

ATAC-STARR-seq lymphoblastoid active region 21324
ATAC-STARR-seq lymphoblastoid silent region 15284
ATAC-STARR-seq lymphoblastoid silent region 15285
H3K27ac hESC enhancer GRCh37_chr4:13485939-13486846
Sharpr-MPRA regulatory region 1971
Sharpr-MPRA regulatory region 3941

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.