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LOC112577525 Sharpr-MPRA regulatory region 13804 [ Homo sapiens (human) ]

Gene ID: 112577525, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112577525
Gene description
Sharpr-MPRA regulatory region 13804
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion 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 unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also includes two accessible chromatin subregions that were validated as silencers based on their ability to repress 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 LOC112577525 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (2391550..2392585)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1830819..1831854)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2322989..2324024)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2246747-2247500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2253541-2254148 Neighboring gene MORN repeat containing 1 Neighboring gene small nuclear ribonucleoprotein polypeptide N pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2306674-2306868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 55 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 56 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2340121-2340621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2342650-2343230 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:2343231-2343811 to GRCh37_chr1:2344393-2344972 Neighboring gene retention in endoplasmic reticulum sorting receptor 1 Neighboring gene peroxisomal biogenesis factor 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2361610-2361787 Neighboring gene phospholipase C eta 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2377030-2377864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2378700-2379534 Neighboring gene Sharpr-MPRA regulatory region 13638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383066-2383714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383715-2384362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2423421-2423982 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:2430511-2431710

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. 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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 115
  • ATAC-STARR-seq lymphoblastoid silent region 116
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2323152-2324024

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_060444.2 

    Range
    101..1136
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    2391550..2392585
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    1830819..1831854
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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