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LOC125078059 Sharpr-MPRA regulatory region 4108 [ Homo sapiens (human) ]

Gene ID: 125078059, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078059
Gene description
Sharpr-MPRA regulatory region 4108
Gene type
biological region
Feature type(s)
regulatory: 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 a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its 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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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (38251248..38251542)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (36056547..36056831)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene transmembrane and coiled-coil domains 5A Neighboring gene long intergenic non-protein coding RNA 2345 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:38364669-38365534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6298 Neighboring gene long intergenic non-protein coding RNA 1852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6304 Neighboring gene MPRA-validated peak2297 silencer Neighboring gene sprouty related EVH1 domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:38679220-38679403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9203 Neighboring gene CTD small phosphatase 2 pseudogene Neighboring gene family with sequence similarity 98 member B

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 6299

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_080195.1 

    Range
    101..395
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    38251248..38251542
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    36056547..36056831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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