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LOC121627865 Sharpr-MPRA regulatory region 5939 [ Homo sapiens (human) ]

Gene ID: 121627865, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627865
Gene description
Sharpr-MPRA regulatory region 5939
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. A 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 K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). Another subregion was validated as an enhancer by the ChIP-STARR-seq MPRA in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. 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 ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18636699..18637466)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18771766..18772533)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18747509..18747803)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18724873-18725393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14329 Neighboring gene transmembrane protein 59 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18748277-18748791 Neighboring gene RNA, 7SL, cytoplasmic 155, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18758904-18759714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18759715-18760525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18762196-18762783 Neighboring gene kelch like family member 26 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18768110-18768641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18768642-18769172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18771679-18772215 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18783189-18783923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18806569-18807467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18810877-18811723 Neighboring gene CREB regulated transcription coactivator 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18820620-18821614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18859933-18860916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18878537-18879414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18879415-18880291 Neighboring gene Sharpr-MPRA regulatory region 9725 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18900694-18901273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18901274-18901854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18901855-18902433 Neighboring gene cartilage oligomeric matrix protein

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
  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 10415
  • H3K4me1 hESC enhancer GRCh37_chr19:18747762-18748276

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_075056.2 

    Range
    101..868
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    18636699..18637466
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18771766..18772533
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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