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LOC128927814 STARR-seq mESC enhancer starr_44732 [ Mus musculus (house mouse) ]

Gene ID: 128927814, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128927814
Gene description
STARR-seq mESC enhancer starr_44732
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Rr370382
Summary
This genomic region represents an enhancer that was validated by the STARR-seq (self-transcribing active regulatory region sequencing) reporter assay in ground-state (2iL) and metastable (SL) mouse embryonic stem cells, where it was defined as a C1 class enhancer that overlaps an active chromatin signature. This locus also includes two candidate cis-regulatory modules (CRMs) that were identified in developing mouse thymocytes based on a combination of DNase I hypersensitivity and transcription factor binding. Those CRMs were validated as active enhancers by high-throughput CapStarr-seq reporter assays, with both having strong activity in NIH3T3 fibroblasts, and one additionally having weak activity in P5424 T cells. [provided by RefSeq, Jul 2023]
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Genomic context

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See LOC128927814 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (60974253..60977404)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene 40S ribosomal protein S16 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E2509 Neighboring gene STARR-positive B cell enhancer ABC_E1960 Neighboring gene STARR-positive B cell enhancer ABC_E2510 Neighboring gene STARR-positive B cell enhancer ABC_E8719 Neighboring gene CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated) Neighboring gene microRNA 5107 Neighboring gene treacle ribosome biogenesis factor 1 Neighboring gene STARR-positive B cell enhancer ABC_E3230 Neighboring gene predicted gene, 41744 Neighboring gene CapStarr-seq enhancer MGSCv37_chr18:61036982-61037190 Neighboring gene CapStarr-seq enhancer MGSCv37_chr18:61044121-61044304 Neighboring gene predicted gene, 41745

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. STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells. Peng T, et al. Genome Biol, 2020 Sep 10. PMID 32912294, Free PMC Article
  2. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Vanhille L, et al. Nat Commun, 2015 Apr 15. PMID 25872643

GeneRIFs: Gene References Into Functions

General gene information

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Other Names

  • CapStarr-seq enhancer MGSCv37_chr18:61003555-61003738
  • CapStarr-seq enhancer MGSCv37_chr18:61003794-61003947
  • regulatory region 370382

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_153423.2 

    Range
    101..3252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000084.7 Reference GRCm39 C57BL/6J

    Range
    60974253..60977404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version