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LOC128927427 STARR-seq mESC enhancer starr_39650 [ Mus musculus (house mouse) ]

Gene ID: 128927427, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128927427
Gene description
STARR-seq mESC enhancer starr_39650
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
Rr370005
Summary
This genomic region represents an enhancer that was validated by the STARR-seq (self-transcribing active regulatory region sequencing) reporter assay in 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 a candidate cis-regulatory module (CRM) that was identified in developing mouse thymocytes based on a combination of DNase I hypersensitivity and transcription factor binding. That CRM was validated as an active enhancer by high-throughput CapStarr-seq reporter assays showing weak activity in P5424 T cells and NIH3T3 fibroblasts. [provided by RefSeq, Jul 2023]
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Genomic context

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See LOC128927427 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (97990586..97991658)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 41395 Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:97898039-97898148 Neighboring gene predicted gene, 25668 Neighboring gene STARR-seq mESC enhancer starr_39649 Neighboring gene STARR-positive B cell enhancer ABC_E10879 Neighboring gene STARR-positive B cell enhancer ABC_E5514 Neighboring gene phosphofructokinase, muscle Neighboring gene STARR-seq mESC enhancer starr_39651 Neighboring gene STARR-seq mESC enhancer starr_39652 Neighboring gene ankyrin repeat and SOCS box-containing 8 Neighboring gene STARR-seq mESC enhancer starr_39654 Neighboring gene STARR-positive B cell enhancer ABC_E5515 Neighboring gene coiled-coil domain containing 184

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. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Vanhille L, et al. Nat Commun, 2015 Apr 15. PMID 25872643
  2. 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

GeneRIFs: Gene References Into Functions

General gene information

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Other Names

  • CapStarr-seq enhancer MGSCv37_chr15:97923720-97923907
  • regulatory region 370005

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_153057.2 

    Range
    101..1173
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    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_000081.7 Reference GRCm39 C57BL/6J

    Range
    97990586..97991658
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version