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LOC128925118 STARR-seq mESC enhancer starr_11747 [ Mus musculus (house mouse) ]

Gene ID: 128925118, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128925118
Gene description
STARR-seq mESC enhancer starr_11747
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
Rr367755
Summary
This genomic region includes 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 three 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 all three having weak activity in P5424 T cells, and two additionally having weak activity in NIH3T3 fibroblasts. [provided by RefSeq, Jul 2023]
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Genomic context

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See LOC128925118 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (135904451..135906162)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E4687 Neighboring gene STARR-seq mESC enhancer starr_11745 Neighboring gene predicted gene, 42329 Neighboring gene inhibitor of DNA binding 3 Neighboring gene STARR-positive B cell enhancer ABC_E10267 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:135727983-135728166 Neighboring gene STARR-positive B cell enhancer ABC_E3530 Neighboring gene STARR-positive B cell enhancer ABC_E6237 Neighboring gene STARR-positive B cell enhancer ABC_E427 Neighboring gene E2F transcription factor 2 Neighboring gene STARR-seq mESC enhancer starr_11748 Neighboring gene STARR-seq mESC enhancer starr_11749 Neighboring gene ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 Neighboring gene STARR-seq mESC enhancer starr_11750 Neighboring gene transcription elongation factor A (SII), 3 Neighboring gene STARR-positive B cell enhancer ABC_E9604

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_chr4:135733055-135733263
  • CapStarr-seq enhancer MGSCv37_chr4:135733290-135733529
  • CapStarr-seq enhancer MGSCv37_chr4:135733652-135733916
  • regulatory region 367755

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_150838.2 

    Range
    101..1812
    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_000070.7 Reference GRCm39 C57BL/6J

    Range
    135904451..135906162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version