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LOC128927794 STARR-seq mESC enhancer starr_44331 [ Mus musculus (house mouse) ]

Gene ID: 128927794, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128927794
Gene description
STARR-seq mESC enhancer starr_44331
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
Rr370363
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 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. This locus additionally includes a B cell regulatory element that was identified by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and which was validated as an enhancer by STARR-seq in lipopolysaccharide-activated mouse splenic B cells. [provided by RefSeq, Oct 2023]
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Genomic context

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See LOC128927794 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 (38012502..38017570)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene protocadherin alpha 4B Neighboring gene predicted gene, 38666 Neighboring gene predicted gene, 38667 Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene STARR-seq mESC enhancer starr_44324 Neighboring gene protocadherin gamma subfamily B, 8 Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene STARR-seq mESC enhancer starr_44330 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene predicted gene, 29994 Neighboring gene STARR-seq mESC enhancer starr_44332 Neighboring gene STARR-positive B cell enhancer ABC_E8711 Neighboring gene microRNA 6979 Neighboring gene diaphanous related formin 1 Neighboring gene STARR-seq mESC enhancer starr_44334 Neighboring gene STARR-positive B cell enhancer ABC_E1953 Neighboring gene FCH and double SH3 domains 1 Neighboring gene histone deacetylase 3 Neighboring gene RELT-like 2

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

GeneRIFs: Gene References Into Functions

General gene information

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Other Names

  • CapStarr-seq enhancer MGSCv37_chr18:38043236-38043419
  • STARR-positive B cell enhancer ABC_E2506
  • regulatory region 370363

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_153403.2 

    Range
    101..5169
    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
    38012502..38017570
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version