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LOC108663994 ES cell cis-regulatory motif 1d [ Mus musculus (house mouse) ]

Gene ID: 108663994, updated on 9-Aug-2024

Summary

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Gene symbol
LOC108663994
Gene description
ES cell cis-regulatory motif 1d
Gene type
biological region
Feature type(s)
misc_feature: conserved_region, nucleotide_motif
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
Rr366738
Summary
This genomic element is located in the 5' regulatory region of the Gnl3 [guanine nucleotide binding protein-like 3 (nucleolar)] gene on chromosome 14, and it also overlaps the Pbrm1 (polybromo 1) gene. A subregion was predicted to be a cis-regulatory sequence based on the presence of a CGTGACG motif through Comparative MobyDick (CompMoby) analysis, which identified conserved overrepresented motifs in genes upregulated in pluripotent cells. It was validated as a functional enhancer in both undifferentiated and differentiated mouse embryonic stem (ES) cells when two copies were used in a reporter construct driven by a heterologous thymidine kinase (TK) promoter. This locus also 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 (self-transcribing active regulatory region sequencing) in lipopolysaccharide-activated mouse splenic B cells. [provided by RefSeq, Oct 2023]
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Genomic context

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See LOC108663994 in Genome Data Viewer
Location:
14 B
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (30741513..30741839)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (31019827..31019882)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 24916 Neighboring gene small nucleolar RNA, C/D box 19 Neighboring gene guanine nucleotide binding protein nucleolar 3 Neighboring gene polybromo 1 Neighboring gene predicted gene 5459 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 5 Neighboring gene STARR-positive B cell enhancer ABC_E934

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. Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. Grskovic M, et al. PLoS Genet, 2007 Aug. PMID 17784790, Free PMC Article
  2. Gene regulatory networks STARR-ing B cells. Martínez de Paz A, et al. Nat Immunol, 2020 Feb. PMID 31873293, Free PMC Article
  3. Charting the cis-regulome of activated B cells by coupling structural and functional genomics. Chaudhri VK, et al. Nat Immunol, 2020 Feb. PMID 31873292

GeneRIFs: Gene References Into Functions

General gene information

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Other Names

  • STARR-positive B cell enhancer ABC_E5428
  • regulatory region 366738

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_051565.2 

    Range
    101..427
    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_000080.7 Reference GRCm39 C57BL/6J

    Range
    30741513..30741839
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Research Materials