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LOC116915294 CRISPRi-validated Tdgf1 proximal enhancer [ Mus musculus (house mouse) ]

Gene ID: 116915294, updated on 8-Feb-2024

Summary

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Gene symbol
LOC116915294
Gene description
CRISPRi-validated Tdgf1 proximal enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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
Rr366852
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 putative enhancer in the 5'-proximal region of the Tdgf1 (teratocarcinoma-derived growth factor 1) gene on chromosome 9. That subregion was validated as a positively-acting cis-regulatory element for Tdgf1 based on CRISPR/Cas9-mediated perturbation (multiplexed editing regulatory assay with target gene GFP knock-in) in mouse embryonic stem cells. [provided by RefSeq, Jul 2023]
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Genomic context

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See LOC116915294 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (110774032..110777712)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (110947851..110947915)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene ALS2 C-terminal like Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:110810109-110810292 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:110810303-110810412 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:110810673-110810995 Neighboring gene family with sequence similarity 240 member A Neighboring gene cripto, EGF-CFC family member Neighboring gene leucine rich repeat containing 2 Neighboring gene predicted gene 10030 Neighboring gene receptor transporter protein 3

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 mapping of regulatory DNA. Rajagopal N, et al. Nat Biotechnol, 2016 Feb. PMID 26807528, Free PMC Article
  2. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, Free PMC Article
  3. 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

  • STARR-seq mESC enhancer starr_25276
  • regulatory region 366852

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_068093.2 

    Range
    101..3781
    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_000075.7 Reference GRCm39 C57BL/6J

    Range
    110774032..110777712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Research Materials