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LOC128925216 CapStarr-seq enhancer MGSCv37_chr5:65397377-65397486 [ Mus musculus (house mouse) ]

Gene ID: 128925216, updated on 8-Feb-2024

Summary

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Gene symbol
LOC128925216
Gene description
CapStarr-seq enhancer MGSCv37_chr5:65397377-65397486
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
Summary
This genomic region was identified as a candidate cis-regulatory module (CRM) in developing mouse thymocytes based on a combination of DNase I hypersensitivity and transcription factor binding. It 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, Mar 2023]
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Genomic context

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See LOC128925216 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (65163481..65163590)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E1051 Neighboring gene toll-like receptor 1 Neighboring gene STARR-positive B cell enhancer ABC_E2745 Neighboring gene STARR-positive B cell enhancer ABC_E2158 Neighboring gene toll-like receptor 6 Neighboring gene family with sequence similarity 114, member A1 Neighboring gene microRNA 574 Neighboring gene STARR-seq mESC enhancer starr_13253 Neighboring gene STARR-seq mESC enhancer starr_13254 Neighboring gene predicted gene, 32374 Neighboring gene STARR-seq mESC enhancer starr_13256 Neighboring gene transmembrane protein 156 Neighboring gene STARR-seq mESC enhancer starr_13258 Neighboring gene STARR-seq mESC enhancer starr_13259 Neighboring gene kelch-like 5 Neighboring gene predicted gene, 54287

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

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_150930.1 

    Range
    101..210
    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_000071.7 Reference GRCm39 C57BL/6J

    Range
    65163481..65163590
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version