U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116803647 CRISPRi-validated cis-regulatory element for Rcc1 and Trnau1ap [ Mus musculus (house mouse) ]

Gene ID: 116803647, updated on 8-Feb-2024

Summary

Go to the top of the page Help
Gene symbol
LOC116803647
Gene description
CRISPRi-validated cis-regulatory element for Rcc1 and Trnau1ap
Gene type
biological region
Feature type(s)
regulatory: 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
Rr366831
Summary
This genomic region overlaps the promoter of the Rcc1 (regulator of chromosome condensation 1) gene. In addition to being necessary for Rcc1 expression, it was validated as a negatively-acting cis-regulatory element for the neighboring Trnau1ap (tRNA selenocysteine 1 associated protein 1) gene based on CRISPR/Cas9-mediated perturbation (multiple sgRNA deletion method) in mouse embryonic stem cells. 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC116803647 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 (132072616..132073463)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (132345305..132346152)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA host gene 12 Neighboring gene small nucleolar RNA, C/D box 99 Neighboring gene tRNA selenocysteine 1 associated protein 1 Neighboring gene regulator of chromosome condensation 1 Neighboring gene small nucleolar RNA, H/ACA box 73b Neighboring gene small nucleolar RNA, H/ACA box 73a Neighboring gene small nucleolar RNA host gene 3

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Engreitz JM, et al. Nature, 2016 Nov 17. PMID 27783602, 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

GeneRIFs: Gene References Into Functions

General gene information

Go to the top of the page Help

Other Names

  • STARR-positive B cell enhancer ABC_E11258
  • regulatory region 366831

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_068054.1 

    Range
    101..948
    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
    132072616..132073463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Research Materials