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Firre functional intergenic repeating RNA element [ Mus musculus (house mouse) ]

Gene ID: 103012, updated on 9-May-2024

Summary

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Official Symbol
Firreprovided by MGI
Official Full Name
functional intergenic repeating RNA elementprovided by MGI
Primary source
MGI:MGI:2147989
See related
Ensembl:ENSMUSG00000085396 AllianceGenome:MGI:2147989
Gene type
ncRNA
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
5830467J12Rik; 6720401G13Rik
Summary
This gene produces a long non-coding RNA that is localized to the nuclear matrix. This RNA contains repeated sequence motifs that mediate interactions with heterogeneous nuclear ribonucleoprotein U (hnRNPU). Loss of expression of this locus disrupts three-dimensional chromosomal associations. Alternative splicing results in multiple splice variants, though the full length nature of these variants is not known. [provided by RefSeq, Mar 2015]
Expression
Ubiquitous expression in bladder adult (RPKM 35.5), limb E14.5 (RPKM 28.4) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Firre in Genome Data Viewer
Location:
X A5; X 26.53 cM
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (49651997..49724198, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (50563120..50635321, complement)

Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_47139 Neighboring gene STARR-seq mESC enhancer starr_47140 Neighboring gene STARR-seq mESC enhancer starr_47141 Neighboring gene olfactory receptor family 1 subfamily AA member 2 Neighboring gene STARR-seq mESC enhancer starr_47143 Neighboring gene STARR-seq mESC enhancer starr_47144 Neighboring gene predicted gene, 35612 Neighboring gene STARR-seq mESC enhancer starr_47145 Neighboring gene STARR-seq mESC enhancer starr_47146 Neighboring gene predicted gene 14620 Neighboring gene STARR-seq mESC enhancer starr_47148 Neighboring gene STARR-seq mESC enhancer starr_47149 Neighboring gene STARR-seq mESC enhancer starr_47152 Neighboring gene STARR-seq mESC enhancer starr_47153 Neighboring gene STARR-seq mESC enhancer starr_47154 Neighboring gene serine/threonine kinase 26 Neighboring gene STARR-seq mESC enhancer starr_47158 Neighboring gene FERM domain containing 7 Neighboring gene STARR-seq mESC enhancer starr_47159 Neighboring gene RAP2C, member of RAS oncogene family

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Fang H, et al. Nat Commun, 2020 Nov 27. PMID 33247132, Free PMC Article
  2. The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Lewandowski JP, et al. Nat Commun, 2019 Nov 13. PMID 31723143, Free PMC Article
  3. Downregulation of lncRNA FIRRE relieved the neuropathic pain of female mice by suppressing HMGB1 expression. Wen Y, et al. Mol Cell Biochem, 2021 Feb. PMID 33151463
  4. In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation. Andergassen D, et al. Elife, 2019 Nov 18. PMID 31738164, Free PMC Article
  5. Regulatory networks of non-coding RNAs in brown/beige adipogenesis. Xu S, et al. Biosci Rep, 2015 Aug 17. PMID 26283634, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Downregulation of lncRNA FIRRE relieved the neuropathic pain of female mice by suppressing HMGB1 expression.
    Title: Downregulation of lncRNA FIRRE relieved the neuropathic pain of female mice by suppressing HMGB1 expression.
  2. Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome.
    Title: Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome.
  3. examined the in vivo contribution of these loci by generating mice carrying a single or double deletion of Firre and Dxz4. We found that these mutants are viable, fertile and show no defect in random or imprinted X-chromosome inactivation
    Title: In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation.
  4. the Firre locus produces a trans-acting long noncoding RNA that has physiological roles in hematopoiesis.
    Title: The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis.
  5. neither the deletion of the CTCF locus nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter topologically associated domains in a sex-specific or allele-specific manner
    Title: A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus.
  6. Firre is X-linked and expressed from a macrosatellite repeat locus associated with a cluster of CTCF and cohesin binding sites, and is preferentially located adjacent to the nucleolus
    Title: The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

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.

RNA

  1. NR_015505.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AK030946, AK032694, BC066100, BP762728, BU704013, CJ052235
    Related
    ENSMUST00000203933.3

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_000086.8 Reference GRCm39 C57BL/6J

    Range
    49651997..49724198 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_026976.1: Suppressed sequence

    Description
    NR_026976.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
Nucleotide Protein Strain
Heading Accession and Version

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Molecular Biology Databases