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    Lrif1 ligand dependent nuclear receptor interacting factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310775, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Lrif1provided by RGD
    Official Full Name
    ligand dependent nuclear receptor interacting factor 1provided by RGD
    Primary source
    RGD:1306520
    See related
    EnsemblRapid:ENSRNOG00000017784 AllianceGenome:RGD:1306520
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1306520
    Summary
    Predicted to enable nuclear retinoic acid receptor binding activity. Predicted to be involved in dosage compensation by inactivation of X chromosome. Predicted to be located in centriolar satellite; chromosome, telomeric region; and nuclear lumen. Human ortholog(s) of this gene implicated in facioscapulohumeral muscular dystrophy 3. Orthologous to human LRIF1 (ligand dependent nuclear receptor interacting factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 92.7), Thymus (RPKM 80.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lrif1 in Genome Data Viewer
    Location:
    2q34
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (196919606..197010713)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (194231397..194322489)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (209358668..209448123)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene choline/ethanolamine phosphotransferase 1 Neighboring gene DNA damage regulated autophagy modulator 2 Neighboring gene uncharacterized LOC134485947 Neighboring gene uncharacterized LOC120100909 Neighboring gene Cd53 molecule Neighboring gene olfactory receptor family 11 subfamily I member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Independent Mechanisms Target SMCHD1 to Trimethylated Histone H3 Lysine 9-Modified Chromatin and the Inactive X Chromosome. Brideau NJ, et al. Mol Cell Biol, 2015 Dec. PMID 26391951, Free PMC Article
    2. Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway. Nozawa RS, et al. Nat Struct Mol Biol, 2013 May. PMID 23542155
    3. A quantitative telomeric chromatin isolation protocol identifies different telomeric states. Grolimund L, et al. Nat Commun, 2013. PMID 24270157
    4. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs RA, et al. Nature, 2004 Apr 1. PMID 15057822
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables nuclear retinoic acid receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in dosage compensation by inactivation of X chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dosage compensation by inactivation of X chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in dosage compensation by inactivation of X chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Barr body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Barr body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Barr body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in centriolar satellite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centriolar satellite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, telomeric region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ligand-dependent nuclear receptor-interacting factor 1
    Names
    receptor interacting factor 1

    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.

    mRNA and Protein(s)

    1. NM_001127485.1 → NP_001120957.1  ligand-dependent nuclear receptor-interacting factor 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/Swiss-Prot
      Q499M7
      UniProtKB/TrEMBL
      F1LMD4
      Related
      ENSRNOP00000024036.5, ENSRNOT00000024036.7
      Conserved Domains (1) summary
      pfam15741
      Location:26 → 747
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      196919606..197010713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006233147.5 → XP_006233209.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JZ59, B0BNF2
      Related
      ENSRNOP00000094264.2, ENSRNOT00000098808.2
      Conserved Domains (1) summary
      pfam15741
      Location:17 → 252
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    2. XM_039102422.2 → XP_038958350.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X1

      UniProtKB/TrEMBL
      A6HUR4
      Conserved Domains (1) summary
      pfam15741
      Location:26 → 511
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q499M7.2 GenPept UniProtKB/Swiss-Prot:Q499M7

    Gene LinkOut

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

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