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    Lrif1 ligand dependent nuclear receptor interacting factor 1 [ Mus musculus (house mouse) ]

    Gene ID: 321000, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Lrif1provided by MGI
    Official Full Name
    ligand dependent nuclear receptor interacting factor 1provided by MGI
    Primary source
    MGI:MGI:2445214
    See related
    Ensembl:ENSMUSG00000056260 AllianceGenome:MGI:2445214
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    2010012G17Rik; 4933421E11Rik
    Summary
    Predicted to enable nuclear retinoic acid receptor binding activity. Predicted to be involved in dosage compensation by inactivation of X chromosome. Located in Barr body. 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, Nov 2024]
    Expression
    Broad expression in testis adult (RPKM 5.9), bladder adult (RPKM 3.3) and 24 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lrif1 in Genome Data Viewer
    Location:
    3 F2.3; 3 46.52 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (106592256..106643893)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (106684942..106736577)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2010016I18 gene Neighboring gene STARR-seq mESC enhancer starr_08649 Neighboring gene DENN domain containing 2D Neighboring gene choline/ethanolaminephosphotransferase 1 Neighboring gene STARR-seq mESC enhancer starr_08650 Neighboring gene STARR-positive B cell enhancer ABC_E6102 Neighboring gene DNA-damage regulated autophagy modulator 2 Neighboring gene STARR-seq mESC enhancer starr_08651 Neighboring gene STARR-seq mESC enhancer starr_08652 Neighboring gene STARR-seq mESC enhancer starr_08653 Neighboring gene STARR-positive B cell enhancer ABC_E10205 Neighboring gene CD53 antigen Neighboring gene STARR-seq mESC enhancer starr_08654 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: 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. 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. Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes. Ostapcuk V, et al. Nature, 2018 May. PMID 29795351
    3. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article
    4. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Tanaka TS, et al. Proc Natl Acad Sci U S A, 2000 Aug 1. PMID 10922068, Free PMC Article
    5. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables nuclear retinoic acid receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Barr body ISO
    Inferred from Sequence Orthology
    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
    		  
    colocalizes_with 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

    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_001039478.1 → NP_001034567.1  ligand-dependent nuclear receptor-interacting factor 1 isoform 3

      See identical proteins and their annotated locations for NP_001034567.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, lacks a portion of the 5' coding region and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK008209, BE954122, DN174290
      Consensus CDS
      CCDS38586.1
      UniProtKB/TrEMBL
      G3X9P5
      Related
      ENSMUSP00000096347.4, ENSMUST00000098751.10
      Conserved Domains (1) summary
      pfam15741
      Location:17 → 255
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    2. NM_001039488.1 → NP_001034577.1  ligand-dependent nuclear receptor-interacting factor 1 isoform 1

      See identical proteins and their annotated locations for NP_001034577.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC117255, AK030201, AK048030, BB611412, BE954122, DN174290
      Consensus CDS
      CCDS17726.1
      UniProtKB/Swiss-Prot
      Q149J0, Q8C893, Q8CDD9
      Related
      ENSMUSP00000096346.3, ENSMUST00000098750.5
      Conserved Domains (1) summary
      pfam15741
      Location:26 → 753
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    3. NM_001286685.1 → NP_001273614.1  ligand-dependent nuclear receptor-interacting factor 1 isoform 2

      See identical proteins and their annotated locations for NP_001273614.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate exon in the 5' UTR, lacks an in-frame portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2 and 4 encode the same protein.
      Source sequence(s)
      AC117255, AK008209, AK030201, BE954122
      Consensus CDS
      CCDS17727.1
      UniProtKB/TrEMBL
      G5E8M8
      Conserved Domains (1) summary
      pfam15741
      Location:1 → 235
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    4. NM_028081.2 → NP_082357.2  ligand-dependent nuclear receptor-interacting factor 1 isoform 2

      See identical proteins and their annotated locations for NP_082357.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR, lacks an in-frame portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2 and 4 encode the same protein.
      Source sequence(s)
      AK008209, AK030201, BB611412, BB617106, BC094643, BE954122
      Consensus CDS
      CCDS17727.1
      UniProtKB/TrEMBL
      G5E8M8
      Related
      ENSMUSP00000102347.3, ENSMUST00000106736.3
      Conserved Domains (1) summary
      pfam15741
      Location:1 → 235
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      106592256..106643893
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017319616.3 → XP_017175105.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X3

      Conserved Domains (1) summary
      pfam15741
      Location:26 → 609
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    2. XM_036163134.1 → XP_036019027.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X1

      UniProtKB/Swiss-Prot
      Q149J0, Q8C893, Q8CDD9
      Conserved Domains (1) summary
      pfam15741
      Location:26 → 753
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    3. XM_006501581.5 → XP_006501644.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

      See identical proteins and their annotated locations for XP_006501644.1

      Conserved Domains (1) summary
      pfam15741
      Location:1 → 728
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    4. XM_036163135.1 → XP_036019028.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

      Conserved Domains (1) summary
      pfam15741
      Location:1 → 728
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    5. XM_011240140.3 → XP_011238442.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

      See identical proteins and their annotated locations for XP_011238442.1

      Conserved Domains (1) summary
      pfam15741
      Location:1 → 728
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    6. XM_036163136.1 → XP_036019029.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

      Conserved Domains (1) summary
      pfam15741
      Location:1 → 728
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    7. XM_006501584.5 → XP_006501647.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X4

      See identical proteins and their annotated locations for XP_006501647.1

      UniProtKB/TrEMBL
      G5E8M8
      Conserved Domains (1) summary
      pfam15741
      Location:1 → 235
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    RNA

    1. XR_003954331.2 RNA Sequence

    2. XR_003954332.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_177309.2: Suppressed sequence

      Description
      NM_177309.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CDD9.2 GenPept UniProtKB/Swiss-Prot:Q8CDD9

    Gene LinkOut

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