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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

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