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    LRIF1 ligand dependent nuclear receptor interacting factor 1 [ Homo sapiens (human) ]

    Gene ID: 55791, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LRIF1provided by HGNC
    Official Full Name
    ligand dependent nuclear receptor interacting factor 1provided by HGNC
    Primary source
    HGNC:HGNC:30299
    See related
    Ensembl:ENSG00000121931 MIM:615354; AllianceGenome:HGNC:30299
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RIF1; FSHD3; HBiX1; C1orf103
    Summary
    Predicted to enable nuclear retinoic acid receptor binding activity. Involved in dosage compensation by inactivation of X chromosome. Located in centriolar satellite; chromosome, telomeric region; and nuclear lumen. Implicated in facioscapulohumeral muscular dystrophy 3. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 11.6), ovary (RPKM 5.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRIF1 in Genome Data Viewer
    Location:
    1p13.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (110874957..110963922, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (110888014..110978737, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (111489812..111506544, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear receptor binding factor 2 pseudogene 3 Neighboring gene olfactory receptor family 11 subfamily I member 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1478 Neighboring gene Sharpr-MPRA regulatory region 4566 Neighboring gene CD53 molecule Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:111506132-111506668 Neighboring gene cyclin T2 pseudogene 1 Neighboring gene RNA, 5S ribosomal pseudogene 54

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action. Šikrová D, et al. Commun Biol, 2023 Jun 28. PMID 37380887, Free PMC Article
    2. LRIF1 interacts with HP1α to coordinate accurate chromosome segregation during mitosis. Akram S, et al. J Mol Cell Biol, 2018 Dec 1. PMID 30016453, Free PMC Article
    3. RIF-1, a novel nuclear receptor corepressor that associates with the nuclear matrix. Li HJ, et al. J Cell Biochem, 2007 Nov 1. PMID 17455211
    4. 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
    5. Analysis of the human HP1 interactome reveals novel binding partners. Rosnoblet C, et al. Biochem Biophys Res Commun, 2011 Sep 23. PMID 21888893

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action.
      Title: SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action.
    2. LRIF1 interacts directly with HP1 alpha chromoshadow domain via an evolutionarily conserved PXVXL motif within its C-terminus. Importantly, the LRIF1-HP1 alpha interaction is critical for Aurora B activity in the inner centromere.
      Title: LRIF1 interacts with HP1α to coordinate accurate chromosome segregation during mitosis.
    3. Thus, the molecular network involving HBiX1 (previously termed C1orf103) and SMCHD1 links the H3K9me3 and XIST-H3K27me3 domains to organize the compact inactive X chromosome structure.
      Title: Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway.
    4. RIF1 is a novel nuclear matrix transcription repressor: a potential role of RIF1 regulation of nuclear receptor transcriptional activity.
      Title: RIF-1, a novel nuclear receptor corepressor that associates with the nuclear matrix.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Facioscapulohumeral muscular dystrophy 3, digenic
    MedGen: C5561959 OMIM: 619477 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of ligand dependent nuclear receptor interacting factor 1 (LRIF1; C1orf103) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11269

    Gene Ontology Provided by GOA

    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 centriolar satellite IDA
    Inferred from Direct Assay
    more info
    		  
    colocalizes_with chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ligand-dependent nuclear receptor-interacting factor 1
    Names
    HP1-binding protein enriched in inactive X chromosome protein 1
    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_001006945.2 → NP_001006946.1  ligand-dependent nuclear receptor-interacting factor 1 isoform 2

      See identical proteins and their annotated locations for NP_001006946.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal coding exon, compared to variant 1, and encodes a shorter predicted isoform (2) compared to isoform 1.
      Source sequence(s)
      AY190122, BQ787643, BU664417, CD686306
      Consensus CDS
      CCDS41366.1
      UniProtKB/Swiss-Prot
      Q5T3J3
      Related
      ENSP00000432290.1, ENST00000485275.2
      Conserved Domains (1) summary
      pfam15741
      Location:1 → 232
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    2. NM_018372.4 → NP_060842.3  ligand-dependent nuclear receptor-interacting factor 1 isoform 1

      See identical proteins and their annotated locations for NP_060842.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AY190122, BQ787643, BU192014
      Consensus CDS
      CCDS30800.1
      UniProtKB/Swiss-Prot
      Q5T3J3, Q86XS4, Q8N3B6, Q96HT4, Q9NUM5, Q9NV32
      Related
      ENSP00000358778.4, ENST00000369763.5
      Conserved Domains (1) summary
      pfam15741
      Location:28 → 768
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      110874957..110963922 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001769.3 → XP_016857258.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

    2. XM_005271029.5 → XP_005271086.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X1

      Conserved Domains (1) summary
      pfam15741
      Location:28 → 767
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      110888014..110978737 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337632.1 → XP_054193607.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

    2. XM_054337631.1 → XP_054193606.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T3J3.1 GenPept UniProtKB/Swiss-Prot:Q5T3J3

    Gene LinkOut

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

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