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

    Gene ID: 55791, updated on 7-Jan-2024

    Summary

    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 retinoic acid receptor binding activity. Involved in dosage compensation by inactivation of X chromosome. Located in Barr body; centriolar satellite; and nucleoplasm. Colocalizes with chromosome, telomeric region. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 11.6), ovary (RPKM 5.5) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See LRIF1 in Genome Data Viewer
    Location:
    1p13.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (110874957..110963922, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (110888014..110978737, complement)
    105.20220307 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

    Expression

    • Project title: 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

    Phenotypes

    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

    HIV-1 interactions

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001006945.2NP_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:1232
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1
    2. NM_018372.4NP_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:28768
      LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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_017001769.3XP_016857258.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

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

      Conserved Domains (1) summary
      pfam15741
      Location:28767
      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_054337632.1XP_054193607.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

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