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

Gene ID: 55791, updated on 5-Aug-2022

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
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Genomic context

See LRIF1 in Genome Data Viewer
Location:
1p13.3
Exon count:
5
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (110874957..110963922, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (110961987..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 Sharpr-MPRA regulatory region 4566 Neighboring gene CD53 molecule 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

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

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_001006945.2NP_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, 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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
    110961987..110978737 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)