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Lrif1 ligand dependent nuclear receptor interacting factor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 310775, updated on 9-Dec-2024

Summary

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Official Symbol
Lrif1provided by RGD
Official Full Name
ligand dependent nuclear receptor interacting factor 1provided by RGD
Primary source
RGD:1306520
See related
EnsemblRapid:ENSRNOG00000017784 AllianceGenome:RGD:1306520
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1306520
Summary
Predicted to enable nuclear retinoic acid receptor binding activity. Predicted to be involved in dosage compensation by inactivation of X chromosome. Predicted to be located in centriolar satellite; chromosome, telomeric region; and nuclear lumen. 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, Dec 2024]
Expression
Biased expression in Testes (RPKM 92.7), Thymus (RPKM 80.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Lrif1 in Genome Data Viewer
Location:
2q34
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (196919606..197010713)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (194231397..194322489)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (209358668..209448123)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene choline/ethanolamine phosphotransferase 1 Neighboring gene DNA damage regulated autophagy modulator 2 Neighboring gene uncharacterized LOC134485947 Neighboring gene uncharacterized LOC120100909 Neighboring gene Cd53 molecule 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

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. 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
  3. A quantitative telomeric chromatin isolation protocol identifies different telomeric states. Grolimund L, et al. Nat Commun, 2013. PMID 24270157
  4. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs RA, et al. Nature, 2004 Apr 1. PMID 15057822
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables nuclear retinoic acid receptor binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in dosage compensation by inactivation of X chromosome IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
located_in Barr body ISO
Inferred from Sequence Orthology
more info
  
located_in Barr body ISS
Inferred from Sequence or Structural Similarity
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
  
located_in 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
Names
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_001127485.1 → NP_001120957.1  ligand-dependent nuclear receptor-interacting factor 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000002
    UniProtKB/Swiss-Prot
    Q499M7
    UniProtKB/TrEMBL
    F1LMD4
    Related
    ENSRNOP00000024036.5, ENSRNOT00000024036.7
    Conserved Domains (1) summary
    pfam15741
    Location:26 → 747
    LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086020.1 Reference GRCr8

    Range
    196919606..197010713
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006233147.5 → XP_006233209.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X2

    UniProtKB/TrEMBL
    A0A0G2JZ59, B0BNF2
    Related
    ENSRNOP00000094264.2, ENSRNOT00000098808.2
    Conserved Domains (1) summary
    pfam15741
    Location:17 → 252
    LRIF1; Ligand-dependent nuclear receptor-interacting factor 1

  2. XM_039102422.2 → XP_038958350.1  ligand-dependent nuclear receptor-interacting factor 1 isoform X1

    UniProtKB/TrEMBL
    A6HUR4
    Conserved Domains (1) summary
    pfam15741
    Location:26 → 511
    LRIF1; Ligand-dependent nuclear receptor-interacting factor 1
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q499M7.2 GenPept UniProtKB/Swiss-Prot:Q499M7

Gene LinkOut

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