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Aliases for LRIF1 Gene

Aliases for LRIF1 Gene

  • Ligand Dependent Nuclear Receptor Interacting Factor 1 2 3 5
  • Receptor-Interacting Factor 1 3 4
  • C1orf103 3 4
  • RIF1 3 4
  • Ligand-Dependent Nuclear Receptor-Interacting Factor 1 3
  • Chromosome 1 Open Reading Frame 103 2
  • Receptor Interacting Factor 1 2

External Ids for LRIF1 Gene

Previous HGNC Symbols for LRIF1 Gene

  • C1orf103

Previous GeneCards Identifiers for LRIF1 Gene

  • GC01M111491
  • GC01M110877

Summaries for LRIF1 Gene

GeneCards Summary for LRIF1 Gene

LRIF1 (Ligand Dependent Nuclear Receptor Interacting Factor 1) is a Protein Coding gene. Diseases associated with LRIF1 include Facioscapulohumeral Muscular Dystrophy 1. GO annotations related to this gene include retinoic acid receptor binding.

UniProtKB/Swiss-Prot for LRIF1 Gene

  • Represses the ligand-induced transcriptional activity of retinoic acid receptor alpha (RARA). This repression may occur through direct recruitment of histone deacetylases.

Gene Wiki entry for LRIF1 Gene

Additional gene information for LRIF1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRIF1 Gene

Genomics for LRIF1 Gene

Regulatory Elements for LRIF1 Gene

Enhancers for LRIF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H110630 1.8 FANTOM5 Ensembl ENCODE dbSUPER 3.5 +328.4 328413 10 HDGF TBL1XR1 BATF RAD21 SCRT2 ZNF143 FOS ATF7 KLF7 ETV6 CD53 KCNA3 KCNA2 KCNA10 KCNC4-AS1 LRIF1 RBM15 ENSG00000259834
GH01H111189 1.9 FANTOM5 Ensembl ENCODE dbSUPER 3.1 -233.9 -233904 16 HDGF PKNOX1 FOXA2 SIN3A ZNF766 GATA2 ZNF143 ZNF207 FOS ATF7 DRAM2 CEPT1 DENND2D CHI3L2 DDX20 CD53 ENSG00000243960 LRIF1 RAP1A C1orf162
GH01H110646 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.7 +316.4 316394 3 FEZF1 ZNF2 FOS ATF7 RUNX3 SP3 JUNB REST TSHZ1 ZNF488 ENSG00000258634 NRBF2P3 ENSG00000235005 HIGD1AP12 KCNA3 STRIP1 CD53 ENSG00000243960 LRIF1 ENSG00000259834
GH01H110645 0.7 FANTOM5 dbSUPER 3.7 +318.6 318570 0 EBF1 SP7 CD53 KCNA3 LRIF1 KCNA2 ENSG00000259834
GH01H110870 1.7 FANTOM5 ENCODE dbSUPER 1.5 +87.2 87223 12 HDGF PKNOX1 ARNT ZNF766 CBX5 ZNF143 ZNF207 FOS JUNB REST CD53 LINC01160 DRAM2 KCNA3 LRIF1 ENSG00000261654
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LRIF1 on UCSC Golden Path with GeneCards custom track

Promoters for LRIF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000011326 297 2200 ZFP64 DMAP1 YY1 SLC30A9 SP3 NFYC PPARGC1A MEF2D GLIS1 NBN
ENSR00000253539 1996 400 SMARCE1 ZNF362 ARNT ZSCAN4 MLLT1

Genomic Location for LRIF1 Gene

Chromosome:
1
Start:
110,947,185 bp from pter
End:
110,964,197 bp from pter
Size:
17,013 bases
Orientation:
Minus strand

Genomic View for LRIF1 Gene

Genes around LRIF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRIF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRIF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRIF1 Gene

Proteins for LRIF1 Gene

  • Protein details for LRIF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5T3J3-LRIF1_HUMAN
    Recommended name:
    Ligand-dependent nuclear receptor-interacting factor 1
    Protein Accession:
    Q5T3J3
    Secondary Accessions:
    • Q86XS4
    • Q8N3B6
    • Q96HT4
    • Q9NUM5
    • Q9NV32

    Protein attributes for LRIF1 Gene

    Size:
    769 amino acids
    Molecular mass:
    84568 Da
    Quaternary structure:
    • Interacts with RARA.
    SequenceCaution:
    • Sequence=AAH08115.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAO43631.1; Type=Frameshift; Positions=23; Evidence={ECO:0000305}; Sequence=BAA92097.1; Type=Frameshift; Positions=667; Evidence={ECO:0000305};

    Alternative splice isoforms for LRIF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRIF1 Gene

Post-translational modifications for LRIF1 Gene

  • Ubiquitination at Lys11, posLast=134134, posLast=259259, Lys279, posLast=290290, posLast=418418, Lys427, posLast=470470, posLast=543543, and Lys578
  • Modification sites at PhosphoSitePlus

Other Protein References for LRIF1 Gene

No data available for DME Specific Peptides for LRIF1 Gene

Domains & Families for LRIF1 Gene

Gene Families for LRIF1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LRIF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LRIF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q5T3J3

UniProtKB/Swiss-Prot:

LRIF1_HUMAN :
  • Belongs to the LRIF1 family.
Family:
  • Belongs to the LRIF1 family.
genes like me logo Genes that share domains with LRIF1: view

Function for LRIF1 Gene

Molecular function for LRIF1 Gene

UniProtKB/Swiss-Prot Function:
Represses the ligand-induced transcriptional activity of retinoic acid receptor alpha (RARA). This repression may occur through direct recruitment of histone deacetylases.

Phenotypes From GWAS Catalog for LRIF1 Gene

Gene Ontology (GO) - Molecular Function for LRIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15383276
GO:0042974 retinoic acid receptor binding IEA --
genes like me logo Genes that share ontologies with LRIF1: view
genes like me logo Genes that share phenotypes with LRIF1: view

Animal Model Products

CRISPR Products

miRNA for LRIF1 Gene

miRTarBase miRNAs that target LRIF1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LRIF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRIF1 Gene

Localization for LRIF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRIF1 Gene

Nucleus matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRIF1 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Microtubule organizing center (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000784 colocalizes_with nuclear chromosome, telomeric region IDA 24270157
GO:0005634 nucleus IDA --
GO:0005815 microtubule organizing center IDA --
GO:0016363 nuclear matrix IEA --
genes like me logo Genes that share ontologies with LRIF1: view

Pathways & Interactions for LRIF1 Gene

SuperPathways for LRIF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with LRIF1: view

No data available for Pathways by source and SIGNOR curated interactions for LRIF1 Gene

Drugs & Compounds for LRIF1 Gene

No Compound Related Data Available

Transcripts for LRIF1 Gene

Unigene Clusters for LRIF1 Gene

Ligand dependent nuclear receptor interacting factor 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LRIF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for LRIF1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3
SP1: -
SP2:

Relevant External Links for LRIF1 Gene

GeneLoc Exon Structure for
LRIF1
ECgene alternative splicing isoforms for
LRIF1

Expression for LRIF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRIF1 Gene

Protein differential expression in normal tissues from HIPED for LRIF1 Gene

This gene is overexpressed in Testis (19.9), Retina (13.0), Blymphocyte (11.8), Spinal cord (9.2), and CD8 Tcells (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LRIF1 Gene



Protein tissue co-expression partners for LRIF1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LRIF1 Gene:

LRIF1

SOURCE GeneReport for Unigene cluster for LRIF1 Gene:

Hs.25245

mRNA Expression by UniProt/SwissProt for LRIF1 Gene:

Q5T3J3-LRIF1_HUMAN
Tissue specificity: Widely expressed, with the highest expression levels in heart, liver and placenta.
genes like me logo Genes that share expression patterns with LRIF1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRIF1 Gene

Orthologs for LRIF1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRIF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRIF1 33 34
  • 99.83 (n)
dog
(Canis familiaris)
Mammalia LRIF1 33 34
  • 91.51 (n)
cow
(Bos Taurus)
Mammalia LRIF1 33 34
  • 91.05 (n)
mouse
(Mus musculus)
Mammalia Lrif1 33 16 34
  • 82.93 (n)
rat
(Rattus norvegicus)
Mammalia Lrif1 33
  • 82.39 (n)
oppossum
(Monodelphis domestica)
Mammalia LRIF1 34
  • 51 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRIF1 34
  • 45 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRIF1 33 34
  • 58.04 (n)
lizard
(Anolis carolinensis)
Reptilia LRIF1 34
  • 29 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492192 33
  • 52.28 (n)
zebrafish
(Danio rerio)
Actinopterygii LRIF1 (1 of 2) 34
  • 18 (a)
OneToMany
LRIF1 (2 of 2) 34
  • 18 (a)
OneToMany
Species where no ortholog for LRIF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRIF1 Gene

ENSEMBL:
Gene Tree for LRIF1 (if available)
TreeFam:
Gene Tree for LRIF1 (if available)

Paralogs for LRIF1 Gene

No data available for Paralogs for LRIF1 Gene

Variants for LRIF1 Gene

Sequence variations from dbSNP and Humsavar for LRIF1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000001229 -- 110,944,713(+) TAAAA(A/C)TTTTA intron-variant
rs1000028461 -- 110,933,323(+) CAAGG(C/T)CACTA intron-variant
rs1000044035 -- 110,943,622(+) AAAGA(A/G)GCCAC intron-variant
rs1000097644 -- 110,908,889(+) AGAAC(A/C/T)CCTGT intron-variant
rs1000132727 -- 110,927,021(+) TTCAA(C/T)TAAGA intron-variant

Variation tolerance for LRIF1 Gene

Residual Variation Intolerance Score: 19.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.77; 78.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRIF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRIF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for LRIF1 Gene

Disorders for LRIF1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LRIF1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
facioscapulohumeral muscular dystrophy 1
  • facioscapulohumeral muscular dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search LRIF1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LRIF1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRIF1
genes like me logo Genes that share disorders with LRIF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRIF1 Gene

Publications for LRIF1 Gene

  1. RIF-1, a novel nuclear receptor corepressor that associates with the nuclear matrix. (PMID: 17455211) Li HJ … Mendelsohn M (Journal of cellular biochemistry 2007) 2 3 4 60
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  5. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 60

Products for LRIF1 Gene

Sources for LRIF1 Gene

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