LRRFIP1 Gene (Protein Coding)

LRR Binding FLII Interacting Protein 1

GC02P237627
GIFtS:
38
See more...

Aliases for LRRFIP1 Gene

Aliases for LRRFIP1 Gene

  • LRR Binding FLII Interacting Protein 1 2 3 5
  • GC-Binding Factor 2 2 3 4
  • GCF2 2 3 4
  • TRIP 2 3 4
  • Leucine-Rich Repeat Flightless-Interacting Protein 1 3 4
  • Leucine Rich Repeat (In FLII) Interacting Protein 1 2 3
  • LRR FLII-Interacting Protein 1 3 4
  • TAR RNA-Interacting Protein 3 4
  • FLIIAP1 2 3
  • FLAP-1 2 3
  • HUFI-1 2 3
  • GCF-2 2 3
  • NEDD8-Conjugating Enzyme 3
  • LRRFIP1 5
  • FLAP1 3

External Ids for LRRFIP1 Gene

Previous GeneCards Identifiers for LRRFIP1 Gene

  • GC02P236649
  • GC02P237282
  • GC02P238617
  • GC02P238823
  • GC02P238887
  • GC02P238382
  • GC02P238265
  • GC02P230392
  • GC02P238536

Summaries for LRRFIP1 Gene

GeneCards Summary for LRRFIP1 Gene

LRRFIP1 (LRR Binding FLII Interacting Protein 1) is a Protein Coding gene. Diseases associated with LRRFIP1 include Marasmus. Among its related pathways are Cytosolic sensors of pathogen-associated DNA and HIV Life Cycle. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and double-stranded RNA binding. An important paralog of this gene is LRRFIP2.

UniProtKB/Swiss-Prot Summary for LRRFIP1 Gene

  • Transcriptional repressor which preferentially binds to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. May control smooth muscle cells proliferation following artery injury through PDGFA repression. May also bind double-stranded RNA. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding.

Gene Wiki entry for LRRFIP1 Gene

Additional gene information for LRRFIP1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRRFIP1 Gene

Genomics for LRRFIP1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for LRRFIP1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRRFIP1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRFIP1

Top Transcription factor binding sites by QIAGEN in the LRRFIP1 gene promoter:
  • COUP
  • COUP-TF
  • COUP-TF1
  • GR
  • GR-alpha
  • HNF-4alpha1
  • HNF-4alpha2
  • Max1

Genomic Locations for LRRFIP1 Gene

Latest Assembly
chr2:237,627,576-237,813,682
(GRCh38/hg38)
Size:
186,107 bases
Orientation:
Plus strand

Previous Assembly
chr2:238,536,230-238,690,286
(GRCh37/hg19 by Entrez Gene)
Size:
154,057 bases
Orientation:
Plus strand

chr2:238,536,219-238,722,325
(GRCh37/hg19 by Ensembl)
Size:
186,107 bases
Orientation:
Plus strand

Genomic View for LRRFIP1 Gene

Genes around LRRFIP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRFIP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRFIP1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for LRRFIP1 Gene

Proteins for LRRFIP1 Gene

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  • Protein details for LRRFIP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q32MZ4-LRRF1_HUMAN
    Recommended name:
    Leucine-rich repeat flightless-interacting protein 1
    Protein Accession:
    Q32MZ4
    Secondary Accessions:
    • E9PGZ2
    • O75766
    • O75799
    • Q32MZ5
    • Q53T49
    • Q6PKG2
    • Q9Y607

    Protein attributes for LRRFIP1 Gene

    Size:
    808 amino acids
    Molecular mass:
    89253 Da
    Quaternary structure:
    • Homodimer. May also form higher oligomers. Interacts with FLII. Interacts with MYD88. Competes with FLII for MyD88-binding, even in the absence of LPS.
    SequenceCaution:
    • Sequence=AAH01385.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAY14672.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LRRFIP1 Gene

    Alternative splice isoforms for LRRFIP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRRFIP1 Gene

Protein Expression for LRRFIP1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LRRFIP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LRRFIP1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for LRRFIP1

No data available for DME Specific Peptides for LRRFIP1 Gene

Domains & Families for LRRFIP1 Gene

Gene Families for LRRFIP1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for LRRFIP1 Gene

InterPro:

Suggested Antigen Peptide Sequences for LRRFIP1 Gene

GenScript: Design optimal peptide antigens:
  • TAR RNA-interacting protein (LRRF1_HUMAN)
  • LRRFIP1 protein (Q05D04_HUMAN)
  • LRR FLI-I interacting protein 1 (Q9Y607_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q32MZ4

UniProtKB/Swiss-Prot:

LRRF1_HUMAN :
  • The DNA-binding domain is intrinsically unstructured.
  • Belongs to the LRRFIP family.
Domain:
  • The DNA-binding domain is intrinsically unstructured.
  • The coiled coil mediates dimerization.
Family:
  • Belongs to the LRRFIP family.
genes like me logo Genes that share domains with LRRFIP1: view

Function for LRRFIP1 Gene

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  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for LRRFIP1 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor which preferentially binds to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. May control smooth muscle cells proliferation following artery injury through PDGFA repression. May also bind double-stranded RNA. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding.
GENATLAS Biochemistry:
leucine rich repeat in FLII-interacting protein 1,identical to the TAR RNA interacting protein,with specific alternatively spliced transcripts,mainly expressed in heart and skeletal muscle

Phenotypes From GWAS Catalog for LRRFIP1 Gene

Gene Ontology (GO) - Molecular Function for LRRFIP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 14522076
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific IBA 21873635
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 14522076
GO:0003677 DNA binding IEA,IDA 23099021
GO:0003725 double-stranded RNA binding TAS 9671805
genes like me logo Genes that share ontologies with LRRFIP1: view
genes like me logo Genes that share phenotypes with LRRFIP1: view

Animal Models for LRRFIP1 Gene

MGI Knock Outs for LRRFIP1:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRFIP1

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRRFIP1 Gene

Localization for LRRFIP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRFIP1 Gene

Nucleus. Cytoplasm.

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 LRRFIP1 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5
cytoskeleton 4
endosome 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRRFIP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm TAS 9671805
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton TAS 9671805
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with LRRFIP1: view

Pathways & Interactions for LRRFIP1 Gene

genes like me logo Genes that share pathways with LRRFIP1: view

Gene Ontology (GO) - Biological Process for LRRFIP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 14522076
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0032481 positive regulation of type I interferon production TAS --
GO:0051092 positive regulation of NF-kappaB transcription factor activity IEA --
genes like me logo Genes that share ontologies with LRRFIP1: view

No data available for SIGNOR curated interactions for LRRFIP1 Gene

Drugs & Compounds for LRRFIP1 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for LRRFIP1 Gene

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mRNA/cDNA for LRRFIP1 Gene

5 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRFIP1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for LRRFIP1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14 ^ 15 ^ 16a · 16b · 16c ^ 17a ·
SP1: - - - - - -
SP2: - -
SP3: -
SP4: - -
SP5: - - - - - - - -
SP6: - - -
SP7: - - -
SP8:
SP9:
SP10: - -
SP11: - -
SP12:
SP13:
SP14:

ExUns: 17b ^ 18 ^ 19 ^ 20a · 20b
SP1:
SP2:
SP3:
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: -
SP12:
SP13: -
SP14:

Relevant External Links for LRRFIP1 Gene

GeneLoc Exon Structure for
LRRFIP1

Expression for LRRFIP1 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRRFIP1 Gene

mRNA expression in normal human tissues for LRRFIP1 Gene
mRNA expression by GTEx for LRRFIP1 GenemRNA expression by BioGPS for LRRFIP1 Gene

Protein differential expression in normal tissues from HIPED for LRRFIP1 Gene

This gene is overexpressed in Nasal epithelium (19.0), Peripheral blood mononuclear cells (9.3), and Lymph node (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRRFIP1 Gene



Protein tissue co-expression partners for LRRFIP1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRFIP1

SOURCE GeneReport for Unigene cluster for LRRFIP1 Gene:

Hs.471779

mRNA Expression by UniProt/SwissProt for LRRFIP1 Gene:

Q32MZ4-LRRF1_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for LRRFIP1 Gene

  • Liver(4.6)
  • Heart(4.5)
  • Lung(3.6)
  • Skin(3.1)
  • Intestine(2.7)
  • Spleen(2.7)
  • Muscle(2.5)
  • Nervous system(2.5)
  • Blood(2.4)
  • Lymph node(2.4)
  • Kidney(2.4)
  • Bone marrow(2.3)
genes like me logo Genes that share expression patterns with LRRFIP1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRFIP1 Gene

Orthologs for LRRFIP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRFIP1 Gene

Organism Taxonomy Gene Similarity Type Details
Dog
(Canis familiaris)
 Mammalia LRRFIP1 29 30
  • 90.66 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia LRRFIP1 29 30
  • 89.31 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Lrrfip1 29 16 30
  • 86.32 (n)
 OneToOne
Chimpanzee
(Pan troglodytes)
 Mammalia LRRFIP1 30
  • 46 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia LRRFIP1 30
  • 39 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia LRRFIP1 30
  • 38 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves LRRFIP1 29 30
  • 78.36 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia LRRFIP1 30
  • 36 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia lrrfip1 29
  • 70.4 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.15436 29
Zebrafish
(Danio rerio)
 Actinopterygii lrrfip1b 29 30
  • 64.33 (n)
 OneToMany
lrrfip1a 30
  • 38 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta CG8578 30
  • 25 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea flap-1 30
  • 17 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.5234 30
  • 14 (a)
 OneToMany
Species where no ortholog for LRRFIP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)

Evolution for LRRFIP1 Gene

ENSEMBL:
Gene Tree for LRRFIP1 (if available)
TreeFam:
Gene Tree for LRRFIP1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRFIP1: view image
Alliance of Genome Resources:
Additional Orthologs for LRRFIP1

Paralogs for LRRFIP1 Gene

Paralogs for LRRFIP1 Gene

(2) SIMAP similar genes for LRRFIP1 Gene using alignment to 4 proteins:

  • LRRF1_HUMAN
  • C9JTC6_HUMAN
  • Q05D04_HUMAN
  • Q9BSL6_HUMAN

Pseudogenes.org Pseudogenes for LRRFIP1 Gene

genes like me logo Genes that share paralogs with LRRFIP1: view

Variants for LRRFIP1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRRFIP1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs113302264 Benign: not provided 237,749,309(+) C/T
NM_001137550.2(LRRFIP1):c.780C>T (p.Ser260=) 		SYNONYMOUS
VAR_036037 A breast cancer sample p.Ser68Cys
rs2001301 -- p.Asn418Ser
rs3213869 -- p.Gln275Arg
rs3739038 -- p.His783Asp

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRRFIP1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LRRFIP1 Gene

Variant ID Type Subtype PubMed ID
dgv1221e212 CNV loss 25503493
dgv2181n106 CNV deletion 24896259
dgv7345n54 CNV loss 21841781
dgv7346n54 CNV loss 21841781
dgv7347n54 CNV loss 21841781
esv1004389 CNV deletion 20482838
esv23602 CNV loss 19812545
esv24426 CNV loss 19812545
esv2660099 CNV deletion 23128226
esv2664469 CNV deletion 23128226
esv2721737 CNV deletion 23290073
esv2721738 CNV deletion 23290073
esv3561236 CNV deletion 23714750
esv3594748 CNV loss 21293372
esv4182 CNV loss 18987735
esv997081 CNV insertion 20482838
nsv1000252 CNV loss 25217958
nsv1010093 CNV gain 25217958
nsv1073026 CNV deletion 25765185
nsv1122022 CNV deletion 24896259
nsv3230 CNV insertion 18451855
nsv507077 OTHER sequence alteration 20534489
nsv508893 CNV insertion 20534489
nsv518573 CNV gain 19592680
nsv519961 CNV loss 19592680
nsv584746 CNV loss 21841781
nsv584752 CNV loss 21841781
nsv584753 CNV loss 21841781
nsv963784 CNV duplication 23825009

Variation tolerance for LRRFIP1 Gene

Residual Variation Intolerance Score: 68.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.41; 77.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRFIP1 Gene

Human Gene Mutation Database (HGMD)
LRRFIP1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRFIP1
Leiden Open Variation Database (LOVD)
LRRFIP1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRFIP1 Gene

Disorders for LRRFIP1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LRRFIP1 Gene - From: COP

Disorder Aliases PubMed IDs
marasmus
  • nutritional atrophy
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LRRFIP1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LRRFIP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRRFIP1 Gene

Publications for LRRFIP1 Gene

  1. GCF2/LRRFIP1 represses tumor necrosis factor alpha expression. (PMID: 16199883) Suriano AR … Sullivan KE (Molecular and cellular biology 2005) 2 3 4
  2. GCF2: expression and molecular analysis of repression. (PMID: 14522076) Rikiyama T … Johnson AC (Biochimica et biophysica acta 2003) 3 4 22
  3. Novel proteins interacting with the leucine-rich repeat domain of human flightless-I identified by the yeast two-hybrid system. (PMID: 10366446) Fong KS … de Couet HG (Genomics 1999) 3 4 22
  4. Molecular cloning and characterization of a transcription regulator with homology to GC-binding factor. (PMID: 9705290) Reed AL … Johnson AC (The Journal of biological chemistry 1998) 2 3 4
  5. Crystal structure of the dimeric coiled-coil domain of the cytosolic nucleic acid sensor LRRFIP1. (PMID: 23099021) Nguyen JB … Modis Y (Journal of structural biology 2013) 3 4

ExternalLinks

View latest publications for LRRFIP1 gene in Mastermind

Products for LRRFIP1 Gene

Sources for LRRFIP1 Gene