NFIL3 Gene (Protein Coding)

Nuclear Factor, Interleukin 3 Regulated

GC09M091409
GIFtS:
40
The protein encoded by this gene is a transcriptional regulator that binds as a homodimer to activating transcription factor (ATF) sites in many cellular and viral promoters. The encoded protein represses PER1 and PER2 expression and therefore plays a role in the regulation of circadian rhythm. Three transcript variants encoding the same protein have been found for this gene. [... See more...

Aliases for NFIL3 Gene

Aliases for NFIL3 Gene

  • Nuclear Factor, Interleukin 3 Regulated 2 3 5
  • E4BP4 2 3 4
  • Interleukin-3 Promoter Transcriptional Activator 3 4
  • Nuclear Factor Interleukin-3-Regulated Protein 3 4
  • Adenovirus E4 Promoter Region Binding Protein 2 3
  • Transcriptional Activator NF-IL3A 3 4
  • Interleukin-3-Binding Protein 1 3 4
  • E4 Promoter-Binding Protein 4 3 4
  • NF-IL3A 2 3
  • IL3BP1 3 4
  • NFIL3A 2 3
  • Interleukin-3 Binding Protein 1 2
  • E4 Promoter-Binding Protein 2
  • NFIL3 5

External Ids for NFIL3 Gene

Previous HGNC Symbols for NFIL3 Gene

  • IL3BP1

Previous GeneCards Identifiers for NFIL3 Gene

  • GC09M085011
  • GC09M085899
  • GC09M087470
  • GC09M089512
  • GC09M091250
  • GC09M093211
  • GC09M094171
  • GC09M063851

Summaries for NFIL3 Gene

Entrez Gene Summary for NFIL3 Gene

  • The protein encoded by this gene is a transcriptional regulator that binds as a homodimer to activating transcription factor (ATF) sites in many cellular and viral promoters. The encoded protein represses PER1 and PER2 expression and therefore plays a role in the regulation of circadian rhythm. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2014]

GeneCards Summary for NFIL3 Gene

NFIL3 (Nuclear Factor, Interleukin 3 Regulated) is a Protein Coding gene. Diseases associated with NFIL3 include Hereditary Sensory Neuropathy and Advanced Sleep Phase Syndrome. Among its related pathways are Development IGF-1 receptor signaling and NF-kappaB Signaling. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription corepressor activity. An important paralog of this gene is NFILZ.

UniProtKB/Swiss-Prot Summary for NFIL3 Gene

  • Acts as a transcriptional regulator that recognizes and binds to the sequence 5'-[GA]TTA[CT]GTAA[CT]-3', a sequence present in many cellular and viral promoters. Represses transcription from promoters with activating transcription factor (ATF) sites. Represses promoter activity in osteoblasts (By similarity). Represses transcriptional activity of PER1 (By similarity). Represses transcriptional activity of PER2 via the B-site on the promoter (By similarity). Activates transcription from the interleukin-3 promoter in T-cells. Competes for the same consensus-binding site with PAR DNA-binding factors (DBP, HLF and TEF) (By similarity). Component of the circadian clock that acts as a negative regulator for the circadian expression of PER2 oscillation in the cell-autonomous core clock (By similarity). Protects pro-B cells from programmed cell death (By similarity). Represses the transcription of CYP2A5 (By similarity). Positively regulates the expression and activity of CES2 by antagonizing the repressive action of NR1D1 on CES2 (By similarity).

Gene Wiki entry for NFIL3 Gene

Additional gene information for NFIL3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NFIL3 Gene

Genomics for NFIL3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for NFIL3 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 NFIL3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NFIL3

Top Transcription factor binding sites by QIAGEN in the NFIL3 gene promoter:
  • aMEF-2
  • C/EBPalpha
  • COUP
  • COUP-TF
  • COUP-TF1
  • CREB
  • deltaCREB
  • HNF-4alpha1
  • HNF-4alpha2

Genomic Locations for NFIL3 Gene

Genomic Locations for NFIL3 Gene
chr9:91,409,045-91,425,063
(GRCh38/hg38)
Size:
16,019 bases
Orientation:
Minus strand
chr9:94,171,327-94,186,144
(GRCh37/hg19)
Size:
14,818 bases
Orientation:
Minus strand

Genomic View for NFIL3 Gene

Genes around NFIL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NFIL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NFIL3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for NFIL3 Gene

Proteins for NFIL3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for NFIL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16649-NFIL3_HUMAN
    Recommended name:
    Nuclear factor interleukin-3-regulated protein
    Protein Accession:
    Q16649
    Secondary Accessions:
    • B2R9Y8
    • Q14211
    • Q6FGQ8
    • Q96HS0

    Protein attributes for NFIL3 Gene

    Size:
    462 amino acids
    Molecular mass:
    51472 Da
    Quaternary structure:
    • Homodimer (PubMed:1620116). Binds DNA as a dimer (PubMed:1620116). Interacts with DR1 (PubMed:8836190). Interacts with PER2 and CRY2 (By similarity). Interacts with NFIL3 and NR0B2 (By similarity).

neXtProt entry for NFIL3 Gene

Protein Expression for NFIL3 Gene

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

Post-translational modifications for NFIL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NFIL3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NFIL3 Gene

Domains & Families for NFIL3 Gene

Gene Families for NFIL3 Gene

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

Protein Domains for NFIL3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NFIL3 Gene

GenScript: Design optimal peptide antigens:
  • Nuclear factor interleukin 3 regulated protein (D9IVD5_HUMAN)
  • Transcriptional activator NF-IL3A (NFIL3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q16649

UniProtKB/Swiss-Prot:

NFIL3_HUMAN :
  • Belongs to the bZIP family. NFIL3 subfamily.
Family:
  • Belongs to the bZIP family. NFIL3 subfamily.
genes like me logo Genes that share domains with NFIL3: view

Function for NFIL3 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for NFIL3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional regulator that recognizes and binds to the sequence 5'-[GA]TTA[CT]GTAA[CT]-3', a sequence present in many cellular and viral promoters. Represses transcription from promoters with activating transcription factor (ATF) sites. Represses promoter activity in osteoblasts (By similarity). Represses transcriptional activity of PER1 (By similarity). Represses transcriptional activity of PER2 via the B-site on the promoter (By similarity). Activates transcription from the interleukin-3 promoter in T-cells. Competes for the same consensus-binding site with PAR DNA-binding factors (DBP, HLF and TEF) (By similarity). Component of the circadian clock that acts as a negative regulator for the circadian expression of PER2 oscillation in the cell-autonomous core clock (By similarity). Protects pro-B cells from programmed cell death (By similarity). Represses the transcription of CYP2A5 (By similarity). Positively regulates the expression and activity of CES2 by antagonizing the repressive action of NR1D1 on CES2 (By similarity).
UniProtKB/Swiss-Prot Induction:
Up-regulated by PHA or TPA.

Phenotypes From GWAS Catalog for NFIL3 Gene

Gene Ontology (GO) - Molecular Function for NFIL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 20093779
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 20093779
GO:0003677 DNA binding TAS 1620116
genes like me logo Genes that share ontologies with NFIL3: view
genes like me logo Genes that share phenotypes with NFIL3: view

Animal Models for NFIL3 Gene

MGI Knock Outs for NFIL3:

Animal Model Products

CRISPR Products

miRNA for NFIL3 Gene

miRTarBase miRNAs that target NFIL3

Transcription Factor Targets for NFIL3 Gene

Selected GeneGlobe predicted Target genes for NFIL3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NFIL3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for NFIL3 Gene

Localization for NFIL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NFIL3 Gene

Nucleus.

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 NFIL3 gene
Compartment Confidence
nucleus 5
plasma membrane 2
extracellular 2
mitochondrion 2
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NFIL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus TAS,IBA 21873635
genes like me logo Genes that share ontologies with NFIL3: view

Pathways & Interactions for NFIL3 Gene

genes like me logo Genes that share pathways with NFIL3: view

Pathways by source for NFIL3 Gene

1 Cell Signaling Technology pathway for NFIL3 Gene

SIGNOR curated interactions for NFIL3 Gene

Activates:
Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for NFIL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 20093779
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0006366 transcription by RNA polymerase II TAS,IEA --
GO:0006955 immune response TAS,IEA --
genes like me logo Genes that share ontologies with NFIL3: view

Drugs & Compounds for NFIL3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for NFIL3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for NFIL3 Gene

3 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NFIL3

Alternative Splicing Database (ASD) splice patterns (SP) for NFIL3 Gene

No ASD Table

Relevant External Links for NFIL3 Gene

GeneLoc Exon Structure for
NFIL3

Expression for NFIL3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NFIL3 Gene

mRNA expression in normal human tissues for NFIL3 Gene
mRNA expression by BioGPS for NFIL3 GenemRNA expression by GTEx for NFIL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NFIL3 Gene

This gene is overexpressed in Whole Blood (x6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NFIL3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NFIL3

SOURCE GeneReport for Unigene cluster for NFIL3 Gene:

Hs.79334

mRNA Expression by UniProt/SwissProt for NFIL3 Gene:

Q16649-NFIL3_HUMAN
Tissue specificity: Expressed in bladder stomach, thyroid, spinal cord, lymph node, trachea, adrenal gland, bone marrow and muscle.

Evidence on tissue expression from TISSUES for NFIL3 Gene

  • Liver(4.7)
  • Blood(4.6)
  • Bone marrow(3.2)
  • Spleen(3.1)
  • Muscle(3.1)
  • Heart(3)
  • Nervous system(3)
  • Intestine(2.8)
  • Lung(2.8)
  • Kidney(2.7)
  • Adrenal gland(2.6)
  • Lymph node(2.5)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with NFIL3: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NFIL3 Gene

Orthologs for NFIL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NFIL3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia NFIL3 30 31
  • 99.78 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia NFIL3 30 31
  • 87.01 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia NFIL3 31
  • 83 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia NFIL3 30 31
  • 79.58 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Nfil3 30 17 31
  • 79.54 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Nfil3 30
  • 79.1 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia NFIL3 31
  • 52 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves NFIL3 30 31
  • 81.51 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia NFIL3 31
  • 81 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia nfil3 30
  • 70.07 (n)
Zebrafish
(Danio rerio)
 Actinopterygii nfil3 30 31
  • 58.35 (n)
 OneToOne
wufk63e10 30
Fruit Fly
(Drosophila melanogaster)
 Insecta vri 31
  • 11 (a)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea atf-2 31
  • 20 (a)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 15 (a)
 OneToOne
Species where no ortholog for NFIL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 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 NFIL3 Gene

ENSEMBL:
Gene Tree for NFIL3 (if available)
TreeFam:
Gene Tree for NFIL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NFIL3: view image

Paralogs for NFIL3 Gene

Paralogs for NFIL3 Gene

Pseudogenes.org Pseudogenes for NFIL3 Gene

genes like me logo Genes that share paralogs with NFIL3: view

Variants for NFIL3 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NFIL3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
720738 Benign: not provided 91,410,710(-) C/T MISSENSE_VARIANT
721540 Benign: not provided 91,409,346(-) T/C SYNONYMOUS_VARIANT
785289 Benign: not provided 91,409,913(-) C/T SYNONYMOUS_VARIANT
785290 Benign: not provided 91,410,201(-) G/C SYNONYMOUS_VARIANT
789774 Benign: not provided 91,410,399(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for NFIL3 Gene

Structural Variations from Database of Genomic Variants (DGV) for NFIL3 Gene

Variant ID Type Subtype PubMed ID
dgv4098n106 CNV deletion 24896259
nsv1075253 CNV deletion 25765185
nsv614857 CNV loss 21841781
nsv824980 CNV gain 20364138
nsv824981 CNV gain 20364138
nsv950890 CNV duplication 24416366

Variation tolerance for NFIL3 Gene

Residual Variation Intolerance Score: 24% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.82; 34.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NFIL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NFIL3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NFIL3 Gene

Disorders for NFIL3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NFIL3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hereditary sensory neuropathy
  • familial dysautonomia, type ii
advanced sleep phase syndrome
  • familial advanced sleep-phase syndrome
attention deficit-hyperactivity disorder
  • adhd
- elite association - COSMIC cancer census association via MalaCards
Search NFIL3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NFIL3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with NFIL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NFIL3 Gene

Publications for NFIL3 Gene

  1. Molecular cloning and characterization of NF-IL3A, a transcriptional activator of the human interleukin-3 promoter. (PMID: 7565758) Zhang W … Nimer SD (Molecular and cellular biology 1995) 2 3 4 23
  2. Protein-protein interaction between the transcriptional repressor E4BP4 and the TBP-binding protein Dr1. (PMID: 8836190) Cowell IG … Hurst HC (Nucleic acids research 1996) 3 4 23
  3. Transcriptional repression by a novel member of the bZIP family of transcription factors. (PMID: 1620116) Cowell IG … Hurst HC (Molecular and cellular biology 1992) 2 3 4
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  5. PER2 variantion is associated with depression vulnerability. (PMID: 19693801) Lavebratt C … Forsell Y (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2010) 3 41

ExternalLinks

View latest publications for NFIL3 gene in Mastermind

Products for NFIL3 Gene

  • Addgene plasmids for NFIL3
  • Boster Bio Antibodies for NFIL3
  • Boster Bio ELISA Kits for NFIL3
  • Signalway Proteins for NFIL3

Sources for NFIL3 Gene