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NFIL3 nuclear factor, interleukin 3 regulated [ Homo sapiens (human) ]

Gene ID: 4783, updated on 27-Nov-2024

Summary

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Official Symbol
NFIL3provided by HGNC
Official Full Name
nuclear factor, interleukin 3 regulatedprovided by HGNC
Primary source
HGNC:HGNC:7787
See related
Ensembl:ENSG00000165030 MIM:605327; AllianceGenome:HGNC:7787
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
E4BP4; IL3BP1; NFIL3A; NF-IL3A
Summary
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]
Expression
Broad expression in bone marrow (RPKM 59.6), adrenal (RPKM 37.4) and 23 other tissues See more
Orthologs
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Genomic context

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See NFIL3 in Genome Data Viewer
Location:
9q22.31
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (91409045..91483497, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (103575185..103649759, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (94171327..94186908, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902208 Neighboring gene Sharpr-MPRA regulatory region 6399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:93956125-93956992 Neighboring gene Sharpr-MPRA regulatory region 9930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28586 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:93979563-93980163 Neighboring gene Sharpr-MPRA regulatory region 15085 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109225 Neighboring gene AU RNA binding methylglutaconyl-CoA hydratase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109279 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr9:94076941-94077442 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr9:94077443-94077942 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94106111-94106766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20025 Neighboring gene MPRA-validated peak7289 silencer Neighboring gene uncharacterized LOC124902209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20026 Neighboring gene synapsin-1 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:94188762-94188958 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:94251258-94252457 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109428 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:94277032-94278231 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94334217-94334753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28587 Neighboring gene phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 2 Neighboring gene microRNA 3910-1 Neighboring gene microRNA 3910-2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Structural basis for specific DNA sequence recognition by the transcription factor NFIL3. Chen S, et al. J Biol Chem, 2024 Mar. PMID 38382670, Free PMC Article
  2. Transcriptional repression by a novel member of the bZIP family of transcription factors. Cowell IG, et al. Mol Cell Biol, 1992 Jul. PMID 1620116, Free PMC Article
  3. Molecular cloning and characterization of NF-IL3A, a transcriptional activator of the human interleukin-3 promoter. Zhang W, et al. Mol Cell Biol, 1995 Nov. PMID 7565758, Free PMC Article
  4. Exclusion of NFIL3 as the gene causing hereditary sensory neuropathy type I by mutation analysis. Hulme DJ, et al. Hum Genet, 2000 Jun. PMID 10942106
  5. Parathyroid hormone-induced E4BP4/NFIL3 down-regulates transcription in osteoblasts. Ozkurt IC, et al. J Biol Chem, 2003 Jul 18. PMID 12743120

See all (77) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Knockdown of NFIL3 modulates the AMPK pathway to suppress excessive cell proliferation, inflammation, and migration in rheumatoid arthritis.
    Title: Knockdown of NFIL3 modulates the AMPK pathway to suppress excessive cell proliferation, inflammation, and migration in rheumatoid arthritis.
  2. Structural basis for specific DNA sequence recognition by the transcription factor NFIL3.
    Title: Structural basis for specific DNA sequence recognition by the transcription factor NFIL3.
  3. The role of basic leucine zipper transcription factor E4BP4 in cancer: a review and update.
    Title: The role of basic leucine zipper transcription factor E4BP4 in cancer: a review and update.
  4. A Potential Role of NFIL3 in Atherosclerosis.
    Title: A Potential Role of NFIL3 in Atherosclerosis.
  5. NFIL3 aggravates human coronary artery endothelial cell injury by promoting ITGAM transcription in Kawasaki disease.
    Title: NFIL3 aggravates human coronary artery endothelial cell injury by promoting ITGAM transcription in Kawasaki disease.
  6. NFIL3 and its immunoregulatory role in rheumatoid arthritis patients.
    Title: NFIL3 and its immunoregulatory role in rheumatoid arthritis patients.
  7. Diurnal Rhythmicity Programs of Microbiota and Transcriptional Oscillation of Circadian Regulator, NFIL3.
    Title: Diurnal Rhythmicity Programs of Microbiota and Transcriptional Oscillation of Circadian Regulator, NFIL3.
  8. E4BP4-mediated inhibition of T follicular helper cell differentiation is compromised in autoimmune diseases.
    Title: E4BP4-mediated inhibition of T follicular helper cell differentiation is compromised in autoimmune diseases.
  9. NFIL3 is highly expressed in osteosarcoma tissues and thus promotes the proliferation, migration, and invasion of osteosarcoma cells. NFIL3 is potential to become a new target for development of novel treatment strategies of osteosarcoma.
    Title: NFIL3 Acts as a Nuclear Factor to Increase Osteosarcoma Progression.
  10. our observations suggest that the NFIL3/PrPc axis, through regulating lamellipodium formation and cell mobility via JNK signaling, plays a critical role in lung cancer invasiveness and metastasis.
    Title: Cellular prion protein transcriptionally regulated by NFIL3 enhances lung cancer cell lamellipodium formation and migration through JNK signaling.
Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to interleukin-4 IEA
Inferred from Electronic Annotation
more info
  
involved_in circadian rhythm IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in natural killer cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
nuclear factor interleukin-3-regulated protein
Names
E4 promoter-binding protein 4
adenovirus E4 promoter region binding protein
interleukin-3 promoter transcriptional activator
interleukin-3-binding protein 1
transcriptional activator NF-IL3A

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_001289999.2 → NP_001276928.1  nuclear factor interleukin-3-regulated protein

    See identical proteins and their annotated locations for NP_001276928.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. All three variants encode the same protein.
    Source sequence(s)
    AL353764, BC008197, DB256817
    Consensus CDS
    CCDS6690.1
    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
    UniProtKB/TrEMBL
    D9IVD5
    Related
    ENSP00000520782.1, ENST00000718345.1
    Conserved Domains (2) summary
    cd14694
    Location:72 → 131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130 → 461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor

  2. NM_001290000.2 → NP_001276929.1  nuclear factor interleukin-3-regulated protein

    See identical proteins and their annotated locations for NP_001276929.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. All three variants encode the same protein.
    Source sequence(s)
    BC008197, DB256817, HY038941
    Consensus CDS
    CCDS6690.1
    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
    UniProtKB/TrEMBL
    D9IVD5
    Conserved Domains (2) summary
    cd14694
    Location:72 → 131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130 → 461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor

  3. NM_005384.3 → NP_005375.2  nuclear factor interleukin-3-regulated protein

    See identical proteins and their annotated locations for NP_005375.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. All three variants encode the same protein.
    Source sequence(s)
    AW163045, BC008197, BQ937243
    Consensus CDS
    CCDS6690.1
    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
    UniProtKB/TrEMBL
    D9IVD5
    Related
    ENSP00000297689.2, ENST00000297689.4
    Conserved Domains (2) summary
    cd14694
    Location:72 → 131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130 → 461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    91409045..91483497 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423425.1 → XP_047279381.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

  2. XM_017014743.2 → XP_016870232.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
    UniProtKB/TrEMBL
    D9IVD5
    Conserved Domains (2) summary
    cd14694
    Location:72 → 131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130 → 461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor

  3. XM_047423426.1 → XP_047279382.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

  4. XM_017014744.2 → XP_016870233.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
    UniProtKB/TrEMBL
    D9IVD5
    Conserved Domains (2) summary
    cd14694
    Location:72 → 131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130 → 461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor

  5. XM_047423423.1 → XP_047279379.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

  6. XM_047423424.1 → XP_047279380.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

  7. XM_047423422.1 → XP_047279378.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    103575185..103649759 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363000.1 → XP_054218975.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

  2. XM_054362998.1 → XP_054218973.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

  3. XM_054363001.1 → XP_054218976.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0

  4. XM_054362999.1 → XP_054218974.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16649.2 GenPept UniProtKB/Swiss-Prot:Q16649

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