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

    Gene ID: 4783, updated on 10-Dec-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
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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
      UniProtKB/TrEMBL
      D9IVD5

    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
      UniProtKB/TrEMBL
      D9IVD5

    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
      UniProtKB/TrEMBL
      D9IVD5

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

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5

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

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5

    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
      UniProtKB/TrEMBL
      D9IVD5

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

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5

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

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5

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

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q16649.2 GenPept UniProtKB/Swiss-Prot:Q16649

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