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

Gene ID: 4783, updated on 10-Oct-2019

Summary

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
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

Genomic context

See NFIL3 in Genome Data Viewer
Location:
9q22.31
Exon count:
5
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (91409045..91425063, complement)
105 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 Sharpr-MPRA regulatory region 6399 Neighboring gene AU RNA binding methylglutaconyl-CoA hydratase Neighboring gene uncharacterized LOC105376146 Neighboring gene phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 2 Neighboring gene microRNA 3910-1 Neighboring gene microRNA 3910-2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystem (from REACTOME)
    BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystemAs inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et...
  • Circadian Clock, organism-specific biosystem (from REACTOME)
    Circadian Clock, organism-specific biosystemAt the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by b...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Development and heterogeneity of the ILC family, organism-specific biosystem (from WikiPathways)
    Development and heterogeneity of the ILC family, organism-specific biosystemDevelopment and heterogeneity of the ILC family. ILCs develop from distinct progenitors in the fetal liver or bone marrow and then develop into mature ILCs in the periphery. Different transcription f...
  • IL-4 Signaling Pathway, organism-specific biosystem (from WikiPathways)
    IL-4 Signaling Pathway, organism-specific biosystemIL-4 is a glycoprotein which is composed of 129 amino acids and has a molecular weight of 20kDa. IL-4 and IL-13 are produced by CD4+ cells and exhibit significant functional overlap. Both these cytok...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cellular response to interleukin-4 IEA
Inferred from Electronic Annotation
more info
 
circadian rhythm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
immune response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001289999.1NP_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
    Q16649
    UniProtKB/TrEMBL
    A0A024R241
    Conserved Domains (2) summary
    cd14694
    Location:72131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor
  2. NM_001290000.1NP_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
    Q16649
    UniProtKB/TrEMBL
    A0A024R241
    Conserved Domains (2) summary
    cd14694
    Location:72131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor
  3. NM_005384.3NP_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
    Q16649
    UniProtKB/TrEMBL
    A0A024R241
    Related
    ENSP00000297689.2, ENST00000297689.4
    Conserved Domains (2) summary
    cd14694
    Location:72131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    91409045..91425063 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    Q16649
    UniProtKB/TrEMBL
    A0A024R241
    Conserved Domains (2) summary
    cd14694
    Location:72131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor
  2. XM_017014744.1XP_016870233.1  nuclear factor interleukin-3-regulated protein isoform X1

    UniProtKB/Swiss-Prot
    Q16649
    UniProtKB/TrEMBL
    A0A024R241
    Conserved Domains (2) summary
    cd14694
    Location:72131
    bZIP_NFIL3; Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain
    pfam06529
    Location:130461
    Vert_IL3-reg_TF; Vertebrate interleukin-3 regulated transcription factor
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