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

    Gene ID: 4783, updated on 17-Jun-2024

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NFIL3 in Genome Data Viewer
    Location:
    9q22.31
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (91409045..91483497, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (103575185..103649759, complement)
    105.20220307 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

    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

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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 
    part_of 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

    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)

    NEW Try the new Transcript table

    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_001289999.2NP_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
      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_001290000.2NP_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: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
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
      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: GCF_000001405.40-RS_2023_10

    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_047423425.1XP_047279381.1  nuclear factor interleukin-3-regulated protein isoform X1

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    2. XM_017014743.2XP_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: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. XM_047423426.1XP_047279382.1  nuclear factor interleukin-3-regulated protein isoform X1

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    4. XM_017014744.2XP_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: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
    5. XM_047423423.1XP_047279379.1  nuclear factor interleukin-3-regulated protein isoform X1

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    6. XM_047423424.1XP_047279380.1  nuclear factor interleukin-3-regulated protein isoform X1

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    7. XM_047423422.1XP_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_054363000.1XP_054218975.1  nuclear factor interleukin-3-regulated protein isoform X1

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    2. XM_054362998.1XP_054218973.1  nuclear factor interleukin-3-regulated protein isoform X1

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    3. XM_054363001.1XP_054218976.1  nuclear factor interleukin-3-regulated protein isoform X1

      UniProtKB/Swiss-Prot
      B2R9Y8, Q14211, Q16649, Q6FGQ8, Q96HS0
      UniProtKB/TrEMBL
      D9IVD5
    4. XM_054362999.1XP_054218974.1  nuclear factor interleukin-3-regulated protein isoform X1

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