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    ILF3 interleukin enhancer binding factor 3, 90kDa [ Homo sapiens (human) ]

    Gene ID: 3609, updated on 24-Aug-2015
    Official Symbol
    ILF3provided by HGNC
    Official Full Name
    interleukin enhancer binding factor 3, 90kDaprovided by HGNC
    Primary source
    HGNC:HGNC:6038
    See related
    Ensembl:ENSG00000129351; HPRD:04420; MIM:603182; Vega:OTTHUMG00000180587
    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
    CBTF; DRBF; MMP4; MPP4; NF90; NFAR; NF110; NF90a; NF90b; NFAR2; TCP80; DRBP76; NF110b; NFAR-1; TCP110; MPHOSPH4; NF-AT-90
    Summary
    This gene encodes a double-stranded RNA (dsRNA) binding protein that complexes with other proteins, dsRNAs, small noncoding RNAs, and mRNAs to regulate gene expression and stabilize mRNAs. This protein (NF90, ILF3) forms a heterodimer with a 45 kDa transcription factor (NF45, ILF2) required for T-cell expression of interleukin 2. This complex has been shown to affect the redistribution of nuclear mRNA to the cytoplasm. Knockdown of NF45 or NF90 protein retards cell growth, possibly by inhibition of mRNA stabilization. In contrast, an isoform (NF110) of this gene that is predominantly restricted to the nucleus has only minor effects on cell growth when its levels are reduced. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Dec 2014]
    Orthologs
    See ILF3 in Epigenomics, MapViewer
    Location:
    19p13.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 19 NC_000019.10 (10654261..10692419)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10764937..10803095)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 44 (choline transporter), member 2 Neighboring gene ILF3 antisense RNA 1 (head to head) Neighboring gene queuine tRNA-ribosyltransferase 1 Neighboring gene microRNA 638 Neighboring gene dynamin 2

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    NHGRI GWA Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify interleukin enhancer binding factor 3 (ILF3, NF90), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify interleukin enhancer binding factor 3 (ILF3, NF90), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify interleukin enhancer binding factor 3 (ILF3, NF90), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify interleukin enhancer binding factor 3 (ILF3, NF90), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Rev rev HIV-1 Rev interacting protein, interleukin enhancer binding factor 3 (ILF3), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with ILF3 is increased by RRE PubMed
    rev NF90 inhibits HIV-1 Rev-dependent activity by interfering with the RNA export function of Rev PubMed
    rev NF90-RRE-RNA interaction alters HIV-1 Rev subcellular localization PubMed
    rev Three specific domains (residues 89-123, 405-593, and 594-670) of NF90 promote Rev-RRE mediated nuclear export of Gag mRNA, which is dependent on CRM1 function PubMed
    rev The C-terminal 67 amino acids (604-671) of NF90 interact with HIV-1 Rev PubMed
    Tat tat NF90ctv-TAR RNA interaction shows significant inhibition of Tat-transactivation of the HIV-1 LTR in cells expressing NF90ctv, as well as changes in histone H3 methylation of HIV chromatin PubMed
    tat The C-terminal variant of nuclear factor 90 (NF90ctv) with strong affinity for HIV-1 TAR RNA, competes with Tat/TAR interaction in vitro PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of interleukin enhancer binding factor 3 (ILF3, NF90) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    capsid gag Expression of NF90 drastically reduces the amount of p24 expression, suggesting inhibition of HIV-1 particle production PubMed

    Go to the HIV-1, Human Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    double-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    poly(A) RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    defense response to virus IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of translation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of viral genome replication ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitochondrion IDA
    Inferred from Direct Assay
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    interleukin enhancer-binding factor 3
    Names
    M-phase phosphoprotein 4
    double-stranded RNA-binding protein, 76 kD
    dsRNA binding protein NFAR-2/MPP4
    interleukin enhancer binding factor 3, 90kD
    nuclear factor associated with dsRNA
    nuclear factor of activated T-cells 90 kDa
    nuclear factor of activated T-cells, 90 kD
    translational control protein 80

    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.

    Genomic

    1. NG_029220.1 RefSeqGene

      Range
      5001..43159
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001137673.1NP_001131145.1  interleukin enhancer-binding factor 3 isoform e

      See identical proteins and their annotated locations for NP_001131145.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 3' UTR and coding region compared to variant 4. The resulting isoform (e) has a distinct C-terminus compared to isoform d.
      Source sequence(s)
      AC011475, AW576353, BC064836, DC320902
      Consensus CDS
      CCDS45967.1
      UniProtKB/Swiss-Prot
      Q12906
      Related
      ENSP00000384660, OTTHUMP00000264707, ENST00000407004, OTTHUMT00000452060
      Conserved Domains (2) summary
      smart00572
      Location:88342
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:402465
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    2. NM_004516.3NP_004507.2  interleukin enhancer-binding factor 3 isoform b

      See identical proteins and their annotated locations for NP_004507.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 4. The resulting isoform (b) has a distinct C-terminus compared to isoform d. This isoform is also called NFAR-1 or DRBP76.
      Source sequence(s)
      AJ271745, AJ271747, AW576353, DC320902, X98264
      Consensus CDS
      CCDS12247.1
      UniProtKB/Swiss-Prot
      Q12906
      Conserved Domains (2) summary
      smart00572
      Location:88342
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:402465
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    3. NM_012218.3NP_036350.2  interleukin enhancer-binding factor 3 isoform a

      See identical proteins and their annotated locations for NP_036350.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate splice site in the 3' coding region compared to variant 4. The resulting isoform (a) has a shorter C-terminus compared to isoform d. This isoform is also called NFAR-2, ILF3-E and NF110.
      Source sequence(s)
      AF167570, AJ271747, BC018633, DC320902, X98264
      Consensus CDS
      CCDS12246.1
      UniProtKB/TrEMBL
      A0A024R7C7
      UniProtKB/Swiss-Prot
      Q12906
      Conserved Domains (2) summary
      smart00572
      Location:88342
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:402465
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    4. NM_017620.2NP_060090.2  interleukin enhancer-binding factor 3 isoform d

      See identical proteins and their annotated locations for NP_060090.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (d).
      Source sequence(s)
      AF167570, AJ271744, AJ271747, BC018633, BC064836, DC320902
      Consensus CDS
      CCDS45965.1
      UniProtKB/Swiss-Prot
      Q12906
      Related
      ENSP00000404121, ENST00000449870
      Conserved Domains (2) summary
      smart00572
      Location:88342
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:402465
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    5. NM_153464.2NP_703194.1  interleukin enhancer-binding factor 3 isoform c

      See identical proteins and their annotated locations for NP_703194.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding region compared to variant 4. The resulting isoform (c) has a distinct C-terminus compared to isoform d. This isoform is also called DRBP76 delta and ILF3-C.
      Source sequence(s)
      AJ271745, AJ271746, AJ271747, AW576353, DC320902, X98264
      Consensus CDS
      CCDS45966.1
      UniProtKB/Swiss-Prot
      Q12906
      Related
      ENSP00000250241, OTTHUMP00000264715, ENST00000250241, OTTHUMT00000452071
      Conserved Domains (2) summary
      smart00572
      Location:88342
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:402465
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p2 Primary Assembly

      Range
      10654261..10692419
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006722742.2XP_006722805.1  

      Conserved Domains (2) summary
      smart00572
      Location:88342
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:402465
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    2. XM_011527985.1XP_011526287.1  

      Conserved Domains (2) summary
      smart00572
      Location:88342
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:402465
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    3. XM_011527984.1XP_011526286.1  

      Conserved Domains (2) summary
      smart00572
      Location:85339
      DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
      cd00048
      Location:399462
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    4. XM_011527987.1XP_011526289.1  

      See identical proteins and their annotated locations for XP_011526289.1

      Conserved Domains (1) summary
      cd00048
      Location:67130
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    5. XM_011527986.1XP_011526288.1  

      See identical proteins and their annotated locations for XP_011526288.1

      Conserved Domains (1) summary
      cd00048
      Location:67130
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    6. XM_005259895.3XP_005259952.1  

      Conserved Domains (2) summary
      cd00048
      Location:137200
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
      cl02675
      Location:177
      DZF; DZF domain

    Alternate CHM1_1.1

    Genomic

    1. NC_018930.2 Alternate CHM1_1.1

      Range
      10766190..10804342
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)