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

Gene ID: 3609, updated on 4-Nov-2018

Summary

Official Symbol
ILF3provided by HGNC
Official Full Name
interleukin enhancer binding factor 3provided by HGNC
Primary source
HGNC:HGNC:6038
See related
Ensembl:ENSG00000129351 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]
Expression
Ubiquitous expression in bone marrow (RPKM 45.0), testis (RPKM 34.6) and 25 other tissues See more
Orthologs

Genomic context

See ILF3 in Genome Data Viewer
Location:
19p13.2
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 member 2 Neighboring gene ILF3 divergent tranacript Neighboring gene queuine tRNA-ribosyltransferase catalytic subunit 1 Neighboring gene microRNA 638 Neighboring gene dynamin 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
AU-rich element binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA binding NAS
Non-traceable Author Statement
more info
PubMed 
double-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
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 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region HDA PubMed 
membrane HDA 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 

General protein information

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
interleukin enhancer binding factor 3, 90kDa
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

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.

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
    ENSP00000384660.2, OTTHUMP00000264707, ENST00000407004.7, OTTHUMT00000452060
    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  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
    Related
    ENSP00000465219.1, OTTHUMP00000264708, ENST00000589998.5, OTTHUMT00000452062
    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  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/Swiss-Prot
    Q12906
    UniProtKB/TrEMBL
    A0A024R7C7
    Related
    ENSP00000468156.1, OTTHUMP00000264718, ENST00000590261.5, OTTHUMT00000452074
    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  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
    ENSP00000404121.1, ENST00000449870.5
    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  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
    ENSP00000250241.8, OTTHUMP00000264715, ENST00000250241.12, OTTHUMT00000452071
    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017026763.1XP_016882252.1  interleukin enhancer-binding factor 3 isoform X1

    UniProtKB/Swiss-Prot
    Q12906
    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  2. XM_006722742.2XP_006722805.1  interleukin enhancer-binding factor 3 isoform X2

    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  3. XM_017026765.1XP_016882254.1  interleukin enhancer-binding factor 3 isoform X6

    Conserved Domains (1) summary
    smart00358
    Location:67131
    DSRM; Double-stranded RNA binding motif
  4. XM_011527985.2XP_011526287.1  interleukin enhancer-binding factor 3 isoform X3

    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  5. XM_024451491.1XP_024307259.1  interleukin enhancer-binding factor 3 isoform X5

    Conserved Domains (2) summary
    smart00358
    Location:137201
    DSRM; Double-stranded RNA binding motif
    cl02675
    Location:177
    DZF; DZF domain
  6. XM_011527984.2XP_011526286.2  interleukin enhancer-binding factor 3 isoform X1

    UniProtKB/Swiss-Prot
    Q12906
    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  7. XM_024451490.1XP_024307258.1  interleukin enhancer-binding factor 3 isoform X4

    Conserved Domains (2) summary
    smart00572
    Location:88342
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00358
    Location:402466
    DSRM; Double-stranded RNA binding motif
  8. XM_011527987.1XP_011526289.1  interleukin enhancer-binding factor 3 isoform X6

    See identical proteins and their annotated locations for XP_011526289.1

    Conserved Domains (1) summary
    smart00358
    Location:67131
    DSRM; Double-stranded RNA binding motif
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