Human Gene NFIL3 (ENST00000297689.4) from GENCODE V44
  Description: Homo sapiens nuclear factor, interleukin 3 regulated (NFIL3), transcript variant 3, mRNA. (from RefSeq NM_005384)
RefSeq Summary (NM_005384): 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].
Gencode Transcript: ENST00000297689.4
Gencode Gene: ENSG00000165030.4
Transcript (Including UTRs)
   Position: hg38 chr9:91,409,045-91,423,832 Size: 14,788 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr9:91,409,346-91,410,734 Size: 1,389 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:91,409,045-91,423,832)mRNA (may differ from genome)Protein (462 aa)
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-  Comments and Description Text from UniProtKB
  ID: NFIL3_HUMAN
DESCRIPTION: RecName: Full=Nuclear factor interleukin-3-regulated protein; AltName: Full=E4 promoter-binding protein 4; AltName: Full=Interleukin-3 promoter transcriptional activator; AltName: Full=Interleukin-3-binding protein 1; AltName: Full=Transcriptional activator NF-IL3A;
FUNCTION: Acts as a transcriptional regulator that recognizes and binds to the sequence 5'-[GA]TTA[CT]GTAA[CT]-3', a sequence present in many cellular and viral promoters. Represses transcription from promoters with activating transcription factor (ATF) sites. Represses promoter activity in osteoblasts (By similarity). Represses transcriptional activity of PER1 (By similarity). Represses transcriptional activity of PER2 via the B- site on the promoter (By similarity). Activates transcription from the interleukin-3 promoter in T-cells. Competes for the same consensus-binding site with PAR DNA-binding factors (DBP, HLF and TEF) (By similarity). Component of the circadian clock that acts as a negative regulator for the circadian expression of PER2 oscillation in the cell-autonomous core clock (By similarity). Protects pro-B cells from programmed cell death (By similarity).
SUBUNIT: Homodimer. Binds DNA as a dimer. Interacts with DR1. Interacts with PER2 and CRY2 (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Expressed in bladder stomach, thyroid, spinal cord, lymph node, trachea, adrenal gland, bone marrow and muscle.
INDUCTION: Up-regulated by PHA or TPA.
SIMILARITY: Belongs to the bZIP family. NFIL3 subfamily.
SIMILARITY: Contains 1 bZIP (basic-leucine zipper) domain.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 98.54 RPKM in Adipose - Visceral (Omentum)
Total median expression: 1572.56 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -120.60365-0.330 Picture PostScript Text
3' UTR -74.30301-0.247 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004827 - bZIP
IPR016743 - TF_bZIP_E4BP4
IPR010533 - Vert_IL3-reg_TF

Pfam Domains:
PF07716 - Basic region leucine zipper
PF06529 - Vertebrate interleukin-3 regulated transcription factor

ModBase Predicted Comparative 3D Structure on Q16649
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006955 immune response
GO:0007623 circadian rhythm
GO:0010628 positive regulation of gene expression
GO:0048511 rhythmic process
GO:0071353 cellular response to interleukin-4

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC008197 - Homo sapiens nuclear factor, interleukin 3 regulated, mRNA (cDNA clone MGC:5038 IMAGE:3048714), complete cds.
S79880 - NF-IL3A=interleukin-3 promoter transcriptional activator [human, mRNA, 1922 nt].
X64318 - H.sapiens E4BP4 gene.
LP895627 - Sequence 491 from Patent EP3253886.
U26173 - Human bZIP protein NF-IL3A (IL3BP1) mRNA, complete cds.
JD507854 - Sequence 488878 from Patent EP1572962.
JD043731 - Sequence 24755 from Patent EP1572962.
HM204564 - Homo sapiens nuclear factor interleukin 3 regulated protein (NFIL3) mRNA, complete cds.
JD363228 - Sequence 344252 from Patent EP1572962.
AK313970 - Homo sapiens cDNA, FLJ94618, highly similar to Homo sapiens nuclear factor, interleukin 3 regulated (NFIL3), mRNA.
DQ891105 - Synthetic construct clone IMAGE:100003735; FLH169373.01X; RZPDo839B0796D nuclear factor, interleukin 3 regulated (NFIL3) gene, encodes complete protein.
HQ447282 - Synthetic construct Homo sapiens clone IMAGE:100070593; CCSB002712_03 nuclear factor, interleukin 3 regulated (NFIL3) gene, encodes complete protein.
KJ891698 - Synthetic construct Homo sapiens clone ccsbBroadEn_01092 NFIL3 gene, encodes complete protein.
AB464645 - Synthetic construct DNA, clone: pF1KB9633, Homo sapiens NFIL3 gene for nuclear factor, interleukin 3 regulated, without stop codon, in Flexi system.
CR542049 - Homo sapiens full open reading frame cDNA clone RZPDo834D0636D for gene NFIL3, nuclear factor, interleukin 3 regulated; complete cds, without stopcodon.
CU678887 - Synthetic construct Homo sapiens gateway clone IMAGE:100019511 5' read NFIL3 mRNA.
JD290657 - Sequence 271681 from Patent EP1572962.
JD235153 - Sequence 216177 from Patent EP1572962.
JD382319 - Sequence 363343 from Patent EP1572962.
JD391479 - Sequence 372503 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9Y8, E4BP4, ENST00000297689.1, ENST00000297689.2, ENST00000297689.3, IL3BP1, NFIL3_HUMAN, NM_005384, Q14211, Q16649, Q6FGQ8, Q96HS0, uc004arh.1, uc004arh.2, uc004arh.3, uc004arh.4
UCSC ID: ENST00000297689.4
RefSeq Accession: NM_005384
Protein: Q16649 (aka NFIL3_HUMAN)
CCDS: CCDS6690.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.