Human Gene EIF4B (uc001sbh.4)
  Description: Homo sapiens eukaryotic translation initiation factor 4B (EIF4B), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:53,400,062-53,435,993 Size: 35,932 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr12:53,400,268-53,434,007 Size: 33,740 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:53,400,062-53,435,993)mRNA (may differ from genome)Protein (611 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: IF4B_HUMAN
DESCRIPTION: RecName: Full=Eukaryotic translation initiation factor 4B; Short=eIF-4B;
FUNCTION: Required for the binding of mRNA to ribosomes. Functions in close association with EIF4-F and EIF4-A. Binds near the 5'- terminal cap of mRNA in presence of EIF-4F and ATP. Promotes the ATPase activity and the ATP-dependent RNA unwinding activity of both EIF4-A and EIF4-F.
SUBUNIT: Self-associates and interacts with EIF3 p170 subunit.
INTERACTION: P53350:PLK1; NbExp=3; IntAct=EBI-970310, EBI-476768;
PTM: Phosphorylated at Ser-422 by RPS6KA1 and RPS6KB1; phosphorylation enhances the affinity of EIF4B for the EIF3 complex.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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
  • D013749 Tetrachlorodibenzodioxin
  • C017947 sodium arsenite
  • C016403 2,4-dinitrotoluene
  • C023514 2,6-dinitrotoluene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C085911 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one
  • C472791 3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid
  • C009505 4,4'-diaminodiphenylmethane
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015127 9,10-Dimethyl-1,2-benzanthracene
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 182.85 RPKM in Ovary
Total median expression: 3630.25 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 -54.50206-0.265 Picture PostScript Text
3' UTR -560.291986-0.282 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WI8 - NMR 2J76 - NMR


ModBase Predicted Comparative 3D Structure on P23588
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003743 translation initiation factor activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0033592 RNA strand annealing activity
GO:0034057 RNA strand-exchange activity
GO:0043024 ribosomal small subunit binding

Biological Process:
GO:0001731 formation of translation preinitiation complex
GO:0006412 translation
GO:0006413 translational initiation
GO:0006446 regulation of translational initiation
GO:0097010 eukaryotic translation initiation factor 4F complex assembly

Cellular Component:
GO:0005829 cytosol
GO:0005844 polysome
GO:0016281 eukaryotic translation initiation factor 4F complex


-  Descriptions from all associated GenBank mRNAs
  AK310244 - Homo sapiens cDNA, FLJ17286.
AK299329 - Homo sapiens cDNA FLJ54492 complete cds, highly similar to Eukaryotic translation initiation factor 4B.
AK222528 - Homo sapiens mRNA for eukaryotic translation initiation factor 4B variant, clone: adSE02039.
AK293731 - Homo sapiens cDNA FLJ59206 complete cds, highly similar to Eukaryotic translation initiation factor 4B.
AK299526 - Homo sapiens cDNA FLJ59405 complete cds, highly similar to Eukaryotic translation initiation factor 4B.
AK299510 - Homo sapiens cDNA FLJ59402 complete cds, highly similar to Eukaryotic translation initiation factor 4B.
BC073154 - Homo sapiens eukaryotic translation initiation factor 4B, mRNA (cDNA clone MGC:88034 IMAGE:6015183), complete cds.
BC073139 - Homo sapiens eukaryotic translation initiation factor 4B, mRNA (cDNA clone MGC:88035 IMAGE:6527540), complete cds.
BC098437 - Homo sapiens eukaryotic translation initiation factor 4B, mRNA (cDNA clone MGC:104867 IMAGE:6459393), complete cds.
BC007745 - Homo sapiens cDNA clone IMAGE:4099384, containing frame-shift errors.
CR627377 - Homo sapiens mRNA; cDNA DKFZp686O21248 (from clone DKFZp686O21248).
CU687250 - Synthetic construct Homo sapiens gateway clone IMAGE:100023247 5' read EIF4B mRNA.
CR456958 - Homo sapiens full open reading frame cDNA clone RZPDo834G0121D for gene EIF4B, eukaryotic translation initiation factor 4B; complete cds, incl. stopcodon.
AB385251 - Synthetic construct DNA, clone: pF1KB9498, Homo sapiens EIF4B gene for eukaryotic translation initiation factor 4B, complete cds, without stop codon, in Flexi system.
KJ896755 - Synthetic construct Homo sapiens clone ccsbBroadEn_06149 EIF4B gene, encodes complete protein.
AB076839 - Homo sapiens eIF4B mRNA for initation factor 4B, complete cds.
JD264465 - Sequence 245489 from Patent EP1572962.
JD163476 - Sequence 144500 from Patent EP1572962.
JD565898 - Sequence 546922 from Patent EP1572962.
JD078291 - Sequence 59315 from Patent EP1572962.
JD196925 - Sequence 177949 from Patent EP1572962.
JD251383 - Sequence 232407 from Patent EP1572962.
JD179009 - Sequence 160033 from Patent EP1572962.
BC001097 - Homo sapiens eukaryotic translation initiation factor 4B, mRNA (cDNA clone IMAGE:3507583), partial cds.
JD130118 - Sequence 111142 from Patent EP1572962.
JD531265 - Sequence 512289 from Patent EP1572962.
JD371874 - Sequence 352898 from Patent EP1572962.
JD043472 - Sequence 24496 from Patent EP1572962.
AK307496 - Homo sapiens cDNA, FLJ97444.
JD269513 - Sequence 250537 from Patent EP1572962.
AK092188 - Homo sapiens cDNA FLJ34869 fis, clone NT2NE2014650, highly similar to EUKARYOTIC TRANSLATION INITIATION FACTOR 4B.
DL491009 - Novel nucleic acids.
JD162569 - Sequence 143593 from Patent EP1572962.
BC064029 - Homo sapiens cDNA clone IMAGE:6173372, partial cds.
BC047302 - Homo sapiens, clone IMAGE:4444787, mRNA.
JD041623 - Sequence 22647 from Patent EP1572962.
JD054921 - Sequence 35945 from Patent EP1572962.
JD435075 - Sequence 416099 from Patent EP1572962.
JD552434 - Sequence 533458 from Patent EP1572962.
JD118406 - Sequence 99430 from Patent EP1572962.
JD024700 - Sequence 5724 from Patent EP1572962.
BC007974 - Homo sapiens cDNA clone IMAGE:4297962, partial cds.
JD035393 - Sequence 16417 from Patent EP1572962.
JD028168 - Sequence 9192 from Patent EP1572962.
BC013994 - Homo sapiens cDNA clone IMAGE:3629020, partial cds.
JD111203 - Sequence 92227 from Patent EP1572962.
JD526037 - Sequence 507061 from Patent EP1572962.
JD114339 - Sequence 95363 from Patent EP1572962.
DL490612 - Novel nucleic acids.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04150 - mTOR signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein P23588 (Reactome details) participates in the following event(s):

R-HSA-165777 Phosphorylation and activation of eIF4B by activated S6K1
R-HSA-72619 eIF2:GTP is hydrolyzed, eIFs are released
R-HSA-429955 CCR4-NOT complex deadenylates mRNA
R-HSA-429992 PARN deadenylates mRNA
R-HSA-72621 Ribosomal scanning
R-HSA-157849 Formation of translation initiation complexes containing mRNA that does not circularize
R-HSA-72697 Start codon recognition
R-HSA-156823 Association of phospho-L13a with GAIT element of Ceruloplasmin mRNA
R-HSA-156808 Formation of translation initiation complexes yielding circularized Ceruloplasmin mRNA in a 'closed-loop' conformation
R-HSA-430021 PAN2-PAN3 complex partially deadenylates mRNA
R-HSA-8941312 ZCCHC6, ZCCHC11 are mRNA uridyltransferases
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S
R-HSA-166208 mTORC1-mediated signalling
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit
R-HSA-429947 Deadenylation of mRNA
R-HSA-72702 Ribosomal scanning and start codon recognition
R-HSA-72649 Translation initiation complex formation
R-HSA-156827 L13a-mediated translation
R-HSA-72737 Cap-dependent Translation Initiation
R-HSA-165159 mTOR signalling
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-72613 Eukaryotic Translation Initiation
R-HSA-162582 Signal Transduction
R-HSA-8953854 Metabolism of RNA
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: IF4B_HUMAN, NM_001417, NP_001408, P23588, Q4G0E3, Q53HQ2, Q6GPH5, Q6IB46, Q8WYK5
UCSC ID: uc001sbh.4
RefSeq Accession: NM_001417
Protein: P23588 (aka IF4B_HUMAN)
CCDS: CCDS41788.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001417.4
exon count: 15CDS single in 3' UTR: no RNA size: 4041
ORF size: 1836CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 3760.00frame shift in genome: no % Coverage: 99.68
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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