Caenorhabditis elegans gene ife-3, encoding translation Initiation Factor 4E eIF4E.
SUMMARY back to top
[Wormbase] ife-3 encodes one of five C. elegans homologs of the mRNA cap-binding protein eIF4E; by homology, IFE-3 is predicted to bind capped mRNA and mediate its recruitment to ribosomes during translation initiation; in vitro, IFE-3 binds a monomethylated guanosine cap structure but does not bind a trimethylated guanosine cap, which suggests that IFE-3 likely mediates translation of those mRNAs that do not contain a spliced-leader sequence; of the C. elegans eIF4E isoforms, IFE-3 is the most similar to human eIF4E and is the only isoform required for viability (homozygous ife-3 mutant embryos arrest in the early division stages of embryogenesis); IFE-3 is enriched in the adult gonad.
Wormbase predicts 3 models, but Caenorhabditis elegans cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 4 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 13.6 times the average gene in this release, in embryos [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 100%, L3 to adult 0%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 48 cDNA clones and 131 elements defined by RNA-seq, some from embryo (seen 6 times). We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 6 distinct gt-ag introns. Transcription produces 4 alternatively spliced mRNAs. Variant a is transpliced to SL1. There are 2 probable alternative promotors and 7 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, overlapping exons with different boundaries. 529 bp of this gene are antisense to spliced gene 5A485, raising the possibility of regulated alternate expression.
Function: There are 7 articles specifically referring to this gene in PubMed. In addition we point below to 3 abstracts. This gene is associated to a phenotype. Functionally, the gene has been proposed to participate in a process (translational initiation). Proteins are expected to have molecular functions (RNA binding activity, translation initiation factor activity) and to localize in cytoplasm. These proteins appear to interact with other proteins (1N443, 4K910, PQN-45).
Protein coding potential: The 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (2 complete, 2 COOH complete), some containing Eukaryotic translation initiation factor 4E (eIF-4E) domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome V, links to other databases and other names
Map: This gene ife-3 maps on chomosome V at position -20.10 (interpolated). In AceView, it covers 1.24 kb, from 7822 to 6581 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5A486, in Wormbase by its cosmid.number name B0348.6, in NextDB, the Nematode expression pattern database, as CEYK2484.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes EIF4E (e=2 10-56), IF4E.0 (e=3 10-55).
The closest mouse gene, according to BlastP, is the AceView gene EG668879andEif4e (e=2 10-10).
The closest A.thaliana gene, according to BlastP, is the AceView gene EIF4E (e=2 10-56)
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene ife-3 5' 3' encoded on minus strand of chromosome V from 7,822 to 6,581 a b c d 500bp 0 172 bp exon 172 bp exon 41 bp [gt-ag] intron 27 GenBank accessions 177 bp exon 39 bp [gt-ag] intron 9 GenBank accessions 236 bp exon 47 bp [gt-ag] intron 21 GenBank accessions 530 bp exon 157 accessions, some from embryo (seen 4 times) Transpliced 5' end, 2 accessions Validated 3' end, 196 accessions Validated 3' end, 457 accessions 530 bp exon 167 bp exon 167 bp exon 41 bp [gt-ag] intron 27 GenBank accessions 177 bp exon 42 bp [gt-ag] intron 4 GenBank accessions 233 bp exon 47 bp [gt-ag] intron 21 GenBank accessions 510 bp exon 4 accessions, some from embryo (seen once) Validated 3' end, 196 accessions 510 bp exon 168 bp exon 41 bp [gt-ag] intron 27 GenBank accessions 177 bp exon 48 bp [gt-ag] intron 17 GenBank accessions 227 bp exon 47 bp [gt-ag] intron 21 GenBank accessions 514 bp exon 17 accessions, some from embryo (seen once) Validated 3' end, 196 accessions 514 bp exon 126 bp exon 126 bp exon 164 bp [gt-ag] intron 1 GenBank accession 504 bp exon 504 bp exon 1 accession Validated 3' end, 196 accessions 504 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
Downstream sequence
a 1115 bp 251 aa 4 bp 355 bp 2kb including Promoter 1242 bp 1kb
b 1087 bp 249 aa 335 bp 2kb probably including promoter 1217 bp 1kb
c 1086 bp 248 aa 339 bp 2kb probably including promoter 1222 bp 1kb
d 630 bp 94 aa 345 bp 2kb 794 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
5A485 C D C I R P ife-3 5kb 0 5A485, 6 accessions egl-8, 72 accessions, 13 variants ife-3, 179 accessions 4 variants ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography back to top
Please see these 7 articles in PubMed.
In addition we found 3 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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