Caenorhabditis elegans essential gene ife-1, encoding translation Initiation Factor 4E eIF4E.
SUMMARY back to top
[Wormbase] The ife-1 gene encodes one of five C. elegans homologs of the mRNA cap-binding protein eIF4E; it is specifically required for spermatogenesis, and is expressed in P granules.
Wormbase predicts one model, 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 2 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 11.2 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 36%, L1 or L2 larvae 14%, L3 to adult 50%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 95 cDNA clones and 53 elements defined by RNA-seq, some from embryo (seen 10 times), mixed (6), l2 (2), l1 (once).
Alternative mRNA variants and regulation: The gene contains 3 distinct gt-ag introns. Transcription produces 4 different mRNAs, 2 alternatively spliced variants and 2 unspliced forms. Variant b is transpliced to SL3, SL1, SL2, SL4, SL5, SL7, c to SL2, SL3, SL4, SL5. There are 2 probable alternative promotors and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end.
Function: There are 6 articles specifically referring to this gene in PubMed. In addition we point below to 5 abstracts. This essential gene is associated to a phenotype (required for male meiosis, required for spermatogenesis). Functionally, the gene has been proposed to participate in a process (translational initiation). Proteins are expected to have molecular functions (DNA binding activity, RNA binding activity, translation initiation factor activity) and to localize in various compartments (cytoplasm, intracellular). These proteins appear to interact with other proteins (1N443, PGL-1).
Protein coding potential: 2 spliced and the unspliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 partial), some containing domains Transcription factor CBF/NF-Y/archaeal histone, histone core, Eukaryotic translation initiation factor 4E (eIF-4E) [Pfam]. The remaining mRNA variant (unspliced; partial) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome III, links to other databases and other names
Map: This essential gene ife-1 maps on chomosome III at position +20.82 (interpolated). In AceView, it covers 1.96 kb, from 13342565 to 13344519 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3O433, in Wormbase by its cosmid.number name F53A2.6, in NextDB, the Nematode expression pattern database, as CEYK4844.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene IF4E.0 (e=10-36).
The closest mouse genes, according to BlastP, are the AceView genes EG668879andEif4e (e=2 10-37), Eif4e1b (e=3 10-35).
The closest A.thaliana genes, according to BlastP, are the AceView genes EIF4E (e=2 10-29), AT1G29550 (e=2 10-27), LSP1 (e=10-26), AT1G29590 (e=2 10-26)
          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-1 5' 3' encoded on plus strand of chromosome III from 13,343,454 to 13,344,508 a c d b 1kb 0 416 bp exon 82 bp [gt-ag] intron 2 GenBank accessions 480 bp exon 480 bp exon 161 bp [gt-ag] intron 6 GenBank accessions 466 bp exon 46 bp [gt-ag] intron 63 GenBank accessions 277 bp exon 38 accessions, some from mixed (seen 2 times) Validated 3' end, 128 accessions 277 bp exon 390 bp exon 390 bp exon 1 accession Transpliced 5' end, 1 accession 390 bp exon 159 bp exon 159 bp exon 3 accessions Validated 3' end, 15 accessions 159 bp exon 466 bp exon 466 bp exon 46 bp [gt-ag] intron 63 GenBank accessions 304 bp exon 106 accessions, some from embryo (seen 10 times) mixed (4), l2 (2), l1 (once) Transpliced 5' end, 5 accessions Validated 3' end, 188 accessions 304 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 1639 bp 231 aa 841 bp 102 bp 2kb possibly including promoter 1928 bp 1kb
b 770 bp 212 aa 129 bp 2kb including Promoter 816 bp 1kb
c 390 bp 125 aa 13 bp 2kb including Promoter 390 bp 1kb
d 159 bp 23 aa 85 bp 2kb 159 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
sdz-20 D P nud-1 D C I P dro-1 C ife-1 D C I P 3O435 D C R P mtm-6 D C I R P C I R P 3O408C I P 3O426 C 3O444 C C 5kb 0 sdz-20, 2 accessions nud-1, 40 accessions dro-1, 0 accession ife-1, 148 accessions 4 variants 3O435, 79 accessions, 3 variants mtm-6, 43 accessions, 6 variants 3O445, 2 accessions 3O408C, 11 accessions 3 variants 3O426, 7 accessions 3O444, 10 accessions, 4 variants 3O450, 13 accessions 3O456, 2 accessions 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 6 articles in PubMed.
In addition we found 5 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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