Caenorhabditis elegans gene ife-5, encoding translation Initiation Factor 4E eIF4E.
SUMMARY back to top
[Wormbase] ife-5 encodes a member of the Initiation Factor 4E (eIF4E) family; it is expressed in the germ line.
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 4 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.8 times the average gene in this release, in L2 and L3 larvae [Kohara cDNAs]. The sequence of this gene is defined by 4 cDNA clones and 6 elements defined by RNA-seq, some from l2 (seen 2 times).
Alternative mRNA variants and regulation: The gene contains 4 distinct introns (2 gt-ag, 2 gc-ag). Transcription produces 4 alternatively spliced mRNAs. Variant b is transpliced to SL2. There are 3 probable alternative promotors and 2 non overlapping alternative last exons (see the diagram). The mRNAs appear to differ by truncation of the 3' end, overlapping exons with different boundaries.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to 3 abstracts. 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.
Protein coding potential: The 4 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (1 complete, 3 partial), 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 II, links to other databases and other names
Map: This gene ife-5 maps on chomosome II at position +7.12 (interpolated). In AceView, it covers 3.47 kb, from 12280577 to 12284049 (WS190), on the direct strand.
Links to: WormBase, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2M573, in Wormbase by its cosmid.number name Y57A10A.30.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene EIF4E (e=4 10-28).
The closest mouse genes, according to BlastP, are the AceView genes EG668879andEif4e (e=3 10-32), Eif4e1b (e=4 10-30).
The closest A.thaliana genes, according to BlastP, are the AceView genes EIF4E (e=4 10-28), LSP1 (e=10-27), AT1G29550 (e=10-26), AT1G29590 (e=2 10-25)
          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-5 5' 3' encoded on plus strand of chromosome II from 12,280,577 to 12,284,041 a b c d 1kb 0 963 bp exon 963 bp exon 30 bp uORF 963 bp exon 963 bp exon 53 bp [gt-ag] intron 5 GenBank accessions 150 bp exon 150 bp exon 1 accession 150 bp exon 119 bp exon 119 bp exon 93 bp uORF 119 bp exon 2579 bp [gt-ag] intron 3 GenBank accessions 458 bp exon 458 bp exon 458 bp exon 53 bp [gt-ag] intron 5 GenBank accessions 264 bp exon 264 bp exon 7 accessions, some from l2 (seen 2 times) Transpliced 5' end, 3 accessions Validated 3' end, 2 accessions 264 bp exon 529 bp exon 529 bp exon 60 bp uORF 529 bp exon 529 bp exon 535 bp [gc-ag] intron 1 GenBank accession 455 bp exon 455 bp exon 1 accession 455 bp exon 529 bp exon 529 bp exon 60 bp uORF 529 bp exon 529 bp exon 95 bp [gc-ag] intron 1 GenBank accession 55 bp exon 1 accession 55 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 uORF Upstream sequence Transcription
Downstream sequence
a 1113 bp 201 aa 508 bp 27 bp 2kb possibly including promoter 1166 bp 1kb
b 841 bp 201 aa 122 bp 113 bp 90 bp 2kb including Promoter 3473 bp 1kb
c 984 bp 178 aa 448 bp 57 bp 2kb possibly including promoter 1519 bp 1kb
d 584 bp 66 aa 386 bp 57 bp 2kb possibly including promoter 679 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2M555 D C R P 2M571 C ife-5 C P 2M589 C I P sre-50 C C 2M548 D C P 2M560 C 2M566 P 2M592 5kb 0 2M555, 73 accessions, 4 variants 2M571, 20 accessions, 5 variants ife-5, 10 accessions, 4 variants 2M589, 18 accessions sre-50, 2 accessions 2M548, 36 accessions, 2 variants 2M560, 26 accessions, 3 variants 2M566, 14 accessions 2M592, 13 accessions 2M596, 16 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 5 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 C

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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