Caenorhabditis elegans essential gene eif-3.F, encoding eukaryotic Initiation Factor.
SUMMARY back to top
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at very high level, 7.7 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 25%, L1 or L2 larvae 10%, L3 to adult (including dauer) 64%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 28 cDNA clones and 74 elements defined by RNA-seq, some from mixed (seen 11 times), embryo (10), l2 (2), l1 (once).
The gene contains 3 distinct gt-ag introns. Transcription produces one spliced mRNA, 1 alternatively spliced variant and 1 unspliced form. Variant a is transpliced to SL4, SL2, SL3, SL5, SL1, SL7, b to SL2, SL3, SL5, SL7. There are 3 validated alternative polyadenylation sites (see the diagram).
Function: There are 4 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (DumPY : shorter than wild-type, Embryonic Lethal, Larval arrest, STerile Progeny, various morphological defects, shared oogenic and spermatogenic protein copurified with chromatin). This protein appears to interact with another protein (LST-3).
Protein coding potential: The spliced mRNAs putatively encode a good protein, containing Mov34/MPN/PAD-1 domain [Pfam], a coiled coil stretch [Psort2]. 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 II, links to other databases and other names
Map: This essential gene eif-3.F maps on chomosome II at position +1.36 (interpolated). In AceView, it covers 2.36 kb, from 9331566 to 9333922 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2J623, in Wormbase by its cosmid.number name D2013.7, in NextDB, the Nematode expression pattern database, as CEYK1718.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes EIF3S5, hCG_15200.
The closest mouse gene, according to BlastP, is the AceView gene Eif3s5.
The closest A.thaliana gene, according to BlastP, is the AceView gene EIF2
          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 eif-3.F 5' 3' encoded on plus strand of chromosome II from 9,331,566 to 9,333,922 a b 1kb 0 172 bp exon 172 bp exon 429 bp [gt-ag] intron 24 GenBank accessions 515 bp exon 54 bp [gt-ag] intron 18 GenBank accessions 139 bp exon 587 bp [gt-ag] intron 24 GenBank accessions 461 bp exon 101 accessions, some from mixed (seen 11 times) embryo (10), l2 (2), l1 (once) Transpliced 5' end, 15 accessions Validated 3' end, 27 accessions Validated 3' end, 9380 accessions Validated 3' end, 361 accessions 461 bp exon 165 bp exon 1 accession Transpliced 5' end, 1 accession 165 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 1287 bp 294 aa 19 bp 383 bp 2kb including Promoter 2357 bp 1kb
b 165 bp 51 aa 12 bp 2kb including Promoter 165 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
wdfy-2 D C I R P 2J613 C eat-3 D C R P 2J621 C I P eif-3.F D C I R P scp-1 D C R P ttll-12 C 2J643 C C 2J608 C P rab-39 D C I P 2J632 D C R P sdhb-1 5kb 0 wdfy-2, 36 accessions 2 variants 2J613, 0 accession eat-3, 112 accessions 5 variants 2J621, 0 accession eif-3.F, 102 accessions 2 variants scp-1, 50 accessions, 7 variants ttll-12, 31 accessions 2 variants 2J643, 43 accessions, 2 variants cam-1, 140 accessions 12 variants 2J608, 8 accessions rab-39, 12 accessions 4 variants 2J632, 34 accessions, 2 variants sdhb-1, 442 accessions 5 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 4 articles in PubMed.
? Gene Summary Gene on genome mRNA:.a, .b 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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