Caenorhabditis elegans gene fut-3, encoding FUcosyl Transferase.
SUMMARY back to top
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 3 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.1 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 12%, L1 or L2 larvae 20%, L3 to adult (including dauer) 68%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 23 cDNA clones and 18 elements defined by RNA-seq, some from mixed (seen 5 times), embryo (2), l2 (2), l1 (once).
Alternative mRNA variants and regulation: The gene contains 9 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL2, SL1, SL3, b to SL7, SL5, SL2, SL3, SL4. There are 2 non overlapping alternative last exons and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of a cassette exon, overlapping exons with different boundaries.
Function: There are 2 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. Functionally, the gene has been proposed to participate in a process (protein amino acid glycosylation). Proteins are expected to have molecular function (fucosyltransferase activity) and to localize in various compartments (extracellular space, membrane).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing Glycosyl transferase, family 10 domain [Pfam]; 1 of the 2 complete proteins appears to be secreted.

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 fut-3 maps on chomosome II at position -1.01 (interpolated). In AceView, it covers 2.07 kb, from 5659747 to 5657678 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2F948, in Wormbase by its cosmid.number name F59E12.13, in NextDB, the Nematode expression pattern database, as CEYK6649.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes FUT6 (e=0.11), NDUFA11andFUT5 (e=0.14), FUT3 (e=0.14), FUT9 (e=0.57)
          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 fut-3 5' 3' encoded on minus strand of chromosome II from 5,659,747 to 5,657,678 a b c 1 2kb 0 278 bp exon 278 bp exon 44 bp [gt-ag] intron 13 GenBank accessions 172 bp exon 42 bp [gt-ag] intron 12 GenBank accessions 226 bp exon 142 bp [gt-ag] intron 13 GenBank accessions 127 bp exon 341 bp [gt-ag] intron 14 GenBank accessions 89 bp exon 47 bp [gt-ag] intron 16 GenBank accessions 90 bp exon 47 bp [gt-ag] intron 16 GenBank accessions 148 bp exon 46 bp [gt-ag] intron 17 GenBank accessions 226 bp exon 34 accessions, some from mixed (seen 3 times) embryo (2), l2 (once) Transpliced 5' end, 3 accessions Validated 3' end, 31 accessions 226 bp exon 270 bp exon 44 bp [gt-ag] intron 13 GenBank accessions 172 bp exon 42 bp [gt-ag] intron 12 GenBank accessions 226 bp exon 142 bp [gt-ag] intron 13 GenBank accessions 127 bp exon 341 bp [gt-ag] intron 14 GenBank accessions 89 bp exon 47 bp [gt-ag] intron 16 GenBank accessions 90 bp exon 47 bp [gt-ag] intron 16 GenBank accessions 148 bp exon 46 bp [gt-ag] intron 17 GenBank accessions 221 bp exon 5 accessions, some from mixed (seen 2 times) l1 (once), l2 (once) Transpliced 5' end, 5 accessions 221 bp exon 123 bp exon 123 bp exon 477 bp [gt-ag] intron 1 GenBank accession 94 bp exon 43 bp [gt-ag] intron 1 GenBank accession 142 bp exon 2 accessions 142 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 1356 bp 400 aa 8 bp 145 bp 2kb including Promoter 2065 bp 1kb
b 1343 bp 400 aa 140 bp 2kb including Promoter 2052 bp 1kb
c 359 bp 53 aa 79 bp 118 bp 2kb possibly including promoter 879 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2F929 C R zyg-1 D C I P 2F947 C R 2F953 D C R P C 2F955 C R flp-27 C C 2F924 C I P 2F930 D C I P ddl-1 D C I P bli-2 C P fut-3 C R 2F950 C R 2F956 D C P 2F960 5kb 0 2F929, 7 accessions zyg-1, 49 accessions, 3 variants 2F947, 72 accessions, 2 variants 2F953, 28 accessions, 5 variants 2F953b, 6 accessions, 2 variants 2F955, 7 accessions flp-27, 38 accessions 2F947a, 1 accession 2F958, 3 accessions, 2 variants 2F924, 0 accession 2F930, 55 accessions, 2 variants ddl-1, 51 accessions, 5 variants bli-2, 6 accessions fut-3, 41 accessions, 3 variants 2F950, 37 accessions, 4 variants 2F956, 29 accessions, 3 variants 2F960, 44 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 2 articles in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c 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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !