Caenorhabditis elegans gene acs-11, encoding putative fatty Acid CoA Synthetase.
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 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, 4.4 times the average gene in this release, mostly from L1 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 7%, L1 or L2 larvae 63%, L3 to adult (including dauer) 31%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 37 cDNA clones and 21 elements defined by RNA-seq, some from l1 (seen 19 times), l2 (9), l4 (3), embryo (2), mixed (2). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 11 distinct introns (10 gt-ag, 1 gc-ag). Transcription produces at least 5 different mRNAs, 4 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL1, b to SL1, SL2, SL11, SL3, SL4, SL5, c to SL1. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 5 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end.
Function:. Functionally, the gene has been proposed to participate in processes (metabolism, vesicle-mediated transport). Proteins are expected to have molecular function (enzyme activity) and to localize in membrane.
Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 partial), some containing domains AMP-dependent synthetase and ligase, Got1-like protein [Pfam], some transmembrane domains [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 gene acs-11 maps on chomosome II at position -2.81 (interpolated). In AceView, it covers 4.97 kb, from 4740399 to 4745369 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2F35, in Wormbase by its cosmid.number name F41C3.3, in NextDB, the Nematode expression pattern database, as CEYK9078.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes GOLT1B, LOC197322.
The closest mouse genes, according to BlastP, are the AceView genes Golt1b (e=4 10-18), Golt1aandKiss1 (e=10-16).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT3G03180, AT3G49420, AT5G01430, AT3G16170
          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 acs-11 5' 3' encoded on plus strand of chromosome II from 4,742,115 to 4,745,279 c a b d e 1 2kb 0 66 bp exon 66 bp exon 47 bp [gt-ag] intron 3 GenBank accessions 92 bp exon 45 bp [gt-ag] intron 4 GenBank accessions 103 bp exon 48 bp [gt-ag] intron 5 GenBank accessions 76 bp exon 152 bp [gt-ag] intron 5 GenBank accessions 82 bp exon 47 bp [gt-ag] intron 5 GenBank accessions 419 bp exon 12 accessions, some from embryo (seen 2 times) l2 (once), mixed (once) Transpliced 5' end, 1 accession Validated 3' end, 544 accessions 419 bp exon 122 bp exon 122 bp exon 54 bp [gt-ag] intron 29 GenBank accessions 99 bp exon 56 bp [gt-ag] intron 29 GenBank accessions 252 bp exon 480 bp [gt-ag] intron 28 GenBank accessions 954 bp exon 892 bp [gc-ag] intron 33 GenBank accessions 232 bp exon 14 accessions, some from l1 (seen 2 times) l4 (2), l2 (once) Transpliced 5' end, 3 accessions Validated 3' end, 3 accessions 232 bp exon 113 bp exon 113 bp exon 54 bp [gt-ag] intron 29 GenBank accessions 99 bp exon 56 bp [gt-ag] intron 29 GenBank accessions 252 bp exon 480 bp [gt-ag] intron 28 GenBank accessions 954 bp exon 892 bp [gc-ag] intron 33 GenBank accessions 346 bp exon 28 accessions, some from l1 (seen 17 times) l2 (7), l4 (once), mixed (once) Transpliced 5' end, 24 accessions Validated 3' end, 2 accessions Validated 3' end, 30 accessions 346 bp exon 79 bp exon 41 bp [gt-ag] intron 1 GenBank accession 190 bp exon 783 bp [gt-ag] intron 1 GenBank accession 113 bp exon 2 accessions 113 bp exon 81 bp exon 81 bp exon 2 accessions Validated 3' end, 10 accessions 81 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 1659 bp 505 aa 11 bp 130 bp 2kb including Promoter 3141 bp 1kb
b 1764 bp 505 aa 244 bp 2kb including Promoter 3246 bp 1kb
c 838 bp 141 aa 35 bp 377 bp 2kb including Promoter 1177 bp 1kb
d 382 bp 127 aa 2kb 1206 bp 1kb
e 81 bp 22 aa 11 bp 2kb 81 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2F29 C R 2F31 D C P acs-11 C 2F41 D C I R P 2F43 C 2F45 D C I R P 2F49 C 2F53 C 2F25 2F27 C R P 2F4 C I P ttr-41 C R P 2F24 C 2F46 C I P ttm-2 5kb 0 2F29, 61 accessions, 3 variants 2F31, 0 accession acs-11, 58 accessions 5 variants 2F41, 26 accessions, 2 variants 2F43, 8 accessions 2F45, 14 accessions 2F49, 3 accessions 2F53, 8 accessions, 3 variants 2F25, 4 accessions, 2 variants 2F27, 14 accessions, 2 variants 2F4, 44 accessions, 2 variants ttr-41, 292 accessions 2 variants 2F24, 11 accessions, 2 variants 2F46, 7 accessions, 2 variants ttm-2, 21 accessions, 3 variants ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e 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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