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
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.
. 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
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
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
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
The closest mouse genes
, according to BlastP, are the AceView genes Golt1b
The closest A.thaliana genes
, according to BlastP, are the AceView genes AT3G03180
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.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line
denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line
denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink
and ] - ] blue
straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags
to any single letter variant of the main . More explanations are given in the gene help file