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Wormbase predicts 4 models from 2 genes, 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 6 spliced variants.
AceView synopsis, each blue text links to tables and details Expression: According to AceView, this gene is expressed at very high level, 9.1 times the average gene in this release, only in embryos, L1, L2 and L3 larvae [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 43%, L1 or L2 larvae 51%, L3 to adult 7%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 41 cDNA clones and 79 elements defined by RNA-seq, some from embryo (seen 13 times), l1 (8), l2 (8), whole animal (2). We annotate structural defects or features in 77 cDNA clones. Alternative mRNA variants and regulation: The gene contains 12 distinct introns (11 gt-ag, 1 gc-ag). Transcription produces at least 7 different mRNAs, 6 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL3, b to SL1, SL2, SL3, SL4, SL11, SL1'. There are 2 probable alternative promotors and 6 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of 3 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron. 133 bp of this gene are antisense to spliced gene 5E192, raising the possibility of regulated alternate expression.
2 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD). Function: There are 14 articles specifically referring to this gene in PubMed. In addition we point below to 13 abstracts. This essential gene is associated to a phenotype (abnormal cell LINeage, Larval arrest, LEThal, Male ABnormal, Sterile adult, NO Germ line, EGg Laying defective, oogenic protein copurified with chromatin). Proteins are expected to have molecular function (DNA binding activity) and to localize in extracellular space. These proteins appear to interact with other proteins (LIN-36, LIN-53). The gene interacts with 2 other genes (EGL-27, LET-60). Protein coding potential: 6 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (4 complete, 1 COOH complete), some containing domains Bromo adjacent region, ELM2, myb, DNA-binding [Pfam], a vacuolar domain, a coiled coil stretch [Psort2]; 2 of the 4 complete proteins appear to be secreted. 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 V, links to other databases and other names Map: This essential gene lin-40 maps on chomosome V at position -8.16 (interpolated). In AceView, it covers 7.81 kb, from 3704982 to 3712789 (WS190), on the direct strand. Links to:WormBase, NextDB, RNAiDB.
as Other names: The gene is also known let-432, nog-1, egr-1, in Wormgenes/AceView by its positional name 5E189, in Wormbase by its cosmid.number name T27C4.4, in NextDB, the Nematode expression pattern database, as CEYK2415. Closest AceView homologs in other species ? The closest human genes, according to BlastP, are the AceView genes MTA1 (e=2 10-57), hCG_1783907andMTA3 (e=2 10-57), EML3andMTA2 (e=6 10-57). The closest mouse genes, according to BlastP, are the AceView genes Mta1 (e=2 10-57), Mta3 (e=3 10-57), Eml3andMta2 (e=6 10-57), Mta2 (e=6 10-57). The closest A.thaliana genes, according to BlastP, are the AceView genes MET2 (e=0.11), AT3G52250 (e=0.12), AT4G08990 (e=0.31), MEE57 (e=0.37)
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.
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. Read more...
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.
Introns 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.
Exons: 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
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash: .a, .b, .c, .d, .e, .f, .g.
or in GIF: .a, .b, .c, .d, .e, .f, .g
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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