[Wormbase] ama-1 encodes the large subunit of RNA polymerase II required for mRNA transcription; AMA-1 is essential for proper embryonic development, particularly for the early division and migration of the endodermal precursor (E) cells that initiate gastrulation; AMA-1 is expressed ubiquitously in the developing embryo until the 550-cell stage.
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 5 spliced variants.
AceView synopsis, each blue text links to tables and details Expression: According to AceView, this gene is expressed at very high level, 4.1 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 46%, L1 or L2 larvae 4%, L3 to adult 50%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 35 cDNA clones and 19 elements defined by RNA-seq, some from embryo (seen 21 times), mixed (10). We annotate structural defects or features in 2 cDNA clones. Alternative mRNA variants and regulation: The gene contains 17 distinct gt-ag introns. Transcription produces at least 5 alternatively spliced mRNAs. Variant b is transpliced to SL1. There are 2 probable alternative promotors and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of a cassette exon, overlapping exons with different boundaries.
Note that mRNA .b was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD). Function: There are 22 articles specifically referring to this gene in PubMed. In addition we point below to 44 abstracts. This essential gene is associated to a phenotype (AMAnitin resistant, Embryonic Lethal, SLow growth, Sterile adult, unhealthy, spindle elongation or integrity abnormal, affects spindle orientation, abundant spermatogenesis enriched protein copurified with chromatin). Functionally, the gene has been proposed to participate in processes (transcription, transcription from Pol II promoter). Proteins are expected to have molecular function (DNA binding activity) and to localize in DNA-directed RNA polymerase II, core complex. These proteins appear to interact with another protein (RGR-1). Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (2 complete, 1 COOH complete, 2 partial), some containing domains RNA polymerase Rpb1, domain 1, RNA polymerase, alpha subunit, RNA polymerase Rpb1, domain 3, RNA polymerase Rpb1, domain 4, RNA polymerase Rpb1, domain 5, RNA polymerase Rpb1, domain 6, RNA polymerase Rpb1, domain 7, RNA polymerase II, heptapeptide repeat, eukaryotic [Pfam], a coiled coil stretch [Psort2]. The remaining mRNA variant (spliced; 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 IV, links to other databases and other names Map: This essential gene ama-1 maps on chomosome IV at position +0.05 (interpolated). In AceView, it covers 10.63 kb, from 4247571 to 4258199 (WS190), on the direct strand. Links to:WormBase, NextDB, RNAiDB. Other names: The gene is also known in Wormgenes/AceView by its positional name 4F21, in Wormbase by its cosmid.number name F36A4.7, in NextDB, the Nematode expression pattern database, as CEYK1310. Closest AceView homologs in other species ? The closest human gene, according to BlastP, is the AceView gene POLR2A (e=0.0). The closest mouse gene, according to BlastP, is the AceView gene Polr2a (e=0.0). The closest A.thaliana gene, according to BlastP, is the AceView gene NRPB1 (e=0.0)
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.
or in GIF: .a, .b, .c, .d, .e
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 !