Summary
[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, 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 summary
Expression: According to AceView, this gene is expressed at high level, 2.7 times the average gene in this release, at all stages of development [Kohara cDNAs]. The sequence of this gene is defined by 35 cDNA clones. We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 14 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. There are 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by by truncation of the 5' end, overlapping exons with different boundaries.
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (1 complete, 2 COOH complete, 1 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].
Function: There are 17 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.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12

Map: This essential gene ama-1 maps on chomosome IV at position +0.05 (interpolated). In AceView, it covers 10.14 kb, from 4248063 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.

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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. 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. Details on tissue of origin for each intron and exon is available from the intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession 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.
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