Caenorhabditis elegans essential gene ama-1, encoding DNA-directed RNA polymerase II largest subunit, AMAnitin resistant.
SUMMARY back to top
[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)
          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 ama-1 5' 3' encoded on plus strand of chromosome IV from 4,248,063 to 4,258,199 a b e c d 1 2kb 0 415 bp exon 415 bp exon 298 bp [gt-ag] intron 5 GenBank accessions 414 bp exon 390 bp [gt-ag] intron 6 GenBank accessions 741 bp exon 454 bp [gt-ag] intron 8 GenBank accessions 1589 bp exon 402 bp [gt-ag] intron 5 GenBank accessions 208 bp exon 420 bp [gt-ag] intron 5 GenBank accessions 186 bp exon 807 bp [gt-ag] intron 10 GenBank accessions 526 bp exon 33 accessions, some from embryo (seen 16 times) mixed (10) Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 28 accessions Validated 3' end, 1 accession 526 bp exon 62 bp exon 56 bp [gt-ag] intron 3 GenBank accessions 84 bp exon 84 bp exon 50 bp [gt-ag] intron 4 GenBank accessions 110 bp exon 110 bp exon 97 bp [gt-ag] intron 4 GenBank accessions 329 bp exon 329 bp exon 484 bp [gt-ag] intron 2 GenBank accessions 709 bp exon 709 bp exon 328 bp [gt-ag] intron 1 GenBank accession 306 bp exon 306 bp exon 306 bp [gt-ag] intron 2 GenBank accessions 781 bp exon 781 bp exon 298 bp [gt-ag] intron 5 GenBank accessions 444 bp exon 444 bp exon 360 bp [gt-ag] intron 1 GenBank accession 731 bp exon 731 bp exon 464 bp [gt-ag] fuzzy intron 1 GenBank accession 1589 bp exon 1589 bp exon 1589 bp exon 1589 bp exon 402 bp [gt-ag] intron 5 GenBank accessions 208 bp exon 208 bp exon 420 bp [gt-ag] intron 5 GenBank accessions 186 bp exon 186 bp exon 807 bp [gt-ag] intron 10 GenBank accessions 102 bp exon 14 accessions, some from embryo (seen 3 times) Transpliced 5' end, 3 accessions 102 bp exon 72 bp exon 72 bp exon 420 bp [gt-ag] intron 1 GenBank accession 57 bp exon 1 accession 57 bp exon 329 bp exon 329 bp exon 484 bp [gt-ag] intron 2 GenBank accessions 721 bp exon 316 bp [gt-ag] intron 1 GenBank accession 306 bp exon 2 accessions 306 bp exon 433 bp exon 433 bp exon 390 bp [gt-ag] intron 6 GenBank accessions 741 bp exon 2445 bp [gt-ag] intron 1 GenBank accession 28 bp exon 4 accessions, some from embryo (seen 2 times) 28 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 4079 bp 1217 aa 424 bp 2kb 6850 bp 1kb
b 5641 bp 1165 aa 62 bp 2081 bp 2kb including Promoter 9713 bp 1kb
664 aa 3646 bp 2kb including Promoter 9713 bp 1kb
c 1356 bp 451 aa 2kb 2156 bp 1kb
d 1202 bp 400 aa 2kb 4037 bp 1kb
e 129 bp 42 aa 2kb 549 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
dpy-13 D C I P ttr-20 C ama-1 D C I R P col-33 C P 4F31 C 4F33 C 4F35 C 4F37 C 4F39 C I P 4F3 4F10 C 4E994 P D C P col-34 D C P nhr-78 5kb 0 dpy-13, 538 accessions 2 variants ttr-20, 13 accessions ama-1, 54 accessions, 5 variants col-33, 31 accessions 9 variants 4F31, 6 accessions, 2 variants 4F33, 16 accessions 4F35, 24 accessions, 2 variants 4F37, 6 accessions, 2 variants 4F39, 20 accessions mir-242, 1 accession 4F3, 0 accession 4F43, 19 accessions, 2 variants 4F2, 2 accessions 4F4, 1 accession 4F10, 0 accession 4E994, 31 accessions, 4 variants 4F6, 3 accessions col-34, 113 accessions 4 variants 4F44, 41 accessions, 9 variants nhr-78, 0 accession ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography back to top
Please see these 22 articles in PubMed.
In addition we found 44 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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