Caenorhabditis elegans gene dom-3, encoding downstream Of Mes (in same operon), protein similar to human HLA class III.
SUMMARY back to top
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 2 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 1.0 times the average gene in this release, 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 2%, L1 or L2 larvae 17%, L3 to adult 81%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 6 cDNA clones and 7 elements defined by RNA-seq, some from mixed (seen 3 times), l1 (once).
Alternative mRNA variants and regulation: The gene contains 4 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. Variant b is transpliced to SL1, SL2, SL3, SL4. There are 2 validated alternative polyadenylation sites (see the diagram). 715 bp of this gene are antisense to spliced gene 1F574, raising the possibility of regulated alternate expression.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to one abstract. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: The 2 spliced mRNAs putatively encode the same good protein, some containing RAI1 like domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This gene dom-3 maps on chomosome I at position -0.51 (interpolated). In AceView, it covers 1.72 kb, from 5003352 to 5005069 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1F573, in Wormbase by its cosmid.number name F54C1.2, in NextDB, the Nematode expression pattern database, as CEYK6806.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene DOM3Z.
The closest mouse gene, according to BlastP, is the AceView gene Dom3z (e=2 10-31).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G17620 (e=2 10-15)
          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 dom-3 5' 3' encoded on plus strand of chromosome I from 5,003,352 to 5,004,937 a b 1kb 0 228 bp exon 228 bp exon 49 bp [gt-ag] intron 4 GenBank accessions 106 bp exon 43 bp [gt-ag] intron 4 GenBank accessions 336 bp exon 48 bp [gt-ag] intron 4 GenBank accessions 85 bp exon 98 bp [gt-ag] intron 7 GenBank accessions 725 bp exon 11 accessions, some from mixed (seen 3 times) l1 (once) capped 5' end, 1 accession Validated 3' end, 1 accession 725 bp exon 129 bp exon 129 bp exon 49 bp [gt-ag] intron 4 GenBank accessions 106 bp exon 43 bp [gt-ag] intron 4 GenBank accessions 336 bp exon 48 bp [gt-ag] intron 4 GenBank accessions 85 bp exon 98 bp [gt-ag] intron 7 GenBank accessions 592 bp exon 2 accessions Transpliced 5' end, 2 accessions 592 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 1480 bp 393 aa 113 bp 185 bp 2kb including Promoter 1718 bp 1kb
b 1248 bp 393 aa 14 bp 52 bp 2kb including Promoter 1486 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
mes-3 D C I R P dom-3 C P spe-5 D C P 1F581 C P 1F591 C C P paf-1 C 1F556 D C R P dyf-1 C 1F574 C 1F582 D C I R P pat-10 5kb 0 snf-1, 25 accessions, 2 variants mes-3, 25 accessions, 5 variants dom-3, 13 accessions, 2 variants spe-5, 15 accessions 1F581, 28 accessions, 3 variants 1F591, 7 accessions, 2 variants lfe-2, 99 accessions, 9 variants paf-1, 23 accessions 1F556, 7 accessions, 2 variants dyf-1, 27 accessions, 3 variants 1F574, 24 accessions 1F582, 7 accessions, 2 variants pat-10, 1347 accessions 4 variants 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 5 articles in PubMed.
In addition we found 1 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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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