Caenorhabditis elegans essential gene cua-1, encoding cu++-ATpase, copper transporter, P-type ATPase similar to human Menkes disease-associated protein.
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SUMMARY back to top
Summary
[Wormbase] The cua-1 gene encodes a putative E1-E2 ATPase orthologous to the human gene KIAA1347 (ATP7A; OMIM:604384), which when mutated leads to Hailey-Hailey disease.
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 8 spliced variants
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AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 21.0 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 9%, L1 or L2 larvae 59%, L3 to adult 32%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 238 cDNA clones and 38 elements defined by RNA-seq, some from l1 (seen 128 times), l2 (38), mixed (24), embryo (18), l4 (11), whole animal (2). We annotate structural defects or features in 12 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 28 distinct gt-ag introns. Transcription produces at least 9 different mRNAs, 8 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL1, SL2, SL3, SL4, b to SL2, SL1, SL1', i to SL1. There are 3 probable alternative promotors, 7 non overlapping alternative last exons and 18 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 6 cassette exons, overlapping exons with different boundaries. 155 bp of this gene are antisense to spliced gene 3O511, 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 5 articles specifically referring to this gene in PubMed. In addition we point below to 4 abstracts. This essential gene is associated to a phenotype (Paralysed, UNCoordinated locomotion, affects axonal growth or guidance). Functionally, the gene has been proposed to participate in processes (metabolism, metal ion transport). Proteins are expected to have molecular functions (ATP binding activity, enzyme activity, hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, metal ion binding activity) and to localize in various compartments (cytoplasm, membrane, plasma membrane).
Protein coding potential: 6 spliced mRNAs putatively encode good proteins, altogether 6 different isoforms (3 complete, 3 COOH complete), some containing domains ABC transporter-like, E1-E2 ATPase-associated region, Heavy metal transport/detoxification protein, haloacid dehalogenase-like hydrolase [Pfam], some transmembrane domains, a second peroximal domain, a coiled coil stretch [Psort2]. The remaining 3 mRNA variants (2 spliced, 1 unspliced; 3 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome III, links to other databases and other names
Map: This essential gene cua-1 maps on chomosome III at position +20.97 (interpolated). In AceView, it covers 44.59 kb, from 13467699 to 13423111 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3O530, in Wormbase by its cosmid.number name Y76A2A.2, in NextDB, the Nematode expression pattern database, as CEYK618.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes ATP7B (e=2 10-08), ATP7A (e=5 10-07), LOC644732 (e=6 10-07).
The closest mouse genes, according to BlastP, are the AceView genes Atp7b (e=2 10-08), Atp7a (e=2 10-07).
The closest A.thaliana genes, according to BlastP, are the AceView genes HMA5 (e=4 10-07), PAA1.1 (e=2 10-05)
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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.
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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
unit
pre-mRNA
Downstream sequence
a 3970 bp 1238 aa 47 bp 206 bp 2kb including Promoter 15593 bp 1kb
b 2420 bp 622 aa 31 bp 520 bp 2kb including Promoter 4556 bp 1kb
c 1549 bp 462 aa 158 bp 2kb 7026 bp 1kb
d 2203 bp 355 aa 482 bp 653 bp 2kb possibly including promoter 10270 bp 1kb
e 421 bp 79 aa 181 bp 2kb 677 bp 1kb
f 1674 bp 114 aa 1329 bp 2kb 4605 bp 1kb
g 432 bp 79 aa 192 bp 2kb 3549 bp 1kb
h 455 bp 63 aa 263 bp 2kb 19870 bp 1kb
i 153 bp 46 aa 14 bp 2kb including Promoter 153 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
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 4 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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 !