Caenorhabditis elegans gene hoe-1, encoding homolog Of ELAC2 (cancer susceptibility locus).
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SUMMARY back to top
Summary
[Wormbase] hoe-1 encodes, by alternative splicing, two isoforms of a putative metal-dependent hydrolase orthologous to human ELAC2 (OMIM:605367, associated with susceptibility to prostate cancer); HOE-1 is required for fertility, normal growth progression during the late larval stages and germ line proliferation; since hoe-1(RNAi) animals do not produce gametes, hoe-1 may be required for mitosis and meiosis; hoe-1 deficiency suppresses the multivulva (Muv) phenotype of activated LET-60/RAS, while having no effect on other RAS pathway members.
Wormbase predicts 2 models, 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 4 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 high level, 2.2 times the average gene in this release, mostly 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 1%, L1 or L2 larvae 24%, L3 to adult 75%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 14 cDNA clones and 15 elements defined by RNA-seq, some from mixed (seen 5 times), l2 (2), l1 (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 9 distinct introns (8 gt-ag, 1 other). Transcription produces at least 5 different mRNAs, 4 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL2, SL3, c to SL1, SL2, SL3, SL7. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end.
Function: There are 3 articles specifically referring to this gene in PubMed. This gene is associated to a phenotype (LONg body length, SLow growth). Proteins are expected to have molecular function (hydrolase activity) and to localize in cytoplasm. The gene interacts with 2 other genes (GLD-1, LET-60).
Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete, 1 partial), some containing beta-lactamase-like domain [Pfam], a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 2 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 IV, links to other databases and other names
Map: This gene hoe-1 maps on chomosome IV at position +1.17 (interpolated). In AceView, it covers 4.79 kb, from 4744258 to 4739474 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 4F504, in Wormbase by its cosmid.number name E04A4.4, in NextDB, the Nematode expression pattern database, as CEYK89.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene ELAC2 (e=10-68).
The closest mouse gene, according to BlastP, is the AceView gene Elac2 (e=5 10-71).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT3G16260, AT1G52160
          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 uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
a 2692 bp 833 aa 17 bp 173 bp 2kb including Promoter 4785 bp 1kb
b 2952 bp 760 aa 671 bp 2kb possibly including promoter 4277 bp 1kb
c 2681 bp 760 aa 246 bp 152 bp 45 bp 2kb including Promoter 4764 bp 1kb
d 194 bp 34 aa 87 bp 2kb probably including promoter 956 bp 1kb
e 62 bp 19 aa 2kb 229 bp 1kb

Gene neighbors and Navigator on chromosome IV 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 3 articles in PubMed.
? 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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