Caenorhabditis elegans gene gck-3, encoding germinal Center Kinase, fray / Ste20 homologue.
SUMMARY back to top
[Wormbase] gck-3 encodes a STE20-related kinase, required for normal excretory canal tubules, that is regulated by WNK-1 and in turn inhibits CLH-3; GCK-3 is expressed in oocytes and the excretory cell; GCK-3 binds the C-terminus of CLH-3B in both two-hybrid and GST affinity assays; GCK-3 inhibits a fast gating process in CLH-3B by phosphorylating it, both reducing the magnitude of CLH-3B's responses to hyperpolarization and slowing them; gck-3(tm1296) mutants are sterile, perhaps because they lose sperm from their spermathecae; gck-3(tm1296) mutants also have defective excretory canal tubules; both the fertility and the excretory canal phenotypes of gck-3(tm1296) are partially suppressible by the null clh-3(ok763) allele; a wnk-1 phenotype similar to gck-3(tm1296)'s is suppressible by constitutively activated GCK-3; and gck-3(RNAi) constitutively activates CLH-3B in immature oocytes; GCK-3 is phosphorylated by WNK-1 in vitro, and gck-3 mutants phenotypically resemble wnk-1.
Wormbase predicts one model from 2 genes, 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 high level, 1.5 times the average gene in this release. The sequence of this gene is defined by 4 cDNA clones and 16 elements defined by RNA-seq, some from l4 (seen once), mixed (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces at least 5 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2, SL3, SL4, SL5, b to SL4, c to SL2. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 2 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 3 cassette exons, overlapping exons with different boundaries.
Function: There is one article specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. Functionally, the gene has been proposed to participate in a process (protein amino acid phosphorylation). Proteins are expected to have molecular functions (ATP binding activity, protein kinase activity, protein tyrosine kinase activity).
Protein coding potential: The 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (2 complete, 3 partial), some containing domains Serine/threonine protein kinase-related, tyrosine protein kinase [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome V, links to other databases and other names
Map: This gene gck-3 maps on chomosome V at position +13.26 (interpolated). In AceView, it covers 13.12 kb, from 17966814 to 17953700 (WS190), on the reverse strand.
Links to: WormBase, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5S434, in Wormbase by its cosmid.number name Y59A8B.23.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes STK39, OXSR1.
The closest mouse gene, according to BlastP, is the AceView gene Stk39 (e= 10-143).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G14720 (e=2 10-78), AT1G79640 (e=6 10-78), AT4G24100 (e=2 10-75), AT4G10730 (e=10-73)
          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 gck-3 5' 3' encoded on minus strand of chromosome V from 17,966,814 to 17,953,700 a b c d e 1 2kb 0 271 bp exon 271 bp exon 1258 bp [gt-ag] intron 4 GenBank accessions 185 bp exon 1396 bp [gt-ag] intron 4 GenBank accessions 228 bp exon 1007 bp [gt-ag] intron 3 GenBank accessions 225 bp exon 3730 bp [gt-ag] intron 3 GenBank accessions 279 bp exon 1652 bp [gt-ag] intron 3 GenBank accessions 472 bp exon 1098 bp [gt-ag] intron 2 GenBank accessions 161 bp exon 711 bp [gt-ag] intron 2 GenBank accessions 442 bp exon 14 accessions, some from mixed (seen once) Transpliced 5' end, 2 accessions Validated 3' end, 5 accessions 442 bp exon 271 bp exon 271 bp exon 1258 bp [gt-ag] intron 4 GenBank accessions 185 bp exon 1396 bp [gt-ag] intron 4 GenBank accessions 228 bp exon 1007 bp [gt-ag] intron 3 GenBank accessions 225 bp exon 3730 bp [gt-ag] intron 3 GenBank accessions 279 bp exon 1430 bp [gt-ag] intron 2 GenBank accessions 179 bp exon 43 bp [gt-ag] intron 2 GenBank accessions 267 bp exon 3 accessions, some from l4 (seen once) Transpliced 5' end, 1 accession Validated 3' end, 1 accession 267 bp exon 165 bp exon 165 bp exon 1258 bp [gt-ag] intron 4 GenBank accessions 185 bp exon 1396 bp [gt-ag] intron 4 GenBank accessions 98 bp exon 1 accession Transpliced 5' end, 1 accession 98 bp exon 274 bp exon 274 bp exon 1325 bp [gt-ag] intron 1 GenBank accession 80 bp exon 1 accession 80 bp exon 274 bp exon 274 bp exon 1220 bp [gt-ag] intron 1 GenBank accession 55 bp exon 1 accession 55 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 2263 bp 596 aa 84 bp 388 bp 2kb including Promoter 13115 bp 1kb
b 1634 bp 440 aa 84 bp 227 bp 2kb including Promoter 10498 bp 1kb
c 448 bp 147 aa 5 bp 2kb including Promoter 3102 bp 1kb
d 354 bp 107 aa 31 bp 2kb probably including promoter 1679 bp 1kb
e 329 bp 99 aa 31 bp 2kb probably including promoter 1549 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
5S433 D C I R P dpy-21 C R P gck-3 C I P 5S448 5kb 0 5S433, 0 accession dpy-21, 34 accessions 3 variants gck-3, 20 accessions, 5 variants 5S448, 23 accessions, 3 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 this 1 article in PubMed.
In addition we found 2 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 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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