Caenorhabditis elegans gene gck-3, encoding germinal Center Kinase, fray / Ste20 homologue.
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SUMMARY
Summary
[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, 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 3 spliced variants.
AceView summary
Expression: According to AceView, this gene is
moderately expressed, only 30.4% of the average gene in this release. The
sequence of this gene is defined by
4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains
9 distinct gt-ag introns. Transcription produces
3 alternatively spliced mRNAs. There are 2 non overlapping alternative last exons and 3 validated
alternative polyadenylation sites (see the
diagram). The mRNAs appear to differ by by truncation of the 3' end, presence or absence of a
cassette exon, overlapping exons with different boundaries.
Protein coding potential: The 3 spliced mRNAs putatively encode
good proteins, altogether
3 different isoforms (2 complete, 1 COOH complete, 1 partial), some containing
domains Serine/threonine protein kinase-related, tyrosine protein kinase [Pfam].
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).
Please quote:
AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
Map on chromosome CHROMOSOME_V, links to other databases and other names
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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 gene, according to BlastP, is the AceView gene
STK39 (e= 10^-142).
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=5 10^-78),
AT4G24100 (e=2 10^-75),
AT4G10730 (e=10^-73)
Complete gene on genome diagram: (in true scale, with colored introns)
This diagram was in previous releases displayed by default on the right of the screen. It shows in true scale the gene on the genome, the mRNAs and the cDNA clones. Opening may be slow for large genes. Please choose between the
zoomable GIF version., and the
Flash version
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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Details on tissue of origin for each intron and exon is available from the
intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
More legend
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron.
]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron).
] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries.
]-[ Pink and
] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal,
blue flags to any single letter variant of the main . More explanations are given in the
gene help file
What is known about the gene and its neighbors on chromosome CHROMOSOME_V
ZOOM OUT
D:disease,
C:conserved,
I:interactions,
R:regulation,
P:publications (see the
Legend)
ZOOM IN
D:disease,
C:conserved,
I:interactions,
R:regulation,
P:publications (see the
Legend)
Annotated mRNA diagrams
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash:
.a, .b, .c.
or in GIF:
.a, .b, .c
Please see this
1 article in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
- GB:AY741200_2 Submitted (02-SEP-2004) Medicine, University of Rochester, 675 Elmwood Ave., Rochester, NY 14620, USA Unpublished
- GB:AY741200_1 A novel STE-20 kinase that interacts with the C. elegans chloride channel CLH-3b Unpublished
To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function and 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 and 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 all variants, their summarized annotations, 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. Merci !