Caenorhabditis elegans essential gene cdk-1, encoding cyclin-Dependent Kinase, cell division control protein CDC2 homolog, Nematode Cell Cycle associated ncc-1.
SUMMARY back to top
[Wormbase] cdk-1 encodes a cyclin-dependent kinase, orthologous to and functionally interchangeable with CDC28 from S. cerevisiae; CDK-1 is required for cell-cycle progression through M phase in both meiosis and mitosis.
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 expressed at very high level, 4.0 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 28%, L1 or L2 larvae 8%, L3 to adult (including dauer) 64%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 32 cDNA clones and 21 elements defined by RNA-seq, some from embryo (seen 6 times), mixed (6), l1 (once). We annotate structural defects or features in one cDNA clone.
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, SL3. There are 2 validated alternative polyadenylation sites (see the diagram).
Function: There are 15 articles specifically referring to this gene in PubMed. In addition we point below to 18 abstracts. This essential gene is associated to a phenotype (abnormal pseudocleavage, catastrophic one cell arrest, Embryonic Lethal, Nematode Cell Cycle associated, osmotic or pressure sensitive, Progress through meiotic divisions, required for M phase in meiotic and mitotic cell divisions, shape of one cell embryos abnormal, Sterile adult, STerile and Uncoordinated, STerile Progeny, UNCoordinated locomotion, oogenic protein copurified with chromatin, polar bodies (female meiosis products) abnormal, slow cell cycle). Functionally, the gene has been proposed to participate in processes (osmoregulation, pseudocleavage (sensu Nematoda), protein amino acid phosphorylation). Proteins are expected to have molecular functions (ATP binding activity, protein kinase activity, protein tyrosine kinase activity) and to localize in cytoplasm. These proteins appear to interact with another protein (PAL-1).
Protein coding potential: The 2 spliced mRNAs putatively encode the same good protein, 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 III, links to other databases and other names
Map: This essential gene cdk-1 maps on chomosome III at position +0.79 (interpolated). In AceView, it covers 1.43 kb, from 9747332 to 9748756 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known ncc-1, in Wormgenes/AceView by its positional name 3K837, in Wormbase by its cosmid.number name T05G5.3, in NextDB, the Nematode expression pattern database, as CEYK2952.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes CDC2, CDK3, CDK2.
The closest mouse genes, according to BlastP, are the AceView genes Cdc2a (e= 10-115), Cdk2 (e= 10-105)
          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 cdk-1 5' 3' encoded on plus strand of chromosome III from 9,747,332 to 9,748,756 a b 1kb 0 222 bp exon 222 bp exon 50 bp [gt-ag] intron 21 GenBank accessions 207 bp exon 48 bp [gt-ag] intron 21 GenBank accessions 156 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 327 bp exon 47 bp [gt-ag] intron 20 GenBank accessions 312 bp exon 19 accessions, some from embryo (seen 5 times) mixed (4) Validated 3' end, 71 accessions 312 bp exon 182 bp exon 182 bp exon 50 bp [gt-ag] intron 21 GenBank accessions 207 bp exon 48 bp [gt-ag] intron 21 GenBank accessions 156 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 327 bp exon 47 bp [gt-ag] intron 20 GenBank accessions 316 bp exon 34 accessions, some from mixed (seen 2 times) embryo (once), l1 (once) Transpliced 5' end, 6 accessions Validated 3' end, 71 accessions 316 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 1224 bp 332 aa 42 bp 183 bp 2kb possibly including promoter 1420 bp 1kb
b 1188 bp 332 aa 187 bp 2kb including Promoter 1384 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
cdk-1 D C I P 3K841 C R rmd-1 D C R P cbp-1 D C I R P C C D C P pqm-96 C I R P hlh-4 D C I P iff-1 C R 3K840 D C I R P ech-6 D C P 3K844 C R 3K848 5kb 0 cdk-1, 53 accessions, 2 variants 3K841, 18 accessions, 2 variants rmd-1, 251 accessions 3 variants cbp-1, 59 accessions, 6 variants 3K839, 0 accession clec-162, 6 accessions 3K814, 8 accessions pqm-96, 5 accessions, 2 variants hlh-4, 40 accessions, 5 variants iff-1, 213 accessions 5 variants 3K840, 161 accessions 3 variants ech-6, 120 accessions 4 variants 3K844, 25 accessions, 2 variants 3K848, 31 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 15 articles in PubMed.
In addition we found 18 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 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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