Caenorhabditis elegans essential gene gpd-1, encoding glyceraldehyde 3-Phosphate Dehydrogenase.
SUMMARY back to top
[Wormbase] gpd-1 encodes one of four C. elegans glyceraldehyde-3-phosphate dehydrogenases (GAPDHs); by homology, GPD-1 is predicted to reversibly catalyze the oxidation and phosphorylation of glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate during glycolysis; GPD-1 is required for embryogenesis, normal body morphology, and gonad development; in C. elegans, GPD-1 and GPD-4 constitute the minor GAPDH isoenzymes and are expressed primarily in embryos, in all cell types.
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at very high level, 14.7 times the average gene in this release, in L3, L4, adult and culminating in embryos [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 80%, L1 or L2 larvae 1%, L3 to adult (including dauer) 19%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 54 cDNA clones and 140 elements defined by RNA-seq, some from embryo (seen 30 times), mixed (3). We annotate structural defects or features in one cDNA clone.
The gene contains 2 distinct gt-ag introns. Transcription produces one spliced mRNA, 1 alternatively spliced variant and 1 unspliced form. Variant a is transpliced to SL1, SL5, b to SL1. There are 2 validated alternative polyadenylation sites (see the diagram).
Function: There are 10 articles specifically referring to this gene in PubMed. In addition we point below to one abstract. This essential gene is associated to a phenotype (abnormal gonad morphology, Embryonic Lethal, SMAll body size, oogenic protein copurified with chromatin). Functionally, the gene has been proposed to participate in a process (glucose metabolism). Proteins are expected to have molecular function (glyceraldehyde 3-phosphate dehydrogenase (phosphorylating) activity) and to localize in cytoplasm.
Protein coding potential: The spliced and the unspliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 partial), some containing domains glyceraldehyde 3-phosphate dehydrogenase, glyceraldehyde 3-phosphate dehydrogenase [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome II, links to other databases and other names
Map: This essential gene gpd-1 maps on chomosome II at position +2.29 (interpolated). In AceView, it covers 1.24 kb, from 10394039 to 10395280 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2K685, in Wormbase by its cosmid.number name T09F3.3, in NextDB, the Nematode expression pattern database, as CEYK2502.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes GAPDH (e= 10-144), GAPDHS (e= 10-132), GAPDHP1 (e= 10-132).
The closest mouse genes, according to BlastP, are the AceView genes LOC654475, LOC654473, LOC380687, LOC626807, Gapdh.1, Gapdh, LOC654474, LOC433921, OTTMUSG00000005300, EG277333, EG629557, Gapdhs.
The closest A.thaliana genes, according to BlastP, are the AceView genes GAPCP-2, GAPCP-1, GAPC-2, GAPC
          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 gpd-1 5' 3' encoded on plus strand of chromosome II from 10,394,050 to 10,395,280 a b 500bp 0 531 bp exon 531 bp exon 52 bp [gt-ag] intron 31 GenBank accessions 433 bp exon 48 bp [gt-ag] intron 40 GenBank accessions 167 bp exon 188 accessions, some from embryo (seen 29 times) mixed (2) Transpliced 5' end, 16 accessions Validated 3' end, 1 accession Validated 3' end, 937 accessions 167 bp exon 542 bp exon 542 bp exon 6 accessions, some from embryo (seen once) mixed (once) Transpliced 5' end, 1 accession 542 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 1131 bp 341 aa 8 bp 97 bp 2kb including Promoter 1231 bp 1kb
b 542 bp 174 aa 19 bp 2kb including Promoter 542 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
ztf-27 C I P 2K683 C P gpd-1 D C R P 2K687 C 2K689 C R 2K703 C 2K709 D C R P 5kb 0 ztf-27, 20 accessions 2 variants 2K683, 53 accessions, 3 variants gpd-1, 194 accessions 2 variants 2K687, 9 accessions 2K689, 28 accessions, 4 variants 2K703, 11 accessions, 2 variants 2K709, 74 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 these 10 articles in PubMed.
In addition we found 1 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 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'.

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