Caenorhabditis elegans essential gene gpd-4, encoding glyceraldehyde 3-Phosphate Dehydrogenase.
SUMMARY back to top
[Wormbase] gpd-4 encodes one of four C. elegans glyceraldehyde-3-phosphate dehydrogenases (GAPDHs); by homology, GPD-4 is predicted to reversibly catalyze the oxidation and phosphorylation of glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate during glycolysis; GPD-4 is required for embryonic and larval development; in C. elegans, GPD-4 and GPD-1 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, 7.4 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 74%, L1 or L2 larvae 1%, L3 to adult 25%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 26 cDNA clones and 72 elements defined by RNA-seq, some from embryo (seen 14 times), mixed (2).
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, b to SL1.
Function: There are 9 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. This essential gene is associated to a phenotype (Embryonic Lethal, Larval arrest, 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-4 maps on chomosome II at position +2.07 (interpolated). In AceView, it covers 1.25 kb, from 10171181 to 10172427 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2K461, in Wormbase by its cosmid.number name F33H1.2, 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= 10-131), GAPDHP1 (e= 10-131).
The closest mouse genes, according to BlastP, are the AceView genes LOC626807, LOC380687, Gapdh.1, Gapdh, LOC654475, LOC654473, 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-4 5' 3' encoded on plus strand of chromosome II from 10,171,192 to 10,172,427 a b 500bp 0 533 bp exon 533 bp exon 52 bp [gt-ag] intron 14 GenBank accessions 433 bp exon 48 bp [gt-ag] intron 21 GenBank accessions 170 bp exon 94 accessions, some from embryo (seen 14 times) mixed (2) Transpliced 5' end, 6 accessions Validated 3' end, 284 accessions 170 bp exon 544 bp exon 544 bp exon 4 accessions Transpliced 5' end, 1 accession 544 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 1136 bp 341 aa 10 bp 100 bp 2kb including Promoter 1236 bp 1kb
b 544 bp 174 aa 21 bp 2kb including Promoter 544 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
pax-3 D C I P C 2K453 R gpd-4 D C P 2K463 D C I P 2K469 D C R P 2K481 C srb-6 D C I R P daf-19 D C P srd-1 C P srd-2 C P cdc-25.4 5kb 0 pax-3, 22 accessions 2K445, 2 accessions 2K453, 1 accession gpd-4, 98 accessions, 2 variants 2K463, 13 accessions, 3 variants 2K469, 113 accessions 2K481, 3 accessions srb-6, 2 accessions 2K478, 1 accession daf-19, 61 accessions 6 variants srd-1, 4 accessions srd-2, 0 accession cdc-25.4, 8 accessions 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 9 articles 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 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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