Caenorhabditis elegans essential gene gpi-1, encoding glucose phosphate isomerase, affects lifespan as part of the insulin/FOXO pathway.
SUMMARY back to top
[Wormbase] gpi-1 encodes two isoforms of a putative glucose 6-phosphate isomerase orthologous to human GPI (OMIM:172400, mutated in chronic hemolytic anemia); gpi-1 is required both for embryonic viability and (paradoxically) for normally short lifespan; gpi-1 is expressed in neurons and intestine.
Wormbase predicts 2 models, 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 6 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 13.3 times the average gene in this release, at all stages of development [Kohara cDNAs], in most tissues, including intestine, gonad and nervous system [Kohara in situ hybridisation to RNA, see NextDB]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 7%, L1 or L2 larvae 36%, L3 to adult 56%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 89 cDNA clones and 86 elements defined by RNA-seq, some from l2 (seen 27 times), l4 (15), l1 (14), mixed (12), embryo (7). We annotate structural defects or features in 9 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces at least 7 different mRNAs, 6 alternatively spliced variants and 1 unspliced form. Variant b is transpliced to SL1, SL2, SL3, SL4, SL12, SL7, e to SL1, SL2, SL3, SL4, SL5, SL7, SL8. There are 3 probable alternative promotors, 4 non overlapping alternative last exons and 8 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.
Function: There are 3 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (extends adult lifespan, abnormal DAuer Formation, Embryonic Lethal). Functionally, the gene has been proposed to participate in processes (gluconeogenesis, glycolysis). Proteins are expected to have molecular functions (glucose-6-phosphate isomerase activity, ubiquitin-like-protein ligase activity). These proteins appear to interact with another protein (ABU-11). The gene interacts with 5 other genes (DAF-2, DAF-12, DAF-16, GLP-1, UBC-14).
Protein coding potential: 5 spliced and the unspliced mRNAs putatively encode good proteins, altogether 6 different isoforms (4 complete, 2 COOH complete), some containing domains Phosphoglucose isomerase (PGI), Ubiquitin-conjugating enzyme, E2 [Pfam], a second peroximal domain [Psort2]. The remaining mRNA variant (spliced) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This essential gene gpi-1 maps on chomosome I at position +19.18 (interpolated). In AceView, it covers 9.24 kb, from 13576051 to 13585291 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1O173, in Wormbase by its cosmid.number name Y87G2A.8, in NextDB, the Nematode expression pattern database, as CEYK3744.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes GPIandPDCD2L, UBE2G2.
The closest mouse gene, according to BlastP, is the AceView gene Gpi1 (e=0.0).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G42740, UBC7, UBC13, UBC14
          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 gpi-1 5' 3' encoded on plus strand of chromosome I from 13,576,141 to 13,581,635 a e b g c d f 1 2kb 0 328 bp exon 328 bp exon 27 bp uORF 328 bp exon 328 bp exon 264 bp [gt-ag] intron 10 GenBank accessions 121 bp exon 121 bp exon 832 bp [gt-ag] intron 65 GenBank accessions 293 bp exon 293 bp exon 602 bp [gt-ag] intron 61 GenBank accessions 851 bp exon 851 bp exon 964 bp [gt-ag] intron 61 GenBank accessions 272 bp exon 272 bp exon 720 bp [gt-ag] intron 64 GenBank accessions 338 bp exon 338 bp exon 52 accessions, some from mixed (seen 11 times) l4 (4), embryo (3), l1 (3) l2 (2) Validated 3' end, 1 accession Validated 3' end, 107 accessions 338 bp exon 55 bp exon 55 bp exon 868 bp [gt-ag] intron 8 GenBank accessions 143 bp exon 988 bp [gt-ag] intron 8 GenBank accessions 199 bp exon 1135 bp [gt-ag] intron 8 GenBank accessions 213 bp exon 70 accessions, some from embryo (seen 3 times) l2 (2) Transpliced 5' end, 4 accessions Validated 3' end, 263 accessions 213 bp exon 121 bp exon 121 bp exon 832 bp [gt-ag] intron 65 GenBank accessions 293 bp exon 602 bp [gt-ag] intron 61 GenBank accessions 851 bp exon 964 bp [gt-ag] intron 61 GenBank accessions 272 bp exon 720 bp [gt-ag] intron 64 GenBank accessions 282 bp exon 47 accessions, some from l2 (seen 22 times) l1 (11), l4 (11), embryo (once) mixed (once) Transpliced 5' end, 41 accessions Validated 3' end, 1 accession Validated 3' end, 107 accessions 282 bp exon 119 bp exon 225 bp [gt-ag] intron 1 GenBank accession 341 bp exon 1 accession 341 bp exon 1001 bp exon 1001 bp exon 1 accession 1001 bp exon 687 bp exon 1956 bp [gt-ag] intron 1 GenBank accession 201 bp exon 1 accession Validated 3' end, 1 accession 201 bp exon 119 bp exon 4534 bp [gt-ag] intron 1 GenBank accession 201 bp exon 201 bp exon 187 bp [gt-ag] intron 1 GenBank accession 2 accessions Validated 3' end, 1 accession Validated 3' end, 65 accessions 54 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 uORF Upstream sequence Transcription
Downstream sequence
a 2203 bp 586 aa 225 bp 217 bp 24 bp 2kb possibly including promoter 5585 bp 1kb
b 1819 bp 551 aa 161 bp 2kb including Promoter 4937 bp 1kb
c 1001 bp 324 aa 25 bp 2kb 1001 bp 1kb
d 888 bp 230 aa 195 bp 2kb 2844 bp 1kb
e 610 bp 170 aa 12 bp 85 bp 2kb including Promoter 3601 bp 1kb
f 374 bp 79 aa 134 bp 2kb probably including promoter 5095 bp 1kb
g 460 bp 45 aa 322 bp 2kb probably including promoter 685 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
C C 1O167 C I P gpi-1 D C I R P ubc-14 D C I P 1O187 C R cyn-15 D C P vps-28 C 1O180 C 1O194 5kb 0 1O153, 6 accessions, 2 variants grd-15, 5 accessions 1O167, 25 accessions, 2 variants gpi-1, 175 accessions 7 variants ubc-14, 0 accession 1O187, 5 accessions vrs-2, 58 accessions, 2 variants cyn-15, 43 accessions 2 variants vps-28, 74 accessions 1O180, 8 accessions 1O194, 10 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 3 articles in PubMed.
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g 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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