Caenorhabditis elegans gene gdi-1, encoding rab GDP Dissociation Inhibitor.
SUMMARY back to top
[Wormbase] gdi-1 encodes a member of the Rab GDP dissociation inhibitor (GDI) family with high similarity to Drosophila Gdi; expressed around the pharyngeal, vulval, and tail regions.
Wormbase predicts 2 models

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 19.8 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 10%, L1 or L2 larvae 42%, L3 to adult 48%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 221 cDNA clones and 39 elements defined by RNA-seq, some from l2 (seen 64 times), l1 (52), l4 (39), embryo (26), mixed (15). We annotate structural defects or features in 12 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 3 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL7, b to SL2, SL1, SL3, SL4, SL7, SL5, SL8, SL9, SL10, SL11, SL12. There are 6 validated alternative polyadenylation sites (see the diagram). 729 bp of this gene are antisense to spliced gene 4P555, raising the possibility of regulated alternate expression.
Function: There are 2 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. This gene is associated to a phenotype (oogenic protein copurified with chromatin). Functionally, the gene has been proposed to participate in a process (regulation of GTPase activity). Proteins are expected to localize in cytoplasm.
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing Rab GTPase activator domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome IV, links to other databases and other names
Map: This gene gdi-1 maps on chomosome IV at position +12.91 (interpolated). In AceView, it covers 2.40 kb, from 14792846 to 14790451 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 4P556, in Wormbase by its cosmid.number name Y57G11C.10, in NextDB, the Nematode expression pattern database, as CEYK73.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes GDI2 (e= 10-128), GDI1 (e= 10-127).
The closest mouse genes, according to BlastP, are the AceView genes Gdi1 (e= 10-159), Gdi2 (e= 10-158).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G09550 (e= 10-132), ATGDI2 (e= 10-128), ATGDI1 (e= 10-127)
          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 gdi-1 5' 3' encoded on minus strand of chromosome IV from 14,792,846 to 14,790,765 a b 500bp 0 1074 bp exon 1074 bp exon 276 bp [gt-ag] intron 2 GenBank accessions 254 bp exon 57 bp [gt-ag] intron 181 GenBank accessions 407 bp exon 4 accessions, some from l1 (seen 2 times) l2 (once), l4 (once) Transpliced 5' end, 2 accessions Validated 3' end, 56 accessions Validated 3' end, 22 accessions Validated 3' end, 247 accessions 407 bp exon 1029 bp exon 1029 bp exon 321 bp [gt-ag] intron 158 GenBank accessions 254 bp exon 57 bp [gt-ag] intron 181 GenBank accessions 735 bp exon 253 accessions, some from l2 (seen 60 times) l1 (50), l4 (38), embryo (26) mixed (15) Transpliced 5' end, 138 accessions Validated 3' end, 56 accessions Validated 3' end, 22 accessions Validated 3' end, 247 accessions 735 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 1735 bp 459 aa 35 bp 320 bp 2kb including Promoter 2068 bp 1kb
b 2018 bp 444 aa 35 bp 648 bp 2kb including Promoter 2396 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
4P531 D C R P C 4P547 C R 4P555 D C I R P arl-8 D C R P 4P565 C 4P573 C R C R C P 4P536 P C D C R P gdi-1 C P coq-3 D C R P nuo-3 C R 5kb 0 4P531, 28 accessions, 2 variants 4P533, 37 accessions, 3 variants 4P547, 0 accession 4P555, 188 accessions 10 variants arl-8, 66 accessions, 2 variants 4P565, 41 accessions 4P573, 10 accessions, 4 variants 4P528, 7 accessions 4P534, 0 accession 4P536, 24 accessions, 6 variants 4P538, 12 accessions 4P548, 12 accessions, 3 variants gdi-1, 260 accessions 2 variants coq-3, 32 accessions, 7 variants nuo-3, 101 accessions 4 variants 4P576, 11 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 2 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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