Caenorhabditis elegans essential complex locus idi-1C, encoding isopentenyl Diphosphate Isomerase, needed for protein prenylation, affects lysosomes and autophagy, and is possibly required for fusion of cytoplasmic vesicles.
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SUMMARY back to top
Summary
[Wormbase] idi-1 encodes an isopentyl-diphosphate isomerase that, by sequence similarity, is predicted to function in the synthesis of lipophilic molecules; in C. elegans, idi-1 activity is required for larval growth, movement and development and for removal of apoptotic cell corpses produced by the normal course of programmed cell death; in addition, idi-1 is required for normal morphology and size of vesicular organelles such as lysosomes and autophagosomes, suggesting that IDI-1 activity is essential for proper membrane dynamics.
Wormbase predicts 2 models from 2 genes, 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 4 spliced variants
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AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 4.8 times the average gene in this release, mostly from L1 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 1%, L1 or L2 larvae 20%, L3 to adult (including dauer) 79%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 25 cDNA clones and 38 elements defined by RNA-seq, some from mixed (seen 12 times), l2 (4), l1 (2), l4 (once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 15 distinct gt-ag introns. Transcription produces at least 5 different mRNAs, 4 alternatively spliced variants and 1 unspliced form. Variant b is transpliced to SL4, SL5, SL2, SL10, SL3, SL7, c to SL1, SL2, SL3, SL4, e to SL2. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 2 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 2 cassette exons.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to one abstract. This essential gene is associated to a phenotype (CEll Death abnormality, cells accumulate lysosomes and autophagosomes, early larval arrest, Paralysed, persistance of cell corpses, affects autophagy). Proteins are expected to have molecular function (hydrolase activity) and to localize in nucleus. The gene interacts with CUP-5.
Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 partial), some containing NUDIX hydrolase, core domain [Pfam], a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 1 partial) appear not to encode good proteins.

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 idi-1C maps on chomosome III at position -0.30 (interpolated). In AceView, it covers 4.57 kb, from 8088408 to 8092975 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known idi-1, in Wormgenes/AceView by its positional name 3J183, in Wormbase by its cosmid.number name K06H7.3, K06H7.9, in NextDB, the Nematode expression pattern database, as CEYK1224.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes ANKZF1, IDI1, C10orf110, flawroby, IDI2.
The closest mouse gene, according to BlastP, is the AceView gene Ankzf1 (e=6 10-14).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT1G01930, IDI2\/IPIAT1\/IPP2, IPP1
          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 idi-1C 5' 3' encoded on plus strand of chromosome III from 8,088,408 to 8,092,975 a b c e d 1 2kb 0 203 bp exon 203 bp exon 49 bp [gt-ag] intron 16 GenBank accessions 112 bp exon 43 bp [gt-ag] intron 16 GenBank accessions 80 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 121 bp exon 392 bp [gt-ag] intron 16 GenBank accessions 114 bp exon 48 bp [gt-ag] intron 15 GenBank accessions 126 bp exon 50 bp [gt-ag] intron 10 GenBank accessions 493 bp exon 202 bp [gt-ag] intron 9 GenBank accessions 174 bp exon 59 bp [gt-ag] intron 17 GenBank accessions 240 bp exon 47 bp [gt-ag] intron 16 GenBank accessions 153 bp exon 1156 bp [gt-ag] intron 1 GenBank accession 331 bp exon 76 bp [gt-ag] intron 5 GenBank accessions 124 bp exon 7 accessions, some from mixed (seen once) 124 bp exon 150 bp exon 150 bp exon 49 bp [gt-ag] intron 16 GenBank accessions 112 bp exon 43 bp [gt-ag] intron 16 GenBank accessions 80 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 121 bp exon 392 bp [gt-ag] intron 16 GenBank accessions 114 bp exon 48 bp [gt-ag] intron 15 GenBank accessions 126 bp exon 50 bp [gt-ag] intron 10 GenBank accessions 493 bp exon 202 bp [gt-ag] intron 9 GenBank accessions 174 bp exon 59 bp [gt-ag] intron 17 GenBank accessions 240 bp exon 47 bp [gt-ag] intron 16 GenBank accessions 153 bp exon 141 bp [gt-ag] intron 16 GenBank accessions 240 bp exon 44 accessions, some from mixed (seen 10 times) l2 (4), l1 (2), l4 (once) Transpliced 5' end, 13 accessions Validated 3' end, 95 accessions 240 bp exon 179 bp exon 179 bp exon 50 bp [gt-ag] intron 2 GenBank accessions 80 bp exon 373 bp [gt-ag] intron 2 GenBank accessions 331 bp exon 76 bp [gt-ag] intron 5 GenBank accessions 248 bp exon 10 accessions, some from mixed (seen once) Transpliced 5' end, 2 accessions Validated 3' end, 10 accessions 248 bp exon 120 bp exon 120 bp exon 1 accession Transpliced 5' end, 1 accession 120 bp exon 151 bp exon 182 bp [gt-ag] intron 1 GenBank accession 176 bp exon 176 bp exon 1 accession 176 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.
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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
unit
pre-mRNA
Downstream sequence
a 2271 bp 737 aa 58 bp 2kb possibly including promoter 4439 bp 1kb
b 2003 bp 618 aa 5 bp 141 bp 2kb including Promoter 3080 bp 1kb
c 838 bp 236 aa 4 bp 123 bp 2kb including Promoter 1337 bp 1kb
d 327 bp 57 aa 155 bp 2kb 509 bp 1kb
e 120 bp 26 aa 33 bp 6 bp 2kb including Promoter 120 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
ceh-26 D C I R P apc-2 D C I R P grp-1 C I R P idi-1C D C I R P 3J185 C 3J189 D C P plk-1 D C I R P 3J199 C R 3J195 3J197 D C I R P dcr-1 C R 3J172 D C P 3J186 5kb 0 ceh-26, 21 accessions 3 variants apc-2, 89 accessions, 3 variants grp-1, 20 accessions, 2 variants idi-1C, 63 accessions 5 variants 3J185, 10 accessions 3J189, 7 accessions plk-1, 103 accessions 3 variants 3J199, 79 accessions, 2 variants 3J195, 0 accession 3J197, 0 accession dcr-1, 124 accessions 4 variants 3J172, 45 accessions, 3 variants 3J186, 12 accessions gei-8, 40 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 5 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, .c, .d, .e 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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