Caenorhabditis elegans gene gro-1, abnormal GROwth rate, encoding tRNA isopentenyl transferase, metabolic activity and lifespan regulator.
SUMMARY back to top
Wormbase predicts one model, 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 high level, 2.5 times the average gene in this release, down regulated in dauer [SAGE, Jones et al, 2001]. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 7 cDNA clones and 26 elements defined by RNA-seq, some from embryo (seen once), mixed (once). We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 18 distinct introns (17 gt-ag, 1 gc-ag). Transcription produces at least 6 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2, SL3, SL4, SL11, b to SL1, SL2, SL3, SL4, SL5, SL7. There are 4 probable alternative promotors, 5 non overlapping alternative last exons and 6 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 a cassette exon. 107 bp of this gene are antisense to spliced gene 3G356, raising the possibility of regulated alternate expression.
Function: There are 10 articles specifically referring to this gene in PubMed. In addition we point below to 21 abstracts. This gene is associated to a phenotype (abnormal GROwth rate, maternal rescue, regulates metabolic activity, SLow growth, extends adult lifespan). Functionally, the gene has been proposed to participate in a process (tRNA processing). Proteins are expected to have molecular functions (ATP binding activity, hydrolase activity, tRNA isopentenyltransferase activity). The gene interacts with 3 other genes (AGE-1, CLK-1, CUX-7+CLK-2).
Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (3 complete, 1 COOH complete), some containing domains Ham1-like protein, tRNA isopentenyltransferase [Pfam]. The remaining 2 mRNA variants (2 spliced; 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 gene gro-1 maps on chomosome III at position -1.89 (interpolated). In AceView, it covers 3.49 kb, from 5263902 to 5267389 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3G355, in Wormbase by its cosmid.number name ZC395.6, in NextDB, the Nematode expression pattern database, as CEYK7921.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene TRIT1 (e=5 10-46).
The closest mouse gene, according to BlastP, is the AceView gene Trit1 (e=10-47).
The closest A.thaliana gene, according to BlastP, is the AceView gene ATIPT2 (e=4 10-33)
          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 gro-1 5' 3' encoded on plus strand of chromosome III from 5,265,072 to 5,267,259 a b c e d f 1 2kb 0 192 bp exon 192 bp exon 49 bp [gt-ag] intron 3 GenBank accessions 140 bp exon 51 bp [gt-ag] intron 3 GenBank accessions 283 bp exon 55 bp [gt-ag] intron 4 GenBank accessions 197 bp exon 191 bp [gt-ag] intron 4 GenBank accessions 131 bp exon 48 bp [gt-ag] intron 5 GenBank accessions 94 bp exon 211 bp [gt-ag] intron 5 GenBank accessions 108 bp exon 53 bp [gt-ag] intron 5 GenBank accessions 98 bp exon 44 bp [gt-ag] intron 5 GenBank accessions 153 bp exon 13 accessions, some from mixed (seen once) Transpliced 5' end, 2 accessions Validated 3' end, 2 accessions Validated 3' end, 5 accessions 153 bp exon 87 bp exon 87 bp exon 220 bp [gt-ag] intron 4 GenBank accessions 105 bp exon 42 bp [gt-ag] intron 4 GenBank accessions 106 bp exon 38 bp [gt-ag] intron 4 GenBank accessions 84 bp exon 99 bp [gt-ag] intron 4 GenBank accessions 346 bp exon 13 accessions, some from embryo (seen once) Transpliced 5' end, 1 accession Validated 3' end, 5 accessions Validated 3' end, 11 accessions 346 bp exon 283 bp exon 45 bp [gt-ag] intron 1 GenBank accession 207 bp exon 1 accession 207 bp exon 32 bp exon 44 bp [gt-ag] intron 5 GenBank accessions 295 bp exon 295 bp exon 50 bp [gt-ag] intron 1 GenBank accession 2 accessions 28 bp exon 93 bp exon 52 bp [gc-ag] intron 1 GenBank accession 106 bp exon 106 bp exon 221 bp [gt-ag] intron 1 GenBank accession 110 bp exon 279 bp [gt-ag] intron 1 GenBank accession 188 bp exon 3 accessions 188 bp exon 32 bp exon 48 bp [gt-ag] intron 1 GenBank accession 291 bp exon 291 bp exon 1 accession Validated 3' end, 2 accessions Validated 3' end, 4 accessions 291 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 1396 bp 430 aa 23 bp 80 bp 2kb including Promoter 2098 bp 1kb
b 728 bp 184 aa 6 bp 167 bp 2kb including Promoter 1127 bp 1kb
c 490 bp 102 aa 181 bp 2kb 535 bp 1kb
d 497 bp 70 aa 123 bp 161 bp 2kb possibly including promoter 1049 bp 1kb
e 355 bp 34 aa 250 bp 2kb 449 bp 1kb
f 323 bp 34 aa 42 bp 176 bp 2kb 371 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
gop-1 D C R P gop-2 D C I P gop-3 D C R P hap-1 C I P gro-1 D C I P 3G357 C 3G359 C toc-1 D C R P clk-1 D C I R P 3G374 C I P 3G340 C 3G350 D C I R P ztf-8 D C P 3G364 5kb 0 gop-1, 31 accessions, 6 variants gop-2, 138 accessions 2 variants gop-3, 48 accessions, 3 variants hap-1, 0 accession gro-1, 33 accessions, 6 variants 3G357, 37 accessions, 3 variants 3G359, 7 accessions, 2 variants toc-1, 46 accessions, 5 variants clk-1, 112 accessions 3 variants 3G387, 44 accessions, 7 variants 3G330, 1 accession 3G356, 4 accessions, 2 variants 3G362, 5 accessions 3G374, 0 accession cnd-1, 14 accessions 3G340, 67 accessions, 5 variants 3G350, 6 accessions, 3 variants ztf-8, 50 accessions, 5 variants 3G364, 74 accessions, 2 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 21 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f 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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