Caenorhabditis elegans gene frs-3, encoding phenylalanyl tRNA synthetase.
SUMMARY back to top
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 4 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.8 times the average gene in this release. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 33%, L1 or L2 larvae 8%, L3 to adult (including dauer) 58%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 21 cDNA clones and 16 elements defined by RNA-seq, some from embryo (seen 9 times), mixed (5), l4 (2), l1 (once), l2 (once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces 4 alternatively spliced mRNAs. Variant a is transpliced to SL7, SL3, SL1, SL2, SL6, SL4, b to SL1. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 3 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, overlapping exons with different boundaries.
Function: There is zero article specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. Functionally, the gene has been proposed to participate in processes (phenylalanyl-tRNA aminoacylation, protein biosynthesis, tRNA processing). Proteins are expected to have molecular functions (ATP binding activity, magnesium ion binding activity, nucleotide binding activity, phenylalanine-tRNA ligase activity, tRNA binding activity) and to localize in various compartments (mitochondrion, cytoplasm).
Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 COOH complete), some containing domains Phenylalanyl-tRNA synthetase, beta subunit, ferrodoxin-fold anticodon-binding, Phenylalanyl-tRNA synthetase, class IIc [Pfam], a coiled coil stretch [Psort2]. The remaining mRNA variant (spliced; partial) 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 V, links to other databases and other names
Map: This gene frs-3 maps on chomosome V at position +23.71 (interpolated). In AceView, it covers 9.59 kb, from 19902822 to 19893238 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5U368, in Wormbase by its cosmid.number name Y60A3A.13, in NextDB, the Nematode expression pattern database, as CEYK5194.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene FARS2.
The closest mouse gene, according to BlastP, is the AceView gene Fars2 (e= 10-118).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT3G58140
          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 frs-3 5' 3' encoded on minus strand of chromosome V from 19,902,822 to 19,893,453 a c d b 1 2kb 0 151 bp exon 151 bp exon 800 bp [gt-ag] intron 19 GenBank accessions 157 bp exon 241 bp [gt-ag] intron 19 GenBank accessions 103 bp exon 713 bp [gt-ag] intron 19 GenBank accessions 166 bp exon 617 bp [gt-ag] intron 16 GenBank accessions 273 bp exon 1560 bp [gt-ag] intron 15 GenBank accessions 155 bp exon 260 bp [gt-ag] intron 19 GenBank accessions 97 bp exon 696 bp [gt-ag] intron 19 GenBank accessions 210 bp exon 3007 bp [gt-ag] intron 17 GenBank accessions 379 bp exon 32 accessions, some from embryo (seen 9 times) mixed (5), l4 (2), l1 (once) l2 (once) Transpliced 5' end, 10 accessions Validated 3' end, 19 accessions Validated 3' end, 2 accessions 379 bp exon 148 bp exon 804 bp [gt-ag] intron 1 GenBank accession 153 bp exon 1 accession 153 bp exon 99 bp exon 99 bp exon 724 bp [gt-ag] intron 1 GenBank accession 1 accession 155 bp exon 210 bp exon 210 bp exon 1241 bp [gt-ag] intron 1 GenBank accession 316 bp exon 1450 bp [gt-ag] intron 1 GenBank accession 156 bp exon 3 accessions Transpliced 5' end, 1 accession 156 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 1691 bp 458 aa 313 bp 2kb including Promoter 9585 bp 1kb
b 682 bp 163 aa 51 bp 139 bp 2kb including Promoter 3373 bp 1kb
c 301 bp 82 aa 54 bp 2kb probably including promoter 1105 bp 1kb
d 254 bp 55 aa 89 bp 2kb 978 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
5U389 C R 5U391 C skr-4 C I P 5U355 5U369 C R P gly-4 C P frs-3 D C P chk-2 C 5U390 C nhr-240 5kb 0 5U389, 17 accessions, 6 variants 5U391, 17 accessions, 2 variants skr-4, 0 accession 5U343, 0 accession 5U355, 0 accession 5U369, 0 accession 5U340, 2 accessions gly-4, 37 accessions, 4 variants frs-3, 37 accessions, 4 variants chk-2, 18 accessions, 2 variants 5U390, 10 accessions, 2 variants nhr-240, 6 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
In addition we found 2 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !