Caenorhabditis elegans essential gene fib-1, encoding FIBrillarin.
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SUMMARY back to top
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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 very high level, 24.3 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 39%, L1 or L2 larvae 22%, L3 to adult 39%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 70 cDNA clones and 250 elements defined by RNA-seq, some from embryo (seen 21 times), mixed (7), l2 (6), l1 (5), l4 (2), whole animal (once). We annotate structural defects or features in 7 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 10 distinct introns (9 gt-ag, 1 gc-ag). Transcription produces at least 6 alternatively spliced mRNAs. Variant a is transpliced to SL1, b to SL1, c to SL1. There are 2 probable alternative promotors and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 2 introns.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant a, b).
Function: There are 10 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (embryonic lethal, partial, Larval arrest, SLow growth, Sterile adult, STerile Progeny, unhealthy, shared oogenic and spermatogenic protein copurified with chromatin, HYPoxia resistant). Functionally, the gene has been proposed to participate in a process (rRNA processing). Proteins are expected to have molecular function (RNA binding activity) and to localize in nucleus. These proteins appear to interact with another protein (SMN-1).
Protein coding potential: 5 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (2 complete, 2 partial), some containing fibrillarin domain [Pfam]. 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 essential gene fib-1 maps on chomosome V at position +6.92 (interpolated). In AceView, it covers 1.47 kb, from 15002083 to 15000619 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5P482, in Wormbase by its cosmid.number name T01C3.7, in NextDB, the Nematode expression pattern database, as CEYK1723.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene FBL (e= 10-105).
The closest mouse gene, according to BlastP, is the AceView gene Fbl (e= 10-105).
The closest A.thaliana genes, according to BlastP, are the AceView genes FIB1, FIB2
          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 fib-1 5' 3' encoded on minus strand of chromosome V from 15,002,083 to 15,000,619 a b c d e f 1kb 0 82 bp exon 82 bp exon 24 bp uORF 82 bp exon 56 bp [gt-ag] intron 3 GenBank accessions 41 bp exon 41 bp exon 41 bp exon 48 bp [gt-ag] intron 22 GenBank accessions 190 bp exon 190 bp exon 41 bp [gt-ag] intron 1 GenBank accession 551 bp exon 551 bp exon 47 bp [gt-ag] intron 48 GenBank accessions 387 bp exon 387 bp exon 6 accessions, some from embryo (seen once) l4 (once) Transpliced 5' end, 2 accessions 387 bp exon 82 bp exon 82 bp exon 24 bp uORF 82 bp exon 56 bp [gt-ag] intron 3 GenBank accessions 41 bp exon 41 bp exon 41 bp exon 48 bp [gt-ag] intron 22 GenBank accessions 184 bp exon 184 bp exon 47 bp [gt-ag] intron 28 GenBank accessions 551 bp exon 551 bp exon 47 bp [gt-ag] intron 48 GenBank accessions 300 bp exon 300 bp exon 7 accessions, some from embryo (seen once) l1 (once) Transpliced 5' end, 1 accession 300 bp exon 41 bp exon 41 bp exon 48 bp [gt-ag] intron 22 GenBank accessions 184 bp exon 47 bp [gt-ag] intron 28 GenBank accessions 551 bp exon 47 bp [gt-ag] intron 48 GenBank accessions 409 bp exon 297 accessions, some from embryo (seen 19 times) mixed (6), l2 (5), l1 (4) l4 (once) Transpliced 5' end, 7 accessions Validated 3' end, 25610 accessions 409 bp exon 51 bp exon 60 bp [gt-ag] intron 1 GenBank accession 19 bp exon 49 bp [gt-ag] intron 1 GenBank accession 549 bp exon 7 accessions, some from l2 (seen once) mixed (once) 549 bp exon 51 bp exon 128 bp [gt-ag] intron 1 GenBank accession 1 accession 60 bp exon 18 bp exon 120 bp [gt-ag] intron 1 GenBank accession 33 bp exon 92 bp [gc-ag] intron 1 GenBank accession 2 accessions 30 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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
a 1251 bp 354 aa 83 bp 103 bp 21 bp 2kb including Promoter 1443 bp 1kb
b 1158 bp 352 aa 83 bp 16 bp 21 bp 2kb including Promoter 1356 bp 1kb
c 1185 bp 352 aa 125 bp 2kb including Promoter 1327 bp 1kb
d 619 bp 206 aa 2kb 728 bp 1kb
e 111 bp 37 aa 2kb 239 bp 1kb
f 81 bp 27 aa 2kb 293 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
grd-12 C R P xbx-1 D C I P 5P467 C R 5P471 C I P fil-1 D C P 5P477 C C mut-15 D C R 5P485 C I P 5P501 C 5P505 C 5P503 5P494 D C P 5P468 C I P 5P472 D C P rps-16 D C I R P fib-1 C P nmr-2 D C P obr-2 C 5P500 5kb 0 grd-12, 7 accessions xbx-1, 37 accessions 5P467, 19 accessions, 4 variants 5P471, 28 accessions fil-1, 8 accessions 5P477, 5 accessions 5P479, 6 accessions mut-15, 31 accessions 5P485, 10 accessions, 2 variants 5P501, 2 accessions 5P505, 3 accessions 5P503, 0 accession 5P494, 0 accession 5P450, 31 accessions 5P468, 28 accessions, 3 variants 5P472, 29 accessions rps-16, 638 accessions 4 variants fib-1, 320 accessions 6 variants nmr-2, 21 accessions, 2 variants obr-2, 39 accessions, 4 variants 5P500, 3 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 10 articles in PubMed.
? 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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