Caenorhabditis elegans essential gene dbr-1, encoding RNA lariat DeBRanching enzyme.
SUMMARY back to top
[Wormbase] dbr-1 encodes a homolog of the RNA lariat-debranching enzyme; DBR-1 is predicted to function in RNA processing by hydrolyzing the 2'-5' phosphodiester bond at the branchpoint of excised lariat intron RNA, thus converting the introns into linear molecules that can subsequently be degraded by exonucleases; in C. elegans, DBR-1 activity is required for embryonic and germline development, as well as for normal rates of postembryonic growth; overexpression of C. elegans DBR-1 in Saccharomyces cerevisiae can complement the RNA processing defects of a dbr1 null mutant strain, restoring debranching activity and intron degradation to near wild-type levels.
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 2 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 1.8 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 55%, L3 to adult 44%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 17 cDNA clones and 7 elements defined by RNA-seq, some from l2 (seen 6 times), l1 (4), l4 (2), mixed (once).
Alternative mRNA variants and regulation: The gene contains 5 distinct introns (4 gt-ag, 1 gc-ag). Transcription produces 2 alternatively spliced mRNAs. Variant a is transpliced to SL2, SL9, SL4, b to SL1, SL2, SL3, SL4, SL5. There are 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by overlapping exons with different boundaries, splicing versus retention of one intron.
Function: There are 2 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (embryonic lethal, partial, SLow growth). Functionally, the gene has been proposed to participate in a process (mRNA processing). Proteins are expected to have molecular functions (hydrolase activity, hydrolase activity, acting on ester bonds) and to localize in nucleus.
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing domains Lariat debranching enzyme, C-terminal, Metallophosphoesterase [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This essential gene dbr-1 maps on chomosome I at position +1.14 (interpolated). In AceView, it covers 2.01 kb, from 6492729 to 6490718 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1H68, in Wormbase by its cosmid.number name C55B7.8, in NextDB, the Nematode expression pattern database, as CEYK9467.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene DBR1 (e=6 10-23).
The closest mouse gene, according to BlastP, is the AceView gene Dbr1 (e=3 10-22).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G31770 (e=3 10-16)
          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 dbr-1 5' 3' encoded on minus strand of chromosome I from 6,492,729 to 6,490,718 a b 1kb 0 175 bp exon 175 bp exon 123 bp [gt-ag] intron 15 GenBank accessions 465 bp exon 46 bp [gt-ag] intron 10 GenBank accessions 150 bp exon 49 bp [gt-ag] intron 13 GenBank accessions 147 bp exon 74 bp [gc-ag] intron 14 GenBank accessions 264 bp exon 63 bp [gt-ag] intron 15 GenBank accessions 454 bp exon 10 accessions, some from l2 (seen 5 times) l1 (2), l4 (once) Transpliced 5' end, 8 accessions 454 bp exon 175 bp exon 123 bp [gt-ag] intron 15 GenBank accessions 661 bp exon 661 bp exon 49 bp [gt-ag] intron 13 GenBank accessions 147 bp exon 74 bp [gc-ag] intron 14 GenBank accessions 264 bp exon 63 bp [gt-ag] intron 15 GenBank accessions 456 bp exon 14 accessions, some from l1 (seen 2 times) l2 (once), l4 (once) mixed (once) Transpliced 5' end, 5 accessions Validated 3' end, 1 accession Validated 3' end, 8 accessions 456 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 uORF Upstream sequence Transcription
Downstream sequence
a 1655 bp 500 aa 151 bp 2kb including Promoter 2010 bp 1kb
b 1703 bp 282 aa 701 bp 153 bp 642 bp 2kb including Promoter 2012 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
1H45 C I P 1H51 C R sulp-1 D C P uri-1 D C I R P acdh-1 D C I R P 1H77 D C P gly-2 D C R P glh-2 D C R P D C I R P cdc-25.1 C I R P 1H54 D C R P dbr-1 D C I R P mdt-18 C R 1H78 D C P 1H88 5kb 0 1H43, 50 accessions 1H45, 35 accessions 1H51, 27 accessions sulp-1, 17 accessions 4 variants uri-1, 19 accessions, 2 variants acdh-1, 235 accessions 13 variants 1H77, 0 accession gly-2, 20 accessions, 2 variants glh-2, 27 accessions, 3 variants acdh-3, 53 accessions 3 variants cdc-25.1, 33 accessions 5 variants 1H54, 35 accessions, 5 variants dbr-1, 24 accessions, 2 variants mdt-18, 20 accessions 2 variants 1H78, 9 accessions, 3 variants 1H88, 8 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 2 articles in PubMed.
? 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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