Caenorhabditis elegans gene bas-1, encoding L-amino acid decarboxylase required for serotonin and dopamine synthesis.
SUMMARY back to top
[Wormbase] bas-1 encodes a serotonin- and dopamine-synthetic aromatic amino acid decarboxylase (AAADC) that is required for the synthesis of serotonin from 5-hydroxytryptophan in vivo; mutations of bas-1 impair the turning step in male mating, the migration of AVM, SDQR, ALM, and BDU neurons during development.
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 very high level, 4.8 times the average gene in this release, at all stages, except in embryos [Kohara cDNAs] and dauers [SAGE, Jones et al, 2001]. 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 40%, L3 to adult (including dauer) 61%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 32 cDNA clones and 31 elements defined by RNA-seq, some from l2 (seen 6 times), l4 (3), l1 (2), mixed (2). We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 10 distinct gt-ag introns. Transcription produces 4 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL6, b to SL1. There are 2 probable alternative promotors (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of a cassette exon, overlapping exons with different boundaries.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to 10 abstracts. This gene is associated to a phenotype (Male mating abnormal). Functionally, the gene has been proposed to participate in a process (carboxylic acid metabolism). Proteins are expected to have molecular functions (carboxy-lyase activity, pyridoxal phosphate binding activity) and to localize in cytoplasm. These proteins appear to interact with other proteins (BAS-1, SGN-1). The gene interacts with NEP-1.
Conspicuous RNA editing was observed in this gene by inspection of the cDNA sequencing traces.
Protein coding potential: 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing Pyridoxal phosphate-dependent decarboxylase domain [Pfam]. The remaining 2 mRNA variants (2 spliced; 2 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 bas-1 maps on chomosome III at position -1.66 (interpolated). In AceView, it covers 2.42 kb, from 5612228 to 5614649 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3G703, in Wormbase by its cosmid.number name C05D2.4, in NextDB, the Nematode expression pattern database, as CEYK9023.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes DDC, HDC.
The closest mouse genes, according to BlastP, are the AceView genes Ddc (e= 10-117), Hdc (e= 10-106).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT2G20340 (e=6 10-89), AT4G28680 (e=2 10-87)
          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 bas-1 5' 3' encoded on plus strand of chromosome III from 5,612,228 to 5,614,618 a b c d 1 2kb 0 138 bp exon 138 bp exon 139 bp [gt-ag] intron 14 GenBank accessions 468 bp exon 126 bp [gt-ag] intron 3 GenBank accessions 27 bp exon 212 bp [gt-ag] intron 3 GenBank accessions 210 bp exon 46 bp [gt-ag] intron 12 GenBank accessions 354 bp exon 46 bp [gt-ag] intron 15 GenBank accessions 99 bp exon 69 bp [gt-ag] intron 16 GenBank accessions 105 bp exon 105 bp [gt-ag] intron 16 GenBank accessions 238 bp exon 7 accessions, some from l1 (seen once) l2 (once), mixed (once) Transpliced 5' end, 4 accessions 238 bp exon 138 bp exon 138 bp exon 139 bp [gt-ag] intron 14 GenBank accessions 468 bp exon 365 bp [gt-ag] intron 9 GenBank accessions 210 bp exon 46 bp [gt-ag] intron 12 GenBank accessions 354 bp exon 46 bp [gt-ag] intron 15 GenBank accessions 99 bp exon 69 bp [gt-ag] intron 16 GenBank accessions 105 bp exon 105 bp [gt-ag] intron 16 GenBank accessions 278 bp exon 54 accessions, some from l2 (seen 5 times) l4 (3), l1 (once), mixed (once) Transpliced 5' end, 7 accessions Validated 3' end, 86 accessions 278 bp exon 120 bp exon 120 bp exon 21 bp uORF 120 bp exon 59 bp [gt-ag] intron 1 GenBank accession 270 bp exon 270 bp exon 1 accession 270 bp exon 120 bp exon 120 bp exon 21 bp uORF 120 bp exon 119 bp [gt-ag] intron 1 GenBank accession 210 bp exon 210 bp exon 1 accession 210 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 1639 bp 523 aa 15 bp 52 bp 2kb including Promoter 2382 bp 1kb
b 1652 bp 514 aa 15 bp 92 bp 2kb including Promoter 2422 bp 1kb
c 390 bp 63 aa 201 bp 18 bp 2kb 449 bp 1kb
d 330 bp 63 aa 141 bp 18 bp 2kb 449 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
ucr-1 D C R P ced-6 D C I R P xnd-1 D C I R P bas-1 D C I R P 3G707 C P daf-4 D C I R P 3G717 D C R P 3G680 C I R P 3G688 C R 3G690 C R 3G698 5kb 0 3G677, 33 accessions, 2 variants ucr-1, 257 accessions 2 variants ced-6, 27 accessions xnd-1, 21 accessions bas-1, 63 accessions, 4 variants 3G707, 11 accessions, 2 variants daf-4, 71 accessions, 7 variants ckk-1, 32 accessions, 4 variants 3G685, 1 accession 3G717, 2 accessions 3G690a, 1 accession 3G680, 97 accessions, 4 variants 3G688, 0 accession 3G690, 83 accessions, 6 variants 3G698, 38 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 10 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 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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