Summary
[Wormbase] aps-1 encodes an adaptin: specifically, it encodes an ortholog of the sigma1 subunit of adaptor protein complex 1 (AP-1).
Wormbase predicts 3 models, but Caenorhabditis elegans cDNA sequences in GenBank, 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 summary
Expression: According to AceView, this gene is expressed at very high level, 4.1 times the average gene in this release, at all stages of development [Kohara cDNAs]. The sequence of this gene is defined by 54 cDNA clones, some from whole animal (seen once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 9 distinct gt-ag introns. Transcription produces 4 alternatively spliced mRNAs. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by by truncation of the 5' end, truncation of the 3' end.
Protein coding potential: The 4 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (3 complete, 3 COOH complete), some containing domains Clathrin adaptor, sigma subunit/coatomer, zeta subunit, Uncharacterized conserved proteins (DUF2216) [Pfam], a coiled coil stretch [Psort2]. 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).
Function: There is one article specifically referring to this gene in PubMed. In addition we point below to one abstract. This essential gene is associated to a phenotype (CLeaR, translucent appearance, Embryonic Lethal, Larval arrest, Sterile adult, unhealthy, resistant to aldicarb, Resistance to Inhibitors of Cholinesterase, affects synaptic transmission). Functionally, the gene has been proposed to participate in processes (intracellular protein transport, vesicle-mediated transport). Proteins are expected to have molecular function (protein binding activity) and to localize in various compartments (cytoplasm, mitochondrion, membrane coat).

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12

Map: This essential gene aps-1C maps on chomosome V at position -0.78 (interpolated). In AceView, it covers 8.37 kb, from 6017953 to 6026324 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known aps-1, apt-2, in Wormgenes/AceView by its positional name 5G505, in Wormbase by its cosmid.number name F29G9.2, F29G9.3, in NextDB, the Nematode expression pattern database, as CEYK5522.

The closest human gene, according to BlastP, is the AceView gene CCDC85A (e=3 10^-26).
The closest mouse gene, according to BlastP, is the AceView gene Ccdc85a (e=3 10^-27).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT4G35410 (e=5 10^-50), AP19 (e=10^-49)

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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Details on tissue of origin for each intron and exon is available from the intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
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