Summary
[Wormbase] The fem-1 gene encodes an ankyrin repeat-containing protein orthologous to human FEM1A and is required for masculinization of germline and somatic tissues; FEM-1 is widely expressed and functions as a second messenger in the sex determination pathway, connecting the membrane protein TRA-2A to the transcription factor TRA-1A which it negatively regulates; FEM-1 may also play a role in apoptosis, as it is a substrate for the CED-3 protease and can induce apoptosis when overexpressed in mammalian cells.
Wormbase predicts 2 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 3 spliced variants.

AceView summary
Expression: According to AceView, this gene is well expressed, 1.1 times the average gene in this release, at all stages of development [Kohara cDNAs]. The sequence of this gene is defined by 15 cDNA clones. We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. 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 by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, splicing versus retention of 2 introns.
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (2 complete, 2 COOH complete, 1 partial), some containing ankyrin domain [Pfam], a second peroximal domain [Psort2].
Isoform fem-1.c is annotated using as Met a Kozak-compatible a..TTGg start, thereby gaining 94 amino acids N-terminal to the first AUG. 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 c).
Function: There are 16 articles specifically referring to this gene in PubMed. In addition we point below to 80 abstracts. This essential gene is associated to a phenotype (FEMinization of XX and XO animals, STerile Progeny). Proteins are expected to localize in cytoplasm.

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

Map: This essential gene fem-1 maps on chomosome IV at position +2.34 (interpolated). In AceView, it covers 4.84 kb, from 5537962 to 5533120 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known isx-1, in Wormgenes/AceView by its positional name 4G298, in Wormbase by its cosmid.number name F35D6.1, in NextDB, the Nematode expression pattern database, as CEYK198.

The closest human gene, according to BlastP, is the AceView gene FEM1C (e=7 10^-08).
The closest mouse gene, according to BlastP, is the AceView gene Fem1c (e=5 10^-08).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT3G04710 (e=3 10^-16), AT2G31820 (e=3 10^-14), AKT1 (e=7 10^-14), AT1G07710 (e=2 10^-13), AT2G03430 (e=2 10^-13)

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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