Caenorhabditis elegans essential gene fem-1, encoding fem-1 homolog, FEMinization of XX and XO animals.
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SUMMARY back to top
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, 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 3 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.2 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 14%, L1 or L2 larvae 14%, L3 to adult (including dauer) 72%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 15 cDNA clones and 27 elements defined by RNA-seq, some from mixed (seen 7 times), embryo (3), l2 (2). 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 4 different mRNAs, 3 alternatively spliced variants and 1 unspliced form. Variant d is transpliced to SL1. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, 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 c).
Function: There are 19 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. These proteins appear to interact with other proteins (CED-3, CED-4). The gene interacts with 7 other genes (FEM-3, FOG-3, GLD-1, SEL-10, TRA-1, TRA-2, TRA-3).
Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 partial), some containing ankyrin domain [Pfam], a second peroximal domain [Psort2]. The remaining mRNA variant (unspliced) appears not to encode a good protein.
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.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome IV, links to other databases and other names
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.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene FEM1C (e=10-07).
The closest mouse gene, according to BlastP, is the AceView gene Fem1c (e=8 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)
          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 fem-1 5' 3' encoded on minus strand of chromosome IV from 5,537,969 to 5,533,120 a b c d 1 2kb 0 194 bp exon 194 bp exon 53 bp [gt-ag] intron 10 GenBank accessions 126 bp exon 44 bp [gt-ag] intron 12 GenBank accessions 61 bp exon 49 bp [gt-ag] intron 12 GenBank accessions 47 bp exon 50 bp [gt-ag] intron 13 GenBank accessions 106 bp exon 47 bp [gt-ag] intron 13 GenBank accessions 89 bp exon 55 bp [gt-ag] intron 12 GenBank accessions 366 bp exon 46 bp [gt-ag] intron 2 GenBank accessions 117 bp exon 1473 bp [gt-ag] intron 3 GenBank accessions 146 bp exon 66 bp [gt-ag] intron 2 GenBank accessions 716 bp exon 599 bp [gt-ag] intron 11 GenBank accessions 393 bp exon 38 accessions, some from mixed (seen 6 times) embryo (2), l2 (2) capped 5' end, 4 accessions Validated 3' end, 56 accessions 393 bp exon 689 bp exon 689 bp exon 46 bp [gt-ag] intron 2 GenBank accessions 795 bp exon 1 accession from embryo Validated 3' end, 1 accession 795 bp exon 63 bp exon 44 bp [gt-ag] intron 12 GenBank accessions 61 bp exon 61 bp exon 42 bp [gt-ag] intron 2 GenBank accessions 54 bp exon 50 bp [gt-ag] intron 13 GenBank accessions 106 bp exon 47 bp [gt-ag] intron 13 GenBank accessions 89 bp exon 55 bp [gt-ag] intron 12 GenBank accessions 17 bp exon 2 accessions, some from mixed (seen once) 17 bp exon 139 bp exon 139 bp exon 1 accession Transpliced 5' end, 1 accession 139 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 2361 bp 656 aa 119 bp 271 bp 2kb including Promoter 4843 bp 1kb
b 1484 bp 124 aa 464 bp 645 bp 2kb possibly including promoter 1530 bp 1kb
c 390 bp 106 aa 70 bp 30 bp 2kb possibly including promoter 628 bp 1kb
d 139 bp 18 aa 43 bp 39 bp 2kb including Promoter 139 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
drp-1 D C I R P 4G309 C 4G311 C 4G323 C P D C I R P fem-1 5kb 0 drp-1, 85 accessions, 5 variants 4G309, 18 accessions, 2 variants 4G311, 32 accessions, 2 variants 4G323, 41 accessions, 2 variants unc-5, 34 accessions, 6 variants fem-1, 42 accessions, 4 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 19 articles in PubMed.
In addition we found 80 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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