Caenorhabditis elegans essential gene frh-1, encoding FRataxin Homolog, loss of function increases sensitivity to oxidative stress, impairs respiration, reduces lifespan, and causes lethality in a mitochondrial complex II mutant.TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS SUMMARY
Summary
[Wormbase] frh-1 encodes the C. elegans frataxin ortholog; by homology, FRH-1 is predicted to be a mitochondrial protein required for biogenesis of iron-sulfur clusters, co-factors necessary for proper function of electron transport chain proteins; in C. elegans, loss of frh-1 activity via RNAi results in small body size, pale coloration, reduced egg-laying and fertility, altered responses to oxidative stress, and a significant lifespan extension.
Wormbase predicts one model.
AceView synopsis, each blue text links to tables and details
According to AceView, this gene is well expressed, 0.8 times the average gene in this release. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 7 cDNA clones and 4 elements defined by RNA-seq, some from l1 (seen once), l2 (once).
The gene contains 2 distinct gt-ag introns. Transcription produces one mRNA. Variant a is transpliced to SL5, SL9, SL2, SL1, SL3, SL4. Function: There are 6 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. This essential gene is associated to a phenotype (embryonic lethal, partial, SLow growth, UNCoordinated locomotion, EGg Laying defective, EATing: abnormal pharyngeal pumping, abnormal oxidative stress response, shortens adult lifespan). Proteins are expected to localize in mitochondrion. This protein appears to interact with another protein (VAB-21). The gene interacts with MEV-1.
The spliced mRNA putatively encodes a good protein, containing Frataxin-like domain [Pfam].
Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12. Map on chromosome II, links to other databases and other names Map: This essential gene frh-1 maps on chomosome II at position -0.67 (interpolated). In AceView, it covers 1.14 kb, from 5917388 to 5918529 (WS190), on the direct strand. Links to:WormBase, NextDB, RNAiDB. Other names: The gene is also known in Wormgenes/AceView by its positional name 2G207, in Wormbase by its cosmid.number name F59G1.7, in NextDB, the Nematode expression pattern database, as CEYK9540. Closest AceView homologs in other species ? The closest human gene, according to BlastP, is the AceView gene FXN. The closest mouse gene, according to BlastP, is the AceView gene Fxn (e=2 10-16). The closest A.thaliana gene, according to BlastP, is the AceView gene ATFH\/FH
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.
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. Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
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. Proteins supported by a single continuous cDNA sequence 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.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink and ] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags to any single letter variant of the main . More explanations are given in the gene help file
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash: .a.
or in GIF: .a
Please see these 6 articles in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
pm19123269
GB:AY048153_2 Submitted (20-JUL-2001) Laboratory of Genetics and Molecular Medicine, Instituto de Biomedicina de Valencia (CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
GB:AY048153_1 Characterization of the Caenorhabditis elegans ortholog of the frataxin Unpublished
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 see the mRNA diagram, sequence and annotation, click the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.
If you know more about this gene, or found errors, please share your knowledge. Thank you !
