Mus musculus complex locus Fxn, encoding frataxin.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Mus musculus 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 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is well expressed, 1.1 times the average gene in this release. The sequence of this gene is defined by 114 GenBank accessions from 103 cDNA clones, some from whole joints (seen 11 times), whole body (6), visual cortex (5), thymus (4), brain (3), embryo (3), pancreas (3) and 27 other tissues. We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 7 distinct gt-ag introns. Transcription produces 6 different mRNAs, 5 alternatively spliced variants and 1 unspliced form. 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 truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries. 128 bp of this gene are antisense to spliced gene choydoy, raising the possibility of regulated alternate expression.
Note that mRNA .bSep07 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 18 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (behavior/neurological phenotype; cardiovascular system phenotype; cellular phenotype; embryogenesis phenotype; growth/size phenotype; homeostasis/metabolism phenotype; lethality-embryonic/perinatal; life span-post-weaning/aging; muscle phenotype; nervous system phenotype) and proposed to participate in a process (cellular iron ion homeostasis). Proteins are expected to localize in various compartments (extracellular space, mitochondrion).
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_1096879 for in depth functional annotation of this gene.
Protein coding potential: 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (5 complete), some containing Frataxin-like domain [Pfam]. The remaining mRNA variant (unspliced) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 19, links to other databases and other names
Map: This gene Fxn maps on chromosome 19, at 19 C1 according to Entrez Gene. In AceView, it covers 21.33 kb, from 24355098 to 24333765 (NCBI 37a, Aug 2007), on the reverse strand.
Links to: manual annotations from MGI_1096879, the SNP view, gene overviews from Gene 14297, expression data from Gene 14297, molecular and other annotations from UCSC.
Other names: The gene is also known as Fxn, FA, X25, FARR or Frda, LOC14297.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene FXN (e=4 10-67).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene frh-1 (e=2 10-24), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene ATFH\/FH (e=7 10-20), which may contain interesting functional annotation
          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 Fxn 5' 3' encoded on minus strand of chromosome 19 from 24,355,098 to 24,333,765 a [NM] b c d e f-u 1 2kb 0 202 bp exon 202 bp exon 3131 bp [gt-ag] intron 51 GenBank accessions 95 bp exon 4713 bp [gt-ag] intron 70 GenBank accessions 121 bp exon 4947 bp [gt-ag] intron 60 GenBank accessions 98 bp exon 5248 bp [gt-ag] intron 57 GenBank accessions 2779 bp exon 104 accessions, NM_008044 some from whole joints (seen 11 times) whole body (6), thymus (4) embryo (3), pancreas (3) Validated 3' end, 9 accessions Validated 3' end, 7 accessions 2779 bp exon 162 bp exon 162 bp exon 3131 bp [gt-ag] intron 51 GenBank accessions 95 bp exon 4713 bp [gt-ag] intron 70 GenBank accessions 164 bp exon 4904 bp [gt-ag] intron 2 GenBank accessions 98 bp exon 98 bp exon 5248 bp [gt-ag] intron 57 GenBank accessions 2 accessions, some from brain (seen once) brain, mouse, 13.5,14.5 16.5,17.5 dpc (once), whole brain (once) 535 bp exon 991 bp exon 991 bp exon 4713 bp [gt-ag] intron 70 GenBank accessions 121 bp exon 4947 bp [gt-ag] intron 60 GenBank accessions 98 bp exon 5248 bp [gt-ag] intron 57 GenBank accessions 190 bp exon 3 accessions, some from mammary tumor metastatized to lung.mmtv-ltr/wnt1 model. expression driven by an mmtv-ltrenhancer (seen 2 times) lung (once), tumor, metastatic to mammary (once) Validated 3' end, 2 accessions 190 bp exon 160 bp exon 160 bp exon 3131 bp [gt-ag] intron 51 GenBank accessions 95 bp exon 4377 bp [gt-ag] intron 1 GenBank accession 100 bp exon 1 accession 100 bp exon 128 bp exon 128 bp exon 1046 bp [gt-ag] intron 1 GenBank accession 98 bp exon 5248 bp [gt-ag] intron 57 GenBank accessions 226 bp exon 2 accessions, some from visual cortex (seen 2 times) 226 bp exon 567 bp exon 567 bp exon 1 accession 567 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


Click on the headers to reorder the lines
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aSep07 3295 bp 207 aa 43 bp 2628 bp 621 bp 2kb probably including promoter 21334 bp 1kb
bSep07 1054 bp 145 aa   613 bp 435 bp 2kb probably including promoter 19050 bp 1kb
cSep07 1400 bp 145 aa 923 bp 39 bp   2kb possibly including promoter 16308 bp 1kb
dSep07 355 bp 101 aa   48 bp 303 bp 2kb probably including promoter 7863 bp 1kb
eSep07 452 bp 92 aa 98 bp 75 bp   2kb possibly including promoter 6746 bp 1kb
fSep07-unspliced 567 bp 48 aa 417 bp 3 bp   2kb 567 bp 1kb
Gene neighbors and Navigator on chromosome 19 C1 back to top
Apba1 D C R P C C C 1700021P04Rik C R R R E030010A14Rik C R R R C R Gm967 P C R P Tjp2 C D C R P Fxn C R G C D C R P Pip5k1b G C R P 2900009I07Rik R C 100kb 0 Apba1, 234 accessions 7 variants nahoru, 1 accession tahoru, 1 accession tihoru, 1 accession 1700021P04Rik, 3 accessions fufu, 1 accession choydoy, 7 accessions wanaru, 179 accessions E030010A14Rik, 53 accessions mehoru, 1 accession swarfy, 1 accession swawfy, 1 accession sweefy, 1 accession hahoru, 6 accessions huhoru, 2 accessions sweyfy, 2 accessions sworfy, 2 accessions hehoru, 1 accession swoyfy, 1 accession cherdoy, 1 accession bofu, 1 accession beefu, 1 accession berfu, 1 accession tiruru, 2 accessions, 2 variants borfu, 1 accession nuhoru, 1 accession tehoru, 1 accession dawfu, 1 accession sihoru, 1 accession derfu, 1 accession suhoru, 1 accession sohoru, 1 accession kihoru, 2 accessions farfu, 1 accession kehoru, 2 accessions ferfu, 1 accession ranaru, 1 accession gyfu, 1 accession runaru, 1 accession ronaru, 1 accession tururu, 5 accessions yanaru, 1 accession yunaru, 28 accessions geefu, 1 accession gorfu, 3 accessions jofu, 1 accession shadoy, 1 accession munaru, 1 accession hanaru, 1 accession mohoru, 1 accession swerfy, 3 accessions hihoru, 1 accession hohoru, 1 accession bafu, 1 accession byfu, 1 accession bufu, 1 accession barfu, 1 accession bawfu, 1 accession beyfu, 1 accession nehoru, 1 accession cheydoy, 1 accession tuhoru, 1 accession boyfu, 1 accession dafu, 2 accessions tohoru, 3 accessions dyfu, 1 accession dufu, 2 accessions dofu, 1 accession deefu, 1 accession sahoru, 2 accessions deyfu, 1 accession sehoru, 1 accession dorfu, 9 accessions doyfu, 1 accession kahoru, 1 accession fafu, 1 accession fyfu, 1 accession chordoy, 1 accession fofu, 2 accessions kuhoru, 3 accessions fawfu, 3 accessions feefu, 1 accession feyfu, 2 accessions forfu, 5 accessions foyfu, 1 accession gafu, 2 accessions gufu, 1 accession rinaru, 2 accessions renaru, 2 accessions gofu, 2 accessions garfu, 1 accession gawfu, 1 accession gerfu, 1 accession geyfu, 2 accessions yonaru, 6 accessions goyfu, 1 accession jafu, 1 accession jyfu, 1 accession manaru, 16 accessions jufu, 1 accession minaru, 2 accessions menaru, 1 accession jawfu, 1 accession jeefu, 1 accession hinaru, 1 accession jerfu, 3 accessions jeyfu, 1 accession taruru, 2 accessions nihoru, 2 accessions Gm967, 64 accessions, 7 variants nohoru, 19 accessions Tjp2, 575 accessions, 20 variants darfu, 1 accession Fxn, 113 accessions, 6 variants kohoru, 51 accessions LOC667743, 104 accessions Pip5k1b, 112 accessions 7 variants LOC100042457, 2 accessions 2900009I07Rik, 66 accessions jarfu, 2 accessions monaru, 4 accessions Pgm5, 89 accessions, 4 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               18 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !