Homo sapiens gene FCF1, encoding FCF1 small subunit (SSU) processome component homolog (S. cerevisiae).
SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Homo sapiens 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 11 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 1.4 times the average gene in this release. The sequence of this gene is defined by 165 GenBank accessions from 143 cDNA clones, some from lung (seen 12 times), carcinoid (6), kidney (6), liver (6), placenta (6), prostate (6), uterus (5) and 73 other tissues. We annotate structural defects or features in 27 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 15 distinct introns (14 gt-ag, 1 gc-ag). Transcription produces 13 different mRNAs, 11 alternatively spliced variants and 2 unspliced forms. There are 2 probable alternative promotors, 4 non overlapping alternative last exons and 6 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.
3 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
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 cAug10).
Function: There are 5 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a process (rRNA processing). Proteins are expected to localize in various compartments (nucleus, nucleolus).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 8 different isoforms (5 complete, 1 COOH complete, 2 partial), some containing Fcf1 domain [Pfam]. The remaining 4 mRNA variants (2 spliced, 2 unspliced) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 14, links to other databases and other names
Map: This gene FCF1 maps on chromosome 14, at 14q24.3 according to Entrez Gene. In AceView, it covers 25.95 kb, from 75179850 to 75205803 (NCBI 37, August 2010), on the direct strand.
Links to: the SNP view, gene overviews from Entrez Gene 51077, GeneCards, expression data from ECgene, UniGene Hs.579828, Hs.711584, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as FCF1, CGI-35, Bka, MGC99629 or C14orf111, LOC51077. It has been described as rRNA-processing protein FCF1 homolog.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Fcf1 (e=6 10-93), LOC622491 (e=10-88).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 1K80 (e=2 10-61).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT2G46230 (e=2 10-66)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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.
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
Downstream sequence
aAug10 2432 bp 198 aa 51 bp 1784 bp 2kb including Promoter 23568 bp 1kb
bAug10 3509 bp 198 aa 27 bp 2885 bp 2kb probably including promoter 25413 bp 1kb
cAug10 1303 bp 186 aa 122 bp 620 bp 96 bp 2kb including Promoter 23146 bp 1kb
dAug10 848 bp 183 aa 29 bp 267 bp 2kb probably including promoter 22029 bp 1kb
eAug10 483 bp 126 aa 100 bp 2kb 18048 bp 1kb
fAug10 3528 bp 109 aa 279 bp 2919 bp 2kb probably including promoter 25435 bp 1kb
gAug10 571 bp 105 aa 254 bp 195 bp 2kb including Promoter 21750 bp 1kb
hAug10 563 bp 53 aa 402 bp 108 bp 2kb including Promoter 17121 bp 1kb
iAug10-unspliced 2019 bp 62 aa 781 bp 1049 bp 2kb including Promoter 2019 bp 1kb
jAug10-unspliced 1624 bp 37 aa 755 bp 755 bp 2kb including Promoter 1624 bp 1kb
kAug10 1025 bp 157 aa 386 bp 354 bp 2kb including Promoter 21382 bp 1kb
lAug10 604 bp 52 aa 27 bp 418 bp 2kb including Promoter 19642 bp 1kb
mAug10 546 bp 40 aa 88 bp 335 bp 2kb including Promoter 10139 bp 1kb

Gene neighbors and Navigator on chromosome 14q24.3 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               5 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i-u, .j-u, .k, .l, .m Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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 !