RefSeq annotates 3 representative transcripts (NM included in AceView variants .a, .b and .c), 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 4 spliced variants.
AceView synopsis, each blue text links to tables and details 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 134 GenBank accessions from 117 cDNA clones, some from brain (seen 21 times), kidney (6), testis (6), hypothalamus (5), breast (4), cerebellum (4), colon (4) and 45 other tissues. We annotate structural defects or features in 5 cDNA clones. Alternative mRNA variants and regulation: The gene contains 8 distinct gt-ag introns. Transcription produces 5 different mRNAs, 4 alternatively spliced variants and 1 unspliced form. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end, overlapping exons with different boundaries. 249 bp of this gene are antisense to spliced gene LOC728558, raising the possibility of regulated alternate expression.
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 aAug10, bAug10, cAug10). Function: There is one article specifically referring to this gene in PubMed. Proteins are expected to localize in nucleus. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown. Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (3 complete), some containing domains Cyclin, C-terminal domain, Cyclin, N-terminal domain [Pfam]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 2 partial) 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 10, links to other databases and other names Map: This gene CCNJ maps on chromosome 10, at 10pter-q26.12 according to Entrez Gene. In AceView, it covers 18.20 kb, from 97802606 to 97820802 (NCBI 37, August 2010), on the direct strand. Links to: the SNP view, gene overviews from Entrez Gene 54619, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here. Other names: The gene is also known as CCNJ or bA690P14.1, LOC54619. It has been described as cyclin-J. Closest AceView homologs in other species ? The closest mouse gene, according to BlastP, is the AceView gene Ccnj (e=0.0). The closest C.elegans gene, according to BlastP, is the AceView/WormGene cya-1 (e=0.40), which may contain interesting functional annotation. The closest A.thaliana genes, according to BlastP, are the AceView genes CYCA2\;3 (e=0.003), CYCA2\;4 (e=0.003), CYCA1\;2 (e=0.005), CYC1 (e=0.010), which may contain interesting functional annotation
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!. Read more...
About UCSC tracks: you may enjoy the plots for the summed coverage over all primates' libraries (top track), summarizing 3 terabases of stranded RNA-seq. Fragments mapping on the + strand of the genome (from genes on the + strand) are red (or dark), on minus strand blue (or light) and antisense transcribed areas are black or overlaid. The vertical scale for each track is self-adapting. Homozygous SNPs tracks are also presented.
About mapping: Primates body map RNA-seq data were stringently mapped to the human genome using the NCBI Magic pipeline. Normalized results are shown as significant FPKM (sFPKM), which includes corrections on F, K and M, computed from parameters measured directly in each RNA-seq experiment, to render the expression measures more significant and more robust to experimental biases. Only fragments with both reads mapped uniquely and over at least 80+80 bases ending with 8 exact bases on each side of each read, and facing each other in a single site or gene, are included in the computation of the sFPKM/index, in the coverage plots, and in the determination of homozygous SNPs (minimum coverage 10, minimum allele frequency 95%). But be aware that genes whose sequence evolved to become too distant from Human cannot be measured well, this bias can be appreciated in the per-species coverage plots at UCSC.
About libraries: For non-human primates, total RNA libraries used TruSeq, ribozero and the stranded UDG protocol. The human 2010 libraries used the polyA selected non-stranded protocol, with short reads (50, 75 or 50+50 bases); furthermore the insert lengths are larger in human than in the non-human primates (average insert size 187 bp in non-human primates versus 232 bp in human). These protocol differences may impact expression measures for the non polyadenylated genes (or genes with shorter or occasional polyA tails), for the pseudogenes or close gene families (specificity is reduced in humans due to shorter reads), and for the very short genes.
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: .c, .b, .a, .e-u, .d.
or in GIF: .c, .b, .a, .e-u, .d
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 !
