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, 0.5 times the average gene in this release. The sequence of this gene is defined by 53 GenBank accessions from 48 cDNA clones, some from brain (seen 21 times), hippocampus (7), anaplastic oligodendroglioma (2), total brain (2), uterus (2), amygdala (once), brain, hypothalamus (once) and 11 other tissues. We annotate structural defects or features in 2 cDNA clones. Alternative mRNA variants and regulation: The gene contains 27 distinct gt-ag introns. Transcription produces 7 different mRNAs, 5 alternatively spliced variants and 2 unspliced forms. There are 3 probable alternative promotors and 2 non overlapping alternative last exons (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 3 cassette exons, overlapping exons with different boundaries.
Note that mRNA .cAug10 was found in vivo, although it is a predicted target 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, dAug10). Function: There are 12 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Agammaglobulinemia; Bipolar Disorder; Genetic Predisposition to Disease; Schizophrenia) and proposed to participate in a process (central nervous system development). Proteins are expected to have molecular functions (calcium ion binding, protein binding, zinc ion binding) and to localize in various compartments (nucleus, cytoplasm, cytoskeleton, plasma membrane). Putative protein interactors have been described (DAG1, DTNA, PRX, UTRN). Protein coding potential: 4 spliced and the unspliced mRNAs putatively encode good proteins, altogether 5 different isoforms (4 complete, 1 partial), some containing domains EF hand, EF-hand, Spectrin repeat, WW domain, Zinc finger, ZZ type [Pfam], a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 1 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by phosphorylation, as detailed at PhosphoSite.
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
