Expression: According to AceView, this gene is moderately expressed, only 26.8% of the average gene in this release. The sequence of this gene is defined by 34 GenBank accessions from 26 cDNA clones, some from eye (seen 12 times), retina (9), kidney (3), testis (3), fetal brain (once), fetal eyes, lens, eye anterior segment,optic nerve, retina, retina foveal and macular, RPE andchoroid (once), heart (once) and 6 other tissues. Alternative mRNA variants and regulation: The gene contains 14 distinct gt-ag introns. Transcription produces 7 different mRNAs, 5 alternatively spliced variants and 2 unspliced forms. There are 3 probable alternative promotors, 3 non overlapping alternative last exons and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end, presence or absence of 3 cassette exons, overlapping exons with different boundaries.
Note that mRNA .bAug10 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 bAug10). Function: There are 24 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: Deafness, autosomal recessive 35; Other sources: Deafness) and proposed to participate in a process (regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (ligand-dependent nuclear receptor activity, sequence-specific DNA binding, metal ion binding, steroid binding, steroid hormone receptor activity, transcription factor activity, zinc ion binding) and to localize in nucleus. Putative protein interactors have been described (NCOA2, NCOA3). Protein coding potential: 5 spliced and the unspliced mRNAs putatively encode good proteins, altogether 6 different isoforms (4 complete, 1 COOH complete, 1 partial), some containing domains Ligand-binding domain of nuclear hormone receptor, Zinc finger, C4 type (two domains) [Pfam], a peroxisomal domain [Psort2]. The remaining mRNA variant (unspliced; partial) appears not to encode a good protein. Finally proteins from this gene may be modulated by acetylation; phosphorylation; ubiquitination, 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
