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, 0.6 times the average gene in this release. The sequence of this gene is defined by 76 GenBank accessions from 67 cDNA clones, some from kidney (seen 14 times), liver and spleen (14), liver (6), lung (6), 2 pooled tumors (clear cell type) (2), fetal liver (2), primary lung cystic fibrosis epithelialcells (2) and 19 other tissues. We annotate structural defects or features in 2 cDNA clones. Alternative mRNA variants and regulation: The gene contains 34 distinct gt-ag introns. Transcription produces 9 different mRNAs, 7 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 5' end, truncation of the 3' end, presence or absence of 2 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). Function: There are 74 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: Pseudoxanthoma elasticum; Pseudoxanthoma elasticum, forme fruste; Other sources: Aortic Aneurysm, Abdominal; Calcinosis; Cardiovascular Diseases; Celiac disease; Coronary Artery Disease; Family; Genetic Predisposition to Disease and 6 others), proposed to participate in pathway (ABC transporters) and processes (response to drug, transport, response to stimulus, transmembrane transport, visual perception). Proteins are expected to have molecular functions (ATP binding, ATPase activity, ATPase activity, coupled to transmembrane movement of substances, nucleotide binding, transporter activity) and to localize in various compartments (plasma membrane, cytoplasm, apical plasma membrane, integral to membrane, lateral plasma membrane, membrane fraction). Protein coding potential: 7 spliced mRNAs putatively encode good proteins, altogether 8 different isoforms (6 complete, 1 COOH complete, 1 partial), some containing domains ABC transporter transmembrane region, ABC transporter [Pfam], some transmembrane domains [Psort2]. The remaining 2 mRNA variants (2 unspliced; 1 partial) appear not to encode good proteins.
Isoform ABCC6.cAug10 is annotated using as Met a Kozak-compatible a..CTGg start, thereby gaining 71 amino acids N-terminal to the first AUG. 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
