RefSeq annotates one representative transcript (NM included in AceView variant.b), but Mus musculus 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 5 spliced variants.
AceView synopsis, each blue text links to tables and details Expression: According to AceView, this gene is moderately expressed, only 28.1% of the average gene in this release. The sequence of this gene is defined by 31 GenBank accessions from 28 cDNA clones, some from brain (seen 5 times), rathke's pouches (2), whole brain (2), brain, PCR rescued clones (once), branchial arches (once), whole body (once), whole embryo including extraembryonictissues at 13.5-days postcoitum (once). We annotate structural defects or features in one cDNA clone. Alternative mRNA variants and regulation: The gene contains 19 distinct gt-ag introns. Transcription produces 5 alternatively spliced mRNAs. 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 3' end, presence or absence of a cassette exon, overlapping exons with different boundaries. 82 bp of this gene are antisense to spliced gene wychy, raising the possibility of regulated alternate expression. Function: There are 5 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (response to hypoxia, signal transduction, transcription from RNA polymerase II promoter, regulation of transcription, regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (DNA binding, signal transducer activity, transcription factor activity, transcription regulator activity) and to localize in nucleus.
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_1859778 for in depth functional annotation of this gene. Protein coding potential: The 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (1 complete, 2 COOH complete, 2 partial), some containing domains PAS fold, PAS fold-3 [Pfam].
Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12. Map on chromosome 7, links to other databases and other names Map: This gene Hif3a maps on chromosome 7, at 7 A2 according to Entrez Gene. In AceView, it covers 27.07 kb, from 17647776 to 17620703 (NCBI 37a, Aug 2007), on the reverse strand. Links to: manual annotations from MGI_1859778, the SNP view, gene overviews from Entrez Gene 53417, expression data from UniGene, molecular and other annotations from UCSC. Other names: The gene is also known as Hif3a, Ipas or MOP7, LOC53417. Closest AceView homologs in other species ? The closest human gene, according to BlastP, is the AceView gene HIF3A (e= 10-139). The closest C.elegans gene, according to BlastP, is the AceView/WormGene hif-1 (e=3 10-23), which may contain interesting functional annotation
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: .a, .b, .c, .d, .e.
or in GIF: .a, .b, .c, .d, .e
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 !