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We present here a novel methodology for the identification of genome regions potentially spanning one or more protein coding genes. It is based on the detection of clusters of conserved sequence tags whose evolutionary dynamics, based on the observation of an excess bias of synonymous substitutions at nucleotide level and of conservative replacements at protein level, suggests a likely protein coding...
The NCF2 gene encodes p67 phox , an essential component of the multi-protein NADPH oxidase enzyme in phagocytic leukocytes, as well as in certain non-phagocytic cells. In humans, the NCF2 gene is expressed as multiple NCF2 variants that differ in the 5′-untranslated region (5′-UTR). Previously, we reported the presence of four NCF2 5′-UTR mRNA variants (designated as NCF2 exon 1, intron 1a,...
The TRIM37 gene encodes a peroxisomal protein of unknown function. Mutations in TRIM37 underlie mulibrey nanism, a rare autosomal recessively inherited disorder with severe growth failure of prenatal onset, constrictive pericardium, hepatomegaly and characteristic dysmorphic features. Eleven mulibrey nanism-associated mutations have been identified. We here characterised TRIM37 further by mapping...
Human alternative isoform, cryptic, skipped, and constitutive splice sites from the ALTEXTRON database were analysed regarding splice site strength, composition, GC content, position and binding site strength of polypyrimidine tract and branch site. Several features were identified which distinguish alternative isoform and cryptic splice sites, but not skipped splice sites from constitutive ones....
Liver receptor homolog-1 (LRH-1) is a homolog of FTZ-F1, a transcription factor of the fruit fly, and belongs to the orphan nuclear receptor family. LRH-1 is expressed in organs derived from the endoderm, including intestine, liver and exocrine pancreas and plays a predominant role in development, bile-acid homeostasis, and reverse cholesterol transport. Recent research has revealed that mammalian...
Mutations in ectodysplasin-A (EDA) cause loss of hair, sweat glands, and teeth in man and mouse. Isoform EDA-A1 protein shows partial rescue of the affected Tabby mouse phenotypes, suggesting that other isoforms may be required for full function. We describe genomic structure for five EDA isoforms, EDA-A1′, A5, A5′, A6, and A6′, in addition to the previously known EDA-A1, A2, A3, and A4. The novel...
Hax-1 protein, which has been studied in mice and humans, shows a potent anti-apoptotic activity and is involved in regulation of cell motility. Cloning of the rat Hax-1 cDNA has revealed seven alternative transcripts, which differ mostly in their 5′ region. Alternative splicing concerns exon 1, skipped in 5 transcripts, intron 1 which is partially retained in these transcripts, exon 2, which can...
Ohanin, from king cobra venom, is a novel protein which induces hypolocomotion and hyperalgesia in mice [Pung, Y.F., Wong, P.T.H., Kumar, P.P., Hodgson W.C., Kini, R.M., 2005. Ohanin, a novel protein from king cobra venom induces hypolocomotion and hyperalgesia in mice. J. Biol. Chem. 280, 13137–13147.]. It is weakly similar to PRY-SPRY domains (B30.2-like domain). Here we report the complete cDNA...
The 5′- and 3′-UTR regions in pre-mRNAs play a variety of roles in controlling eukaryotic gene expression, including translational modulation. Here we report the results of a systematic study of alternative splicing in rnp-4f, which encodes a Drosophila spliceosomal assembly factor. We show that most of the nine introns are constitutively spliced, but several patterns of alternative splicing are observed...
Down syndrome critical region gene 1-like 2 (DSCR1L2) belongs to the human DSCR1-like gene family, which also includes DSCR1 and DSCR1L1. Both DSCR1 and DSCR1L1 proteins interact with calcineurin, a calcium/calmodulin-dependent phosphatase. To date, no interactor has been described for DSCR1L2. The aim of this work was to perform a first functional study of DSCR1L2 using yeast two-hybrid analysis...
The Ddr1 gene encoding the discoidin domain receptor 1 (DDR1), a member of a small subfamily of receptor tyrosine kinases, is known to be involved in differentiation, proliferation, and cell adhesion. The extracellular discoidin domain is responsible for the binding of the ligand collagen. As the human homologue, the rat Ddr1 gene consists of 17 exons and is located in the major histocompatibility...
Free d-aspartic acid and NMDA are present in the mammalian central nervous system and endocrine glands at significant concentrations, but their physiological role is still matter of debate. The only enzyme known to metabolize in vitro selectively these d-amino acids is d-aspartate oxidase (DDO). To clarify the role in vivo of the enzyme, we generated mice with targeted deletion of Ddo gene by homologous...
Stromal Cell-derived factor 1 (SDF-1) is a CXC chemokine that binds to the CXCR4 receptor. Recent publication indicates that the SDF-1/CXCR4 signaling pathway plays a pivotal role during development and in many patho-physiological conditions including hematopoiesis, blood vessel formation, cancer metastasis, angiogenesis and HIV infection. Two human SDF-1 isoforms, SDF-1α and SDF-1β, have been reported...
The oocyte transcriptome and proteome largely remain a mystery and the important roles of these genes, especially in the bovine, are poorly understood. To better understand specific developmental roles of the bovine oocyte, we sought to characterize a novel oocyte gene. We have sequenced the full-length mRNAs of bovine oocyte-secreted protein 1 (OOSP1) and discovered two splice variants, namely OOSP1_v1...
Toll-Like Receptors (TLRs) have recently emerged as key sensors of invading microbes, acting through recognition of pathogen-associated molecular patterns. It has been demonstrated that TLR9 is involved in the recognition of unmethylated CpG motifs in mice, humans, and pigs. We report here the full-length sequence of TLR9 cDNA in the gilthead sea bream (Sparus aurata L.). The predicted protein (1063...
Expression of POU1F1 gene, a member of the POU homeodomain family of transcription factors, is necessary for normal differentiation, development and survival of three anterior pituitary cell types (thyrotrophs, somatotrophs and lactotrophs) and for the proper expression of growth hormone (GH), prolactin (PRL), thyroid-stimulating hormone (TSH) genes and POU1F1 gene itself. Alternative splicing forms...
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