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Exon-intron Boundaries (exon-intron + boundary)
Selected AbstractsAbstracts of the 8th Meeting of the Italian Peripheral Nerve Study Group: 65JOURNAL OF THE PERIPHERAL NERVOUS SYSTEM, Issue 1 2003E Bellone Mutations in a gene encoding a novel protein of unknown function, the ganglioside-induced differentiation-associated protein 1 gene (GDAP1), are associated with one of the autosomal recessive forms of Charcot-Marie-Tooth disease (CMT4A). Mutations in GDAP1 can cause both axonal and demyelinating inherited peripheral neuropathies. The GDAP1 gene maps on chromosome 8q21.1, encompassing 13.9 kb of genomic DNA. The coding sequence is comprised of six exons. Little is known about the function of GDAP1. The mouse homologue Gdap1 is highly expressed in brain. Northern-blot analysis showed that GDAP1 is also expressed in peripheral nerves, both in neurons and in Schwann cells. A series of Italian patients with demyelinating (n = 42) and axonal (n = 39) peripheral neuropathy with possible recessive inheritance was screened for mutations in the GDAP1 gene. The entire coding region, including exon-intron boundaries, was examined by single strand conformation polymorphism (SSCP) and direct sequencing. All patients were negative for the 17p11.2 duplication and for mutations in the MPZ, GJB1, PMP22 and EGR2 genes. SSCP analysis showed a few electrophoretic variants, in the exon 1, exon 3 and exon 4, respectively. Direct sequencing demonstrated the presence of a common single nucleotide polymorphism in the exon 4 (c.507T > G) and a nucleotide substitution in the exon 3. The latter was found in four patients, belonging to three families, and was not detected in a series of normal subjects. Further studies are in progress to evaluate the possible role of this variant in the pathophysiology of the disease. This work was partially supported by grants MURST 2000 to F.A. and Ministero della Sanità to P.M. [source] cisprimertool: software to implement a comparative genomics strategy for the development of conserved intron scanning (CIS) markersMOLECULAR ECOLOGY RESOURCES, Issue 3 2008B. JAYASHREE Abstract The availability of complete, annotated genomic sequence information in model organisms is a rich resource that can be extended to understudied orphan crops through comparative genomic approaches. We report here a software tool (cisprimertool) for the identification of conserved intron scanning regions using expressed sequence tag alignments to a completely sequenced model crop genome. The method used is based on earlier studies reporting the assessment of conserved intron scanning primers (called CISP) within relatively conserved exons located near exon-intron boundaries from onion, banana, sorghum and pearl millet alignments with rice. The tool is freely available to academic users at http://www.icrisat.org/gt-bt/CISPTool.htm. [source] Study of the mouse sortilin gene: Effects of its transient silencing by RNA interference in TM4 sertoli cellsMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 4 2004Jibin Zeng Abstract Using databases of the mouse genome in combination with a sequence deduced from a mouse sortilin cDNA originated in our laboratory, we found the sortilin gene to map to a region of chromosome 3. The mouse sortilin gene contains 19 short exons separated by introns of various sizes. The study elucidated the exon-intron boundaries. Some introns extend over more than 24 kb. In the cytoplasmic domain of the translation product, we found a dileucine motif and three other motifs known to constitute the active sorting signal of the mannose 6-phosphate receptor (M6P-R). We also tested the hypothesis that sortilin is involved in the sorting of prosaposin (SGP-1) to the lysosomes. Prosaposin was initially identified in Sertoli cells, found in large amounts in the lysosomal compartment and implicated in the degradation of residual bodies released by the spermatids during spermiation. Interestingly, the targeting of prosaposin to the lysosomes is independent of the M6P-R. This investigation demonstrated that sortilin was required for the trafficking of prosaposin to the lysosomes in TM4 cells. The requirement of sortilin was shown using a siRNA probe to block the translation of sortilin mRNA. Sortilin-deficient cells were not able to route prosaposin to the lysosomal compartment but continue to transport cathepsin B, since this hydrolase uses the M6P-R to be routed to the lysosomes. These results indicate that sortilin appears to be involved in the lysosomal trafficking of prosaposin. Mol. Reprod. Dev. 68: 469,475, 2004. © 2004 Wiley-Liss, Inc. [source] Precise prenatal diagnosis of tuberous sclerosis by sequencing the TSC2 genePRENATAL DIAGNOSIS, Issue 7 2005Aubrey Milunsky Abstract Background The presumptive prenatal diagnosis of tuberous sclerosis (TSC) previously depended upon fetal imaging. Cloning of the two TSC genes (TSC1 and TSC2) now enables precise molecular diagnosis by gene sequencing. We used this approach for the prenatal diagnosis of a fetus showing multiple intracardiac tumors. Methods DNA extracted from cultivated amniotic fluid cells underwent sequencing of all coding regions and exon-intron boundaries of the TSC1 and TSC2 genes. Results A mutation (R611Q) was found in exon 16 of the TSC2 gene. Thus far, neither clinically unaffected parents has provided blood samples for mutation analysis. Conclusion For the first time, mutation analysis of a TSC gene enabled a precise prenatal diagnosis. Copyright © 2005 John Wiley & Sons, Ltd. [source] | ||||||||||