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SAGE (serial analysis of gene expression) is a remarkable technique for genome-wide analysis of gene expression. It is crucial to understand the extent to which SAGE can accurately indicate a gene or expressed sequence tag (EST) with a single tag. We analyzed the effect of the size of SAGE tag on gene identification. Our observation indicates that SAGE tags are in general not long enough to achieve...
Serial analysis of gene expression (SAGE) is a powerful technique for global expression profiling without prior knowledge of the genes of interest. We carried out SAGE analysis of purified keratinocytes derived from human skin biopsy specimens, resulting in a partial transcriptome of human epidermis. We identified 7645 unique SAGE tags with quantitative information from 15,131 collected SAGE tags...
During growth, invasion, and metastasis, tumor cells interact extensively with the surrounding stroma. To identify genes that are upregulated during this process, we compared mRNA pooled from tumor cells and fibroblasts cultured separately to mRNA from cells in coculture. Using differential display (DD), a transcript representing a novel gene, designated epithelial–stromal interaction 1 (breast) (EPSTI1),...
Here we report on a genome polymorphism survey using 254 microsatellite markers in ten recently wild-derived inbred strains. Allele size analysis showed that the rate of polymorphism of these wild-derived mouse strains when compared with any of the common laboratory strains is on average 79.8%. We found 632 wild-derived alleles that were not present in the common laboratory strains, representing a...
It is possible to assess positive selection by using the ratio of K a (nonsynonymous substitutions per plausible nonsynonymous sites) to K s (synonymous substitutions per plausible synonymous sites). We have searched candidate genes positively selected during primate evolution by using 5′-end sequences of 21,302 clones derived from cynomolgus monkey (Macaca fascicularis) brain cDNA...
Human L1 retrotransposon has two transcription-regulatory regions: an internal or sense promoter driving transcription of the full-length L1, and an antisense promoter (ASP) driving transcription in the opposite direction into adjacent cellular sequences yielding chimeric transcripts. Both promoters are located in the 5′-untranslated region (5′-UTR) of L1. Chimeric transcripts derived from the L1...
Bone breaking strength is an ultimate measurement of the risk of fracture. For a practical reason, bone mineral density (BMD) has been commonly used for predicting the risk instead. To identify genetic loci influencing femur-breaking strength (FBS), which was measured by three-point bending using an Instron DynaMight Low-Force Testing System, the whole-genome scan was carried out using 119 polymorphic...
The human 13q32–q33 region has been linked to both bipolar disorder and schizophrenia. Before completion of the draft sequences, we developed an ∼15-Mb comprehensive map for the region extending from D13S1300 to ATA35H12. This map was assembled using publicly available mapping data and sequence-tagged site (STS)-based PCR confirmation. We then compared this map with the NCBI, Celera Genomics, and...
We describe the cloning and characterization of a novel member of the immunoglobulin superfamily, Igsf9. The predicted protein structure of IGSF9 closely matches that of the neural cell-adhesion molecule (NCAM) subfamily, consisting of an extracellular region containing five immunoglobulin domains and two fibronectin type III (FnIII) repeats, a transmembrane region, and a cytoplasmic tail. We have...
The human proglucagon gene (GCG) is encoded within a finished 576-kb DNA sequence generated by the Human Genome Project. GCG is flanked by 18 kb and 65 kb of DNA, 5′ and 3′, respectively, that do not encode genes. The genomic sequence that includes GCG was found to have a long history of gene duplication events. Some members of the glucagon-like family of genes, GCG on chromosome 2 and GIP on chromosome...
Drebrin A, a major neuronal actin-binding protein, regulates the dendritic spine shapes of neurons. Here, we have cloned and characterized a novel mouse cDNA clone encoding a truncated form of drebrin A, named s-drebrin A. Analysis of the genomic organization of the mouse drebrin gene (Dbn1), which mapped to the central portion of chromosome 13, revealed that isoforms including s-drebrin A are generated...
Class III myosins are actin-based motors with amino-terminal kinase domains. Expression of these motors is highly enhanced in retinal photoreceptors. As mutations in the gene encoding NINAC, a Drosophila melanogaster class III myosin, cause retinal degeneration, human homologs of this gene are potential candidates for human retinal disease. We have recently reported the cloning of MYO3A, a human myosin...
The objective of this study was to characterize genetic variation in complex cardiovascular traits in two commonly used inbred mouse strains. We performed echocardiography, graded treadmill exercise, tail cuff plethysmography, and telemetry (heart rate, activity, temperature) in age- (∼9 weeks) and sex-matched A/J and C57BL/6J (B6) inbred mice. B6 mice had significantly larger end-diastolic dimension...
The initial analysis of the draft copy of the human genome sequence revealed the presence of several genes that were proposed to have been directly transferred from bacteria. We investigated the human D-1 antigen as a potential lateral transfer event. We report that although the human D-1 antigen seems to be an excellent candidate for lateral transfer, it is a contaminating bacterial sequence present...
Apolipoprotein A-I (apoA-I) is the major apolipoprotein of high-density lipoproteins (HDL) and has an important role in the regulation of the stability, lipid transport, and metabolism of HDL particles. To identify novel proteins that are involved in HDL metabolism, we used mature apoA-I (amino acids 25–267) as a bait for the screening of a human liver two-hybrid cDNA library. Among the identified...
Six novel genes encoding proteins with the interleukin (IL)-1 fold have been identified recently. The classical family members are involved in inflammatory signaling. Previous work has placed the novel genes close to or within the same cluster as IL1A, IL1B, and IL1RN, which occupy an ∼400-kb interval on chromosome 2. We have combined the incomplete public database sequence with our own sequence to...
Recent additions have expanded the interleukin (IL)-1 gene family to 10 members. We have determined the order, orientation, and intergenic distance of the nine IL-1 family genes that lie on human chromosome 2. We report cDNA sequences for the mouse orthologs of three of these genes. The order and orientation of the mouse genes have been mapped, and the mouse locus compared with the human locus. There...
We used in silico (electronic database) subtraction to identify ESTs that are preferentially expressed in the adult mouse germ cells. During our analysis, we identified Obox1 and Obox2 transcripts as preferentially expressed in the mouse unfertilized egg libraries. Obox1 and Obox2 transcripts encode homeodomain proteins of 204 amino acids that share 97% identity with each other. Further characterization...
Down syndrome is caused by an extra copy of human chromosome 21 and the resultant dosage-related overexpression of genes contained within it. To efficiently direct experiments to determine specific gene-phenotype correlations, it is necessary to identify all genes within 21q and assess their functional associations and expression patterns. Analysis of the complete finished sequence of 21q resulted...
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