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Genome Annotation Resource Fields--GARFIELD: a genome browser for Felis catus.
Pontius JU, O'Brien SJ
(2007) J Hered 98: 386-9
MeSH Terms: Animals, Cats, Conserved Sequence, Cosmids, Genome, Mammals
Show Abstract · Added February 22, 2011
Annotation features from the 1.9-fold whole-genome shotgun (WGS) sequences of domestic cat have been organized into an interactive web application, Genome Annotation Resource Fields (GARFIELD) (http://lgd.abcc.ncifcrf.gov) at the Laboratory of Genomic Diversity and Advanced Biomedical Computing Center (ABCC) at The National Cancer Institute (NCI). The GARFIELD browser allows the user to view annotations on a per chromosome basis with unplaced contigs provided on placeholder chromosomes. Various tracks on the browser allow display of annotations. A Genes track on the browser includes 20 285 regions that align to genes annotated in other mammalian genomes: Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris. Also available are tracks that display the contigs that make up the chromosomes and representations of their GC content and repetitive elements as detected using the RepeatMasker (http://www.repeatmasker.org). Data from the browser can be downloaded in FASTA and GFF format, and users can upload their own data to the display. The Felis catus sequences and their chromosome assignments and additional annotations incorporate data analyzed and produced by a multicenter collaboration between NCI, ABCC, Agencourt Biosciences Corporation, Broad Institute of Harvard and Massachusetts Institute of Technology, National Human Genome Research Institute, National Center for Biotechnology and Information, and Texas A&M.
1 Communities
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6 MeSH Terms
The E6-Ap ubiquitin-protein ligase (UBE3A) gene is localized within a narrowed Angelman syndrome critical region.
Sutcliffe JS, Jiang YH, Galijaard RJ, Matsuura T, Fang P, Kubota T, Christian SL, Bressler J, Cattanach B, Ledbetter DH, Beaudet AL
(1997) Genome Res 7: 368-77
MeSH Terms: Amino Acid Sequence, Angelman Syndrome, Animals, Blotting, Northern, Blotting, Southern, Chromosome Aberrations, Chromosome Mapping, Chromosomes, Artificial, Yeast, Chromosomes, Human, Pair 15, Cloning, Molecular, Cosmids, Electrophoresis, Gel, Pulsed-Field, Female, Gene Deletion, Gene Dosage, Gene Expression Regulation, Developmental, Genetic Markers, Genomic Imprinting, Humans, In Situ Hybridization, Ligases, Male, Mice, Mice, Mutant Strains, Molecular Sequence Data, Paternity, Prader-Willi Syndrome, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Tissue Distribution, Transcription, Genetic, Translocation, Genetic, Ubiquitin-Protein Ligases
Show Abstract · Added February 20, 2014
Angelman syndrome (AS) and Prader-Willi syndrome (PWS) are distinct clinical phenotypes resulting from maternal and paternal deficiencies, respectively, in human chromosome 15qll-q13. Although several imprinted, paternally expressed transcripts have been identified within the PWS candidate region, no maternally expressed gene has yet been identified within the AS candidate region. We have developed an integrated physical map spanning the PWS and AS candidate regions and localized two breakpoints, including a cryptic t(14;15) translocation associated with AS and a non-AS 15q deletion, which substantially narrow the AS candidate region to approximately 250 kb. Mapping data indicate that the entire transcriptional unit of the E6-AP ubiquitin-protein ligase (UBE3A) gene lies within the AS region. The UBE3A locus expresses a transcript of approximately 5 kb at low to moderate levels in all tissues tested. The mouse homolog of UBE3A was cloned and sequenced revealing a high degree of conservation at nucleotide and protein levels. Northern and RT-PCR analysis of Ube3a expression in mouse tissues from animals with segmental, paternal uniparental disomy failed to detect substantially reduced or absent expression compared to control animals, failing to provide any evidence for maternal-specific expression from this locus. Recent identification of de novo truncating mutations in UBE3A taken with these observations indicates that mutations in UBE3A can lead to AS and suggests that this locus may encode both imprinted and biallelically expressed products.
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33 MeSH Terms
Dinucleotide repeat polymorphism from a cosmid containing the human anion exchanger isoform 3 (SLC2C) gene.
Klanke CA, Su YR, Varvil TS, Otterud BE, Leppert M, Menon AG
(1994) Hum Mol Genet 3: 2086
MeSH Terms: Alleles, Antiporters, Base Sequence, Chromosome Mapping, Cosmids, Humans, Molecular Sequence Data, Oligodeoxyribonucleotides, Polymerase Chain Reaction, Polymorphism, Genetic
Added December 10, 2013
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10 MeSH Terms
Molecular cloning and physical and genetic mapping of a novel human Na+/H+ exchanger (NHE5/SLC9A5) to chromosome 16q22.1.
Klanke CA, Su YR, Callen DF, Wang Z, Meneton P, Baird N, Kandasamy RA, Orlowski J, Otterud BE, Leppert M
(1995) Genomics 25: 615-22
MeSH Terms: Amino Acid Sequence, Animals, Base Sequence, Blotting, Northern, Chromosome Mapping, Chromosomes, Human, Pair 16, Cloning, Molecular, Cosmids, DNA, Exons, Genetic Markers, Humans, Introns, Mice, Molecular Sequence Data, Polymerase Chain Reaction, Polymorphism, Genetic, RNA, Messenger, Rats, Sequence Homology, Amino Acid, Sodium-Hydrogen Exchangers
Show Abstract · Added December 10, 2013
A human genomic clone for a novel fifth member of the Na+/H+ exchanger (NHE) family, NHE5 (gene symbol SLC9A5), has been isolated and partially sequenced. The deduced amino acid sequence of two exons, containing 154 codons, exhibits 59-73% identity to the other members of the NHE family, with closest similarity to NHE3. Northern blot analysis demonstrated that the NHE5 gene is expressed in brain, testis, spleen, and skeletal muscle. Fluorescence in situ hybridization analysis of a cosmid containing NHE5 to human metaphase chromosomes localized the NHE5 gene to the cytogenetic interval 16q21-q22. A panel of somatic cell hybrids containing various portions of chromosome 16 was used to refine further the placement of NHE5 within band 16q22.1. A polymorphic dinucleotide (GT/CA)n repeat contained in the NHE5 cosmid was identified and developed into a microsatellite PCR marker. This was typed in a subset of the CEPH (Centre d'Etude du Polymorphisme Humain) families to place it on a genetic map of the human genome. Pairwise linkage analysis of this marker showed that it was linked to marker D16S421 with a maximal lod score of 35.21 at a recombination fraction (theta) of 0.000, in complete concordance with its chromosomal localization by physical mapping. Multipoint linkage analysis placed NHE5 between the flanking markers D16S421 and D16S512. The cloning of this new member of the sodium hydrogen exchanger family, its chromosomal localization, and the discovery of a polymorphic marker for it now make it feasible to study the possible involvement of this gene in disorders of Na+/H+ transport.
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21 MeSH Terms
Strategy for molecular cloning of the fragile X site DNA.
Warren ST, Zhang FP, Sutcliffe JS, Peters JF
(1988) Am J Med Genet 30: 613-23
MeSH Terms: Animals, Cloning, Molecular, Cosmids, DNA, Recombinant, Fragile X Syndrome, Humans, Hybrid Cells, Sex Chromosome Aberrations, Translocation, Genetic, X Chromosome
Show Abstract · Added February 20, 2014
Fragile X syndrome is a common form of mental retardation associated with a fragile site on the human X chromosome. We have recently demonstrated that the fragile X chromosome, when isolated within a somatic cell hybrid, often participates in translocations involving rodent chromosome arms. Cytogenetic and molecular evidence strongly suggests that the human breakpoint of these translocations is within the fragile X sequence. Hence, the joining of heterologous DNA (i.e. from two species) may permit the molecular cloning of the fragile X site. We describe here the cloning approach employed to enhance the isolation of interspecific chromosome translocation junctions. The human portion of the translocation junction should be derived from the fragile X site sequence.
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10 MeSH Terms
Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome.
Verkerk AJ, Pieretti M, Sutcliffe JS, Fu YH, Kuhl DP, Pizzuti A, Reiner O, Richards S, Victoria MF, Zhang FP
(1991) Cell 65: 905-14
MeSH Terms: Alleles, Amino Acid Sequence, Base Sequence, Blotting, Northern, Brain, Cosmids, DNA, Exons, Fragile X Mental Retardation Protein, Fragile X Syndrome, Gene Library, Gene Rearrangement, Genetic Variation, Humans, Molecular Sequence Data, Nerve Tissue Proteins, Oligonucleotide Probes, Polymerase Chain Reaction, RNA, RNA-Binding Proteins, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, Restriction Mapping, Translocation, Genetic, X Chromosome
Show Abstract · Added February 20, 2014
Fragile X syndrome is the most frequent form of inherited mental retardation and is associated with a fragile site at Xq27.3. We identified human YAC clones that span fragile X site-induced translocation breakpoints coincident with the fragile X site. A gene (FMR-1) was identified within a four cosmid contig of YAC DNA that expresses a 4.8 kb message in human brain. Within a 7.4 kb EcoRI genomic fragment, containing FMR-1 exonic sequences distal to a CpG island previously shown to be hypermethylated in fragile X patients, is a fragile X site-induced breakpoint cluster region that exhibits length variation in fragile X chromosomes. This fragment contains a lengthy CGG repeat that is 250 bp distal of the CpG island and maps within a FMR-1 exon. Localization of the brain-expressed FMR-1 gene to this EcoRI fragment suggests the involvement of this gene in the phenotypic expression of the fragile X syndrome.
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25 MeSH Terms
Molecular cloning and transformation of cyclodiene resistance in Drosophila: an invertebrate gamma-aminobutyric acid subtype A receptor locus.
Ffrench-Constant RH, Mortlock DP, Shaffer CD, MacIntyre RJ, Roush RT
(1991) Proc Natl Acad Sci U S A 88: 7209-13
MeSH Terms: Amino Acid Sequence, Animals, Cattle, Chromosome Walking, Cloning, Molecular, Cosmids, Crosses, Genetic, DNA, DNA Transposable Elements, Dieldrin, Drosophila, Drug Resistance, Female, Gene Rearrangement, Insecticides, Macromolecular Substances, Male, Molecular Sequence Data, Phenotype, Protein Conformation, Rats, Receptors, GABA-A, Restriction Mapping, Sequence Homology, Nucleic Acid, Transformation, Genetic
Show Abstract · Added June 9, 2010
Cyclodiene resistance represents 60% of the reported cases of insecticide resistance and is also present in vertebrates. Resistance is due to insensitivity of the cyclodiene/picrotoxinin binding site on the gamma-aminobutyric acid subtype A (GABAA) receptor-chloride ionophore complex. Following isolation of cyclodiene-resistant Drosophila mutants, we report the cloning of the locus conferring resistance via a "chromosomal walk" and rescue of the susceptible phenotype by P-element-mediated germ-line transformation. Amino acid sequence analysis of a cDNA from the locus reveals homology with vertebrate GABAA subunits. To our knowledge, this represents the first cloning of an invertebrate GABA receptor and also allows us to manipulate the resistance status of an insect via germ-line transformation. This gene may be useful as a selectable marker in other insect systems.
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25 MeSH Terms
C. elegans unc-4 gene encodes a homeodomain protein that determines the pattern of synaptic input to specific motor neurons.
Miller DM, Shen MM, Shamu CE, B├╝rglin TR, Ruvkun G, Dubois ML, Ghee M, Wilson L
(1992) Nature 355: 841-5
MeSH Terms: Alleles, Amino Acid Sequence, Animals, Base Sequence, Blotting, Southern, Caenorhabditis, Caenorhabditis elegans Proteins, Cosmids, DNA, Genes, Homeobox, Genome, Helminth Proteins, Homeodomain Proteins, Molecular Sequence Data, Motor Neurons, Muscle Proteins, Nuclear Proteins, Polymerase Chain Reaction, Polymorphism, Genetic, Restriction Mapping, Synapses, Transcription, Genetic
Show Abstract · Added February 3, 2014
The creation of neural circuits depends on the formation of synapses between specific sets of neurons. Little is known, however, of the molecular mechanisms governing synaptic choice. A mutation in the unc-4 gene alters the pattern of synaptic input to one class of motor neurons in the Caenorhabditis elegans ventral nerve cord. In unc-4(e120), the presynaptic partners of VA motor neurons are replaced with interneurons appropriate to motor neurons of the VB class. This change in neural specificity is not accompanied by any detectable effects on neuronal morphology or process extension. We show that the absence of a functional unc-4 gene product accounts for the mutant phenotype. The unc-4 gene encodes a homeodomain protein and thus is likely to function as a transcription factor. The limited effect of the unc-4 null mutation on cell fate may mean that unc-4 regulates the expression of a small number of target genes and that the products of these genes are directly involved in the choice of synaptic partners.
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22 MeSH Terms