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At least 1,693 records · Page 94Linked to original sources
PubMed1983

Complete nucleotide sequence of a human c-onc gene: deduced amino acid sequence of the human c-fos protein.

The complete nucleotide sequence of the c-fos(human) gene, the human cellular homolog of the oncogene (v-fos) of Finkel-Biskis-Jinkins murine osteosarcoma virus, has been determined. The c-fos(human) gene contains four discontinuous regions when compared with the v-fos gene. Three of the discontinuities are flanked by sequences characteristic of introns, while the fourth discontinuity is due to a deletion of 104 base pairs in the v-fos gene. As a consequence of the deletion, the predicted c-fos(human) and v-fos gene products differ at their carboxyl termini. Transcripts of 2.2 kilobases from the c-fos(human) gene have been identified in human cells. The sizes of these transcripts are in close agreement with the size expected from the nucleotide sequence after removal of introns.

Amino Acid Sequence↗
PubMed1985

Comparative statistics for DNA and protein sequences: multiple sequence analysis.

Concepts and methods [Karlin, S. & Ghandour, G. (1985) Proc. Natl. Acad. Sci. USA 82, 5800-5804] for the analysis of patterns and relationships are extended to multiple DNA and protein sequences. Functionals include multiple sequence common word occurrence distributions, characterizations of high frequency shared words, and ascertainment of long block identities. Various comparisons of sequences using natural alphabets obtained from grouping nucleotides or amino acids by their chemical and functional characteristics are described. Specific applications are given to globin genes, mitochondrial genomes, and a variety of mammalian viruses.

Amino Acid Sequence↗
PubMed1985

Mutations in direct repeat sequences and in a conserved sequence adjacent to the repeats result in a defective replication origin in plasmid R6K.

Plasmid pMM3 is a pBR322 derivative carrying the gamma origin of replication of the naturally occurring plasmid R6K. We have produced a gamma-origin mutant bank of this plasmid using the single-strand-specific mutagen sodium bisulfite. Members of this bank contain single or multiple mutations in the seven direct repeats and the flanking sequences in the gamma origin. Three mutants with defective gamma origins have been isolated from this mutant bank. Two of these direct repeat mutants, gamma 117 and gamma 120, are unable to replicate and also have lost the ability to bind the R6K initiation protein pi in vitro at one of the seven 22-base-pair direct repeats within their respective origins. Precise deletion of the damaged repeat of either of these mutants restores origin function, suggesting that the primary defect of these mutants involves a disruption of the normal spacing of pi binding and flanking sequences within the gamma origin. The third mutant, gamma 111, binds pi normally but replicates at a greatly reduced copy number due to a mutation near the seventh repeat. This mutation falls within a short sequence that appears to be conserved among a number of other plasmids that contain direct repeats within their origins of replication.

Base Sequence↗
PubMed1986

Nucleic acid sequence of an internal image-bearing monoclonal anti-idiotype and its comparison to the sequence of the external antigen.

The monoclonal anti-idiotypic antibody (mAb2) 87.92.6 directed against the 9B.G5 antibody specific for the virus neutralizing epitope on the mammalian reovirus type 3 hemagglutinin was previously demonstrated to express an internal image of the receptor binding epitope of the reovirus type 3. Furthermore, this mAb2 has autoimmune reactivity to the cell surface receptor of the reovirus. The nucleotide and deduced amino acid sequences of the 87.92.6 mAb2 heavy and light chains are described in this report. The sequence analysis reveals that the same heavy chain variable and joining (VH and JH) gene segments are used by the 87.92.6 anti-idiotypic mAb2 and by the dominant idiotypes of the BALB/c anti-GAT (cGAT) and anti-NP (NPa) responses. [GAT; random polymer that is 60% glutamic acid, 30% alanine, and 10% tyrosine. NP; (4-hydroxy-3-nitrophenyl)-acetyl.] Despite extensive homology at the level of the heavy chain variable regions, the NPa positive BALB/c anti-NP monoclonal antibody 17.2.25 binds neither 9B.G5 nor the cellular receptor for the hemagglutinin. Amino acid sequence comparison between the viral hemagglutinin and the 87.92.6 mAb2 light chain "internal image," reveals an area of significant homology indicating that antigen mimicry by antibodies may be achieved by sharing primary structure.

Amino Acid Sequence↗
PubMed1997

Differential expression and sequence-specific interaction of karyopherin alpha with nuclear localization sequences.

The process of nuclear protein transport requires the interaction of several different proteins, either directly or indirectly with nuclear localization or targeting sequences (NLS). Recently, a number of karyopherins alpha, or NLS-binding proteins, have been identified. We have found that the karyopherins hSRP1 and hSRP1alpha are differentially expressed in various leukocyte cell lines and could be induced in normal human peripheral blood lymphocytes. We show that the two karyopherins bind with varied specificities in a sequence specific manner to different NLSs and that the sequence specificity is modulated by other cytosolic proteins. There was a correlation between binding of karyopherins alpha to different NLSs and their ability to be imported into the nucleus. Taken together, these data provide evidence for multiple levels of control of the nuclear import process.

Amino Acid Sequence↗
PubMed2004

The tumor suppressor gene HIC1 (hypermethylated in cancer 1) is a sequence-specific transcriptional repressor: definition of its consensus binding sequence and analysis of its DNA binding and repressive properties.

HIC1 (hypermethylated in cancer 1) is a tumor suppressor gene located at chromosome 17p13.3, a region frequently hypermethylated or deleted in human tumors and in a contiguous-gene syndrome, the Miller-Dieker syndrome. HIC1 is a transcriptional repressor containing five Krüppel-like C(2)H(2) zinc fingers and an N-terminal dimerization and autonomous repression domain called BTB/POZ. Although some of the HIC1 transcriptional repression mechanisms have been recently deciphered, target genes are still to be discovered. In this study, we determined the consensus binding sequence for HIC1 and investigated its DNA binding properties. Using a selection and amplification of binding sites technique, we identified the sequence 5'-(C)/(G)NG(C)/(G)GGGCA(C)/(A) CC-3' as an optimal binding site. In silico and functional analyses fully validated this consensus and highlighted a GGCA core motif bound by zinc fingers 3 and 4. The BTB/POZ domain inhibits the binding of HIC1 to a single site but mediates cooperative binding to a probe containing five concatemerized binding sites, a property shared by other BTB/POZ proteins. Finally, full-length HIC1 proteins transiently expressed in RK13 cells and more importantly, endogenous HIC1 proteins from the DAOY medulloblastoma cell line, repress the transcription of a reporter gene through their direct binding to these sites, as confirmed by chromatin immunoprecipitation experiments. The definition of the HIC1-specific DNA binding sequence as well as the requirement for multiple sites for optimal binding of the full-length protein are mandatory prerequisites for the identification and analyses of bona fide HIC1 target genes.

Amino Acid Motifs↗
PubMedDate not supplied

Expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs): what large-scale sequencing projects can tell us about ADME.

To date over 800 complete genomes have been sequenced, with many more partially complete. Coupled with the large amount of mRNA transcript sequence data being produced from expression studies, there is now a daunting amount of information available to the research scientist. This review examines how this information may be best used, focusing on examples from sequences encoding absorption, distribution, metabolism and excretion (ADME)-related proteins in particular. Through the use of phylogenetic, splice variant and single nucleotide polymorphism (SNP) analysis, the review examines not only how insights into species-specific responses to drug exposure may be gained, but also how best to utilize this information to predict both individual human responses and the impact of population variance in response.

Alternative Splicing↗
PubMed1998

Sequence of the spacer in the recombination signal sequence affects V(D)J rearrangement frequency and correlates with nonrandom Vkappa usage in vivo.

Functional variable (V), diversity (D), and joining (J) gene segments contribute unequally to the primary repertoire. One factor contributing to this nonrandom usage is the relative frequency with which the different gene segments rearrange. Variation from the consensus sequence in the heptamer and nonamer of the recombination signal sequence (RSS) is therefore considered a major factor affecting the relative representation of gene segments in the primary repertoire. In this study, we show that the sequence of the spacer is also a determinant factor contributing to the frequency of rearrangement. Moreover, the effect of the spacer on recombination rates of various human Vkappa gene segments in vitro correlates with their frequency of rearrangement in vivo in pre-B cells and with their representation in the peripheral repertoire.

B-Lymphocytes↗
PubMed2002

Functional annotation of proteomic sequences based on consensus of sequence and structural analysis.

To maximise the assignment of function of the proteins encoded by a genome and to aid the search for novel drug targets, there is an emerging need for sensitive methods of predicting protein function on a genome-wide basis. GeneAtlas is an automated, high-throughput pipeline for the prediction of protein structure and function using sequence similarity detection, homology modelling and fold recognition methods. GeneAtlas is described in detail here. To test GeneAtlas, a 'virtual' genome was used, a subset of PDB structures from the SCOP database, in which the functional relationships are known. GeneAtlas detects additional relationships by building 3D models in comparison with the sequence searching method PSI-BLAST. Functionally related proteins with sequence identity below the twilight zone can be recognised correctly.

Consensus Sequence↗
PubMed1991

MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences.

This paper presents a method for the multiple alignment of a sequence set. The MASH algorithm uses a non-redundant database of common motifs and an 'alignment priority' criterion that depends on the length and the occurrence frequency of the patterns in the set of sequences. This user-defined criterion allows the determination of the series of the patterns to be aligned. This program is applied to a fragment of envelope gene env gp120 for 20 isolates of the immunodeficiency virus. The multiplicity of alignments obtained by modifying the criterion parameters reveals different aspects of similarity between the sequences.

Algorithms↗
PubMed2005

Sequence specificity of Cr(III)-DNA adduct formation in the p53 gene: NGG sequences are preferential adduct-forming sites.

Hexavalent chromium [Cr(VI)] is a known etiological factor in human lung cancer. Cr(VI) exposure-related lung cancer has a high mutation incidence in the p53 gene. Upon intake in human cells Cr(VI) is reduced to Cr(III), which is able to conjugate with amino acids and consequently form either binary Cr(III)-DNA or ternary Cr(III)-amino acid-DNA adducts. Both binary and ternary Cr(III)-DNA adducts are mutagenic. We have found that the Escherichia coli nucleotide excision enzyme UvrABC nuclease is able to incise Cr(III)- and Cr(III)-histidine-modified plasmid DNA and the extent of incision is proportional to the amount of Cr(III)-DNA adducts in the plasmid. In order to determine the role of Cr(III)-DNA adducts in the mutagenesis of the p53 gene in human cancer using the UvrABC nuclease incision method, we have mapped the Cr(III)-DNA distribution in PCR DNA fragments amplified from exons 5, 7 and 8 of the p53 gene. We have found that the sequence specificities of Cr(III)-DNA and Cr(III)-histidine-DNA adducts in the p53 gene sequence are identical and that both types of adducts are preferentially formed at -NGG- sequences, including codons 245, 248 and 249, the mutational hotspots in human lung cancer. It has been found that Cr(III)-DNA adducts induce mainly G to T mutations. Therefore, these results suggest that Cr(III)-DNA adduct formation contributes to the p53 gene mutations in lung carcinogenesis.

Base Sequence↗
PubMed1985

The nucleotide sequence of the ilvBN operon of Escherichia coli: sequence homologies of the acetohydroxy acid synthase isozymes.

Three acetohydroxy acid synthase isozymes, AHAS I (ilvBN), AHAS II (ilvGM) and AHAS III (ilvIH) catalyze the first step of the parallel isoleucine-valine biosynthetic pathway in Escherichia coli. Previous DNA sequence and protein purification data have shown that AHAS II and AHAS III are composed of large and small subunits encoded in the ilvGMEDA and ilvIH operons, respectively. Recent protein purification and characterization data have demonstrated that the AHAS I isozyme is also composed of large and small subunits (L. Eoyang, L. and P. M. Silverman [1984] J. Bacteriol. 157:184-189). Now the complete DNA sequence of the operon encoding the AHAS I isozyme has been determined. These data show that both AHAS I subunits (Mr 60,400 and Mr 11,100) are encoded in this operon. The coordinant regulation of both genes of the ilvBN operon has also been demonstrated. Comparisons of the DNA sequences of the genes encoding all three AHAS isozymes have been performed. Conserved homologies were observed between both the large and small subunits of all three isozymes. The closest homology was seen between the AHAS I and AHAS II isozymes. On the basis of these comparisons a rationale for the evolution of the AHAS isozymes in E. coli has been proposed.

Acetolactate Synthase↗
PubMed1985

Putative amino acid sequence of chick calcium-binding protein deduced from a complementary DNA sequence.

Two DNA fragments coding for chick CaBP have been isolated and sequenced. cDNA was prepared from enriched intestinal mRNA and cloned in pUC12. The recombinant clones were screened by differential hybridisation with 32P-cDNA probes synthesized from vitamin D replete and deficient chick intestinal mRNA. Two clones had outstanding affinity with the +D probe. Hybrid-arrested and hybrid-selected translation systems showed that both clones hybridised to mRNA coding for immunoprecipitable CaBP. The mRNA for CaBP has a 100 bp G,C rich sequence before a 786 bp coding region followed by 1250 nucleotides 3' untranslated region. Nucleotides coding for the Ca-binding sites show a high degree of homology for Ca-binding sites in chick calmodulin and rat intestinal CaBP. The amino acid sequence specified by the longest open reading frame contains five Ca-binding sites but is too large for the native CaBP; post-translational modification must therefore occur.

Amino Acid Sequence↗
PubMed1985

Nucleotide sequence of mouse IL-2 receptor cDNA and its comparison with the human IL-2 receptor sequence.

We have cloned cDNA encoding the mouse interleukin-2 (IL-2) receptor from a murine T cell line, CTLL using human IL-2 receptor cDNA as probe. COS 7 cells transfected with the cDNA expressed the antigen recognized by the monoclonal antibody against the murine IL-2 receptor. The cDNA identified 4 species of mRNA (4.5, 3.5, 2.2 and 1.5 kb) of the mouse IL-2 receptor in CTLL cells. Difference in the length of mRNA seems to be ascribed to the variable length of the 3' untranslated sequence. Total nucleotide sequence (approximately 1400 bp) of this cDNA was determined and compared with the human receptor. The nucleotide and amino acid sequences of the IL-2 receptor are 70% and 60%, respectively, homologous in average between the two species. The comparison has revealed several conserved regions localized to particular exons such as transmembrane and cytoplasmic portions, suggesting that these regions are important for receptor function and its regulation.

Amino Acid Sequence↗
PubMed1986

Amino acid sequence of the testosterone-regulated mouse kidney RP2 protein deduced from its complementary DNA sequence.

The major forms of testosterone-regulated RP2 messenger RNA (also known as MAK mRNA and pMK908) in the mouse kidney were characterized by examining cDNA and genomic clones. Three sizes of RP2 mRNA are detected by Northern blot analysis and these were shown to result from polyadenylation at three distinct sites within the primary transcript of this single-copy gene. The complete RP2 mRNA sequence was obtained from overlapping cDNA clones, revealing an open reading frame of 357 amino acids that corresponds to a protein of 40,365 daltons. The detection of RP2 mRNA in all tissues examined to date suggests that the RP2 protein may function in a housekeeping role in all cells. This is supported by the finding of a high percentage of G + C residues at the 5' end of the gene, including a sequence homologous to the binding site of the transcription factor Sp1, which has been suggested to affect the regulation of other housekeeping genes that have been characterized. An examination of the amino acid sequence indicates that the RP2 protein is proline-rich and is composed of alternating alpha-helix and beta-sheet regions. RP2 is probably not integrated into a membrane structure in the cell as it does not appear to contain hydrophobic regions capable of spanning a membrane.

Amino Acid Sequence↗
PubMed1988

Impairment of yeast pre-mRNA splicing by potential secondary structure-forming sequences near the conserved branchpoint sequence.

The absolutely conserved TACTAAC box within introns of RNA polymerase II-transcribed genes of the yeast Saccharomyces cerevisiae serves an indispensable role in lariat formation. We show in this report that rather short palindromic sequences inserted into the yeast actin gene intron immediately 3' to the TACTAAC box block the second but not the first splicing step. In contrast, a palindromic sequence inserted some 23 bp 3' of the TACTAAC box did not affect correct and efficient splicing. The data suggest that hairpin structures that might form adjacent to the branchsite sequence interfere with some necessary alteration of the spliceosome required for 3' intron cleavage and exon ligation.

Actins↗
PubMed1999

Histone Sequence Database: sequences, structures, post-translational modifications and genetic loci.

The Histone Sequence Database is an annotated and searchable collection of all available histone and histone fold sequences and structures. Particular emphasis has been placed on documenting conflicts between similar sequence entries from a number of source databases, conflicts that are not necessarily documented in the source databases themselves. New additions to the database include compilations of post-translational modifications for each of the core and linker histones, as well as genomic information in the form of map loci for the human histone gene complement, with the genetic loci linked to Online Mendelian Inheritance in Man (OMIM). The database is freely accessible through the World Wide Web at either http://genome.nhgri.nih.gov/histones/ or http://www.ncbi.nlm.nih. gov/Baxevani/HISTONES

Animals↗
PubMed1980

A rapid enzymatic DNA sequencing technique: determination of sequence alterations in early simian virus 40 temperature sensitive and deletion mutants.

We have adapted a rapid sequencing technique from the enzymatic nick-translation method of Maat and Smith. The Forward-Backward procedure employs both synthetic and 3' to 5' exonucleolytic activities of E. coli DNA polymerase I to achieve greater reliability, especially in reading stretches of the same nucleotide. The technique has been employed to determine sequence alterations in four early SV40 temperature-sensitive (tsA) point mutants and five early SV40 viable deletion mutants. The nucleotide sequence of these mutants provides an insight into their biological properties.

Amino Acid Sequence↗