Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Consensus Sequence”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
PubMed2000

Three novel types of splicing aberrations in the tuberous sclerosis TSC2 gene caused by mutations apart from splice consensus sequences.

Disease causing aberrations in both tuberous sclerosis predisposing genes, TSC1 and TSC2, comprise nearly every type of alteration with a predominance of small truncating mutations distributed over both genes. We performed an RNA based screening of the entire coding regions of both TSC genes applying the protein truncation test (PTT) and identified a high proportion of unusual splicing abnormalities affecting the TSC2 gene. Two cases exhibited different splice acceptor mutations in intron 9 (IVS9-15G-->A and IVS9-3C-->G) both accompanied by exon 10 skipping and simultaneous usage of a cryptic splice acceptor in exon 10. Another splice acceptor mutation (IVS38-18A-->G) destroyed the putative polypyrimidine structure in intron 38 and resulted in simultaneous intron retention and usage of a downstream cryptic splice acceptor in exon 39. Another patient bore a C-->T transition in intron 8 (IVS8+281C-->T) activating a splice donor site and resulting in the inclusion of a newly recognised exon in the mRNA followed by a premature stop. These splice variants deduced from experimental results are additionally supported by RNA secondary structure analysis based on free energy minimisation. Three of the reported splicing anomalies are due to sequence changes remote from exon/intron boundaries, described for the first time in TSC. These findings highlight the significance of investigating intronic changes and their consequences on the mRNA level as disease causing mutations in TSC.

Base Sequence↗
PubMed1998

Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): a consensus sequence for promoters recognized by sigma K RNA polymerase.

The three-dimensional structure of d(GCATATGATAG).d(CTATCATATGC), from the promoter region of a gene regulating sporulation in Bacillus subtilis mother cells, was determined utilizing two-dimensional nuclear Overhauser effect (2D NOE) and double-quantum-filtered COSY (2QF-COSY) spectra. To minimize the effect of methods used to obtain restraints and refine structure, several variables were studied. Interproton distance bounds were calculated very conservatively by running the complete relaxation matrix program MARDIGRAS hundreds of times using 2D NOE spectra for exchangeable and for nonexchangeable protons at different mixing times, assuming different overall correlation times and different starting structures. The 435 distance restraints were used with two different structural refinement methods: restrained molecular dynamics (rMD) and restrained Monte Carlo calculations (rMC). Refinement using different procedures and starting structures resulted in essentially the same structure (<0.8 A rmsd), indicating that the structure is defined by experimental restraints and not the refinement method or variables used. R factors indicate the structures fit the experimental NOE data very well. Some helical parameters, notably large negative X displacement, are characteristic of A-DNA, but others are characteristic of B-DNA. As with TG.CA steps in other duplex DNA sequences studied in our laboratory, the two TG.CA steps have a positive roll, with T6-G7 exhibiting the largest, and consequently a bent helix axis. The converged structure represents a time-averaged structure. However, multiple conformations, especially in deoxyriboses, were evident from vicinal coupling constants obtained from quantitative simulations of 2QF-COSY cross-peaks and from persistent inconsistencies in experimental distances due to nonlinear conformational averaging.

Base Sequence↗
PubMed2005

The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure.

Mouse proline-rich RNA-binding protein (mPrrp) is a mouse ortholog of Xenopus Prrp, which binds to a vegetal localization element (VLE) in the 3'-untranslated region (3'-UTR) of Vg1 mRNA and is expected to be involved in the transport and/or localization of Vg1 mRNA to the vegetal cortex of oocytes. In mouse testis, mPrrp protein is abundantly expressed in the nuclei of pachytene spermatocytes and round spermatids, and shifts to the cytoplasm in elongating spermatids. To gain an insight into the function of mPrrp in male germ cells, we performed in vitro RNA selection (SELEX) to determine the RNA ligand sequence of mPrrp. This analysis revealed that many of the selected clones contained both of two conserved elements, AAAUAG and GU1-3AG. RNA-binding study on deletion mutants and secondary structure analyses of the selected RNA revealed that a two-loop structure containing the conserved elements is required for high-affinity binding to mPrrp. Furthermore, we found that the target mRNAs of Xenopus Prrp contain intact AAAUAG and GU1-3AG sequences in the 3'-UTR, suggesting that these binding sequences are shared by Prrps of Xenopus and mouse.

Animals↗
PubMed1997

A consensus sequence for a functional human endogenous retrovirus K (HERV-K) dUTPase.

Amino acid sequence comparisons have revealed that a potential dUTPase gene is encoded by the retrovirus HERV-K, a defective multicopy virus that is transmitted vertically in humans. This gene is distinct from the human cellular dUTPase gene and thus two potential sources of the enzyme exist in human cells. dUTPases characterized from various sources each contain five conserved amino acid sequence motifs that form the active site of the enzyme. The protein sequence of the putative HERV-K dUTPase deduced from previous DNA sequence data from one proviral clone (HERV-K10) shows marked deviations at highly conserved residues in four of five of these motifs. Therefore, the reported DNA sequence may represent a mutated form of the viral dUTPase gene. To address this possibility, we cloned and sequenced 22 copies of the HERV-K dUTPase gene from human DNA. The results of this analysis indicate that variations evident in the HERV-K10 dUTPase amino acid sequence represent mutations of the wild-type viral DNA sequence. A version of the HERV-K dUTPase gene that corresponds to the ancestral, wild-type DNA sequence was constructed and adapted for expression in Escherichia coli. The resulting enzyme was found to exhibit properties similar to those of dUTPases isolated from other systems. A possible role of the HERV-K dUTPase in human disease is discussed.

Amino Acid Sequence↗
PubMed1983

Essential structure of E. coli promoter: effect of spacer length between the two consensus sequences on promoter function.

A promoter with the consensus sequence(TTGACA and TATAAT) at -35 and -10 regions was constructed, and the distance between the two consensus sequences was independently altered at two restriction sites. In an in vitro transcription system, a maximum activity was observed at the spacer length of 17 base-pairs regardless of the sites of space adjustment. Evidence was also provided that the start point of transcription was fixed by the consensus sequence at the -10 region.

Base Composition↗
PubMed1994

Three-dimensional model of a human interferon-alpha consensus sequence.

A computer-built, three-dimensional, atomic-level model for human interferon-alpha (IFN-alpha) was constructed. This model was prepared using the primary amino acid sequence of consensus IFN-alpha (IFN-alpha Con1) and the alpha-carbon Cartesian coordinates of murine IFN-beta as a homolog guide to the model building. In agreement with an earlier report from this laboratory, the two domains 29-35 and 123-140 are in close spatial proximity in this model, and may constitute a receptor recognition domain, whereas the region bounded by residues 78-95 is somewhat removed from this region on the molecule and may constitute an alternative active site. Extrapolating from the model, we propose that, of the stretch 123-140, the residues that are exposed are 123, 125, 126, 128-130, and 132-139; and of the stretch 29-35, all are accessible. Additionally, we propose that there may be sufficient complexity in the Type 1 IFN receptor to account for the differential sensitivities between IFN-alpha s and IFN-beta that may be associated with residue differences in the region 78-95, specifically at residues 84, 86, and 87. This model conforms with experimental data that identify specific amino acid residues in human IFN-alpha that either do, or do not, affect the active conformation and biological activities of the molecule.

Amino Acid Sequence↗
PubMed1992

Effect of two consensus sequences preceding the translation initiator codon on gene expression in plant protoplasts.

Expression cassettes containing a duplicated cauliflower mosaic virus (CaMV) 35S promoter fused to a polylinker preceded by the CCACCATGG and AACAATGG sequences were constructed. These two sequences correspond to the consensus sequences around the translation start codons in vertebrates and plants respectively. Translational fusions were made with the beta-glucuronidase-coding sequence and transient expression was recorded in tobacco mesophyll protoplasts. Approximately three times more GUS activity was found in protoplasts incubated with the constructs harbouring translational fusions as compared to a control harbouring a transcriptional fusion. No significant difference was observed between GUS activities obtained with the two consensus sequences.

Base Sequence↗
PubMed2006

TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences.

We carried out in vitro selection experiments to systematically probe the effects of TATA-box flanking sequences on its interaction with the TATA-box binding protein (TBP). This study validates our previous hypothesis that the effect of the flanking sequences on TBP/TATA-box interactions is much more significant when the TATA box has a context-dependent DNA structure. Several interesting observations, with implications for protein-DNA interactions in general, came out of this study. (i) Selected sequences are selection-method specific and TATA-box dependent. (ii) The variability in binding stability as a function of the flanking sequences for (T-A)4 boxes is as large as the variability in binding stability as a function of the core TATA box itself. Thus, for (T-A)4 boxes the flanking sequences completely dominate and determine the binding interaction. (iii) Binding stabilities of all but one of the individual selected sequences of the (T-A)4 form is significantly higher than that of their mononucleotide-based consensus sequence. (iv) Even though the (T-A)4 sequence is symmetric the flanking sequence pattern is asymmetric. We propose that the plasticity of (T-A)n sequences increases the number of conformationally distinct TATA boxes without the need to extent the TBP contact region beyond the eight-base-pair long TATA box.

Base Pairing↗
PubMed2003

[Establishment of consensus sequence of PreS/S of hepatitis B virus with genotype B/serotype adw2 or genotype C/serotype adrq+ prevailing in Chongqing of China].

OBJECTIVE: To develop consensus sequence of HBV PreS/S with different subtype in Chongqing of China. METHODS: The gene of PreS/S of HBV in 18 AsC was sequenced. The genotype and serotype of HBV were determined. The main HBV strain prevailing in Chongqing was identified to establish its consensus sequence. RESULTS: It was found that 9 strains were genotype B/serotype adw2, 6 were genotype C/serotype adrq+ and 3 were genotype B/serotype ayw1. The consensus sequence of PreS/S of HBV with genotype B/serotype adw2 and genotype C/serotype adrq+ were established. There were 6 nucleotide variants which causing 4 amino acids change between consensus sequence of PreS/S with genotype B/serotype adw2 in Chongqing and in Southeast of China (homology showed 99.5% and 99.0% respectively). There were 13 different sites that caused 4 amino acids change between consensus sequence of PreS/S with genotype C/serotype adrq+ in Chongqing and in Northeast and South of China (homology showed 98.9% and 99.0% respectively). Comparing the two consensus sequence of PreS/S gene of different subtype HBV in Chongqing, there was 95 variants which caused 40 amino acids variants (the homology was 92.1% and 90.0% respectively). CONCLUSION: The consensus sequence of PreS/S of hepatitis B virus with genotype B/serotype adw2 and genotype C/serotype adrq+ prevailing in Chongqing was established.

Adolescent↗
PubMed1994

Analysis of tandem DNA repeats of cottoid fish in Lake Baikal by direct consensus sequencing.

This paper presents a simple method of consensus sequencing of monomeric repeat units during a single sequencing procedure by the example of a recently found BspMII family of tandemly arrayed repeats of Baikal cottoid fish (Cottoidei). This approach is based on obtaining multimeric repeat forms by the polymerase chain reaction, which eliminates the need of cloning and significantly simplifies the use of tandem repeats in phylogenetic studies. An attempt has been made to derive a phylogenetic evolution pattern of the In1 element of BspMII repeats for eight cottoid species of Lake Baikal. The position of two golomyanka species (Comephorus dybowskii and Comephorus baicalensis) on a phylogenetic tree confirms the theory of their relatively recent origin, based on mitochondrial cytochrome b gene analysis. It was estimated that the tandem repeat element In1 evolves at least one order of magnitude faster than genome coding sequences.

Animals↗
PubMed2001

Features of the 3'-consensus sequence of rotavirus mRNAs critical to minus strand synthesis.

The last seven nucleotides of the 3'-end of rotavirus mRNAs, 5'-UGUGACC-3', are highly conserved and form a cis-acting signal that can promote the synthesis of (-) strand RNA to produce the viral dsRNA genome in vitro. Previous studies have shown that the sequence, location, and strandedness (single- versus double-stranded) of the 3'-consensus sequence of the mRNA affect the efficiency of (-) strand synthesis. In this study, we have used exhaustive mutagenesis of the SA11 gene 8 mRNA and an in vitro replication system to define the importance of each of the residues in the consensus sequence in (-) strand synthesis. The analysis showed that the CC of the consensus sequence was the most critical for (-) strand synthesis. Furthermore, the data revealed that other, but not all, residues of the consensus sequence contributed to efficient (-) strand synthesis in vitro. Mutant gene 8 RNAs supported an intermediate level of (-) strand synthesis when the 15 nt sequence upstream of the CC was replaced with long tracts of poly(A) or poly(U), but not with poly(G). Predictions of the secondary structure of the mutant RNAs suggested that the poly(G)-RNA could not replicate because its 3'-terminus was largely basepaired, instead of extending as a single-stranded tail as is the case for the 3'-termini of the poly(A)- and poly(U)-RNAs and wild-type gene 8 RNA. Subsequent experiments performed with complementary oligonucleotides indicated that efficient RNA replication occurs in vitro only when the last four residues of the 3'-consensus sequence, and most importantly the two terminal C's, existed in a single-stranded form. A single-stranded CC may be crucial for formation of an initiation complex for (-) strand synthesis consisting of viral RdRP, mRNA, and the dinucleotide pGpG.

Animals↗
PubMed2004

A graph based algorithm for generating EST consensus sequences.

MOTIVATION: EST sequences constitute an abundant, yet error prone resource for computational biology. Expressed sequences are important in gene discovery and identification, and they are also crucial for the discovery and classification of alternative splicing. An important challenge when processing EST sequences is the reconstruction of mRNA by assembling EST clusters into consensus sequences. RESULTS: In contrast to the more established assembly tools, we propose an algorithm that constructs a graph over sequence fragments of fixed size, and produces consensus sequences as traversals of this graph. We provide a tool implementing this algorithm, and perform an experiment where the consensus sequences produced by our implementation, as well as by currently available tools, are compared to mRNA. The results show that our proposed algorithm in a majority of the cases produces consensus of higher quality than the established sequence assemblers and at a competitive speed. AVAILABILITY: The source code for the implementation is available under a GPL license from http://www.ii.uib.no/~ketil/bioinformatics/ CONTACT: ketil@ii.uib.no.

Algorithms↗
PubMed1983

Chromosomal replication origin from the marine bacterium Vibrio harveyi functions in Escherichia coli: oriC consensus sequence.

The chromosomal replication origin (oriC) of Vibrio harveyi has been isolated on a plasmid and shown to function as an origin in Escherichia coli. The nucleotide sequence of the V. harveyi oriC was determined. From a comparison of this sequence with oriC sequences of five enteric bacteria, we derived a consensus sequence of bacterial origins that function in E. coli. This consensus sequence identifies 122 positions within oriC where nucleotide substitutions can occur without loss of origin function. These positions are clustered rather than scattered. Four interrelated nine-base-pair repeats and eight of the dam methylation G-A-T-C sites are conserved in the consensus sequence. Very few relative insertion-deletion changes occur, and these are localized to one region of oriC. The genes for three polypeptides linked to the V. harveyi oriC were identified by using in vitro protein synthesis directed by deletion derivative plasmid templates. One of these genes, coding for a 58,000 Mr polypeptide and located 3.0 kilobase pairs from the V. harveyi oriC region, is lethal to E. coli when many copies (approximately 40 per cell) are present (high copy lethal or HCL gene). In addition, nucleotide sequence analysis showed that a different gene, the gid gene to the left of oriC, is highly conserved between E. coli and V. harveyi, whereas the coding region to the right of oriC is much less conserved.

Base Sequence↗