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At least 19 recordsLinked to original sources
PubMed1993

Novel sequences conserved on the human and mouse X chromosomes.

We have cloned and mapped 28 single-copy probes from a pool of cosmids derived from the human X chromosome. Four of the probes detected strongly conserved sequences in murine DNA; all have been localized to the proximal region of the human X chromosome short arm. Comparative mapping of these sequences in the mouse genome demonstrates that, while X linkage is conserved, this region of the human X chromosome is not maintained as a contiguous segment on the mouse X chromosome. The mapping of one novel conserved sequence between Plp and Pdha1 on the mouse X chromosome defines a previously unknown region of homology. The mapping of another probe that detects a novel sequence family (DXF34) close to the X chromosome centromere in both species suggests that a block of pericentromeric material is conserved between the X chromosomes of man and mouse.

Animals↗
PubMed1990

The 5'-flanking region of the synapsin I gene. A G+C-rich, TATA- and CAAT-less, phylogenetically conserved sequence with cell type-specific promoter function.

The 5'-terminal region of the rat gene for the neuron-specific phosphoprotein, synapsin I, was isolated and sequenced. It comprises 1472 nucleotides (nt) of 5'-flanking sequence, 507 nt of the first exon, and 242 nt of the first intron. A single transcription start site was mapped by primer extension and S1 nuclease analysis. A sequence of 340 nt upstream from the transcription start site and the first exon are G+C-rich and enriched in CpG dinucleotides, resembling a CpG island. The 5'-flanking sequence lacks TATA and CAAT consensus elements but contains a consensus motif for the cAMP-responsive element. Furthermore, we notice two potential consensus motifs which are also found in corresponding positions in the genes for the nerve growth factor receptor and the 68-kDa neurofilament protein. The 5'-terminal region of the human synapsin I gene was also cloned and sequenced. A high degree of sequence conservation between rat and human is found in the upstream 340 nt that coincides precisely with the G+C-rich domain and includes the consensus elements, and throughout the first exon including the untranslated sequence. Sequence conservation is also observed further upstream and at the beginning of the first intron. In a transient chloramphenicol acetyltransferase expression assay, 5'-flanking sequences of the rat synapsin I gene function as strong promoters in neuroblastoma cells, but not in fibroblastoid cells. 225 nt of 5'-flanking sequence and 105 nt of 5'-untranslated sequence are sufficient for cell-type specific transcription in this assay.

Amino Acid Sequence↗
PubMedDate not supplied

A short internal eliminated sequence with central conserved sequences interrupting the LA-MSC gene of the 81 locus in the hypotrichous ciliates Oxytricha fallax and O. trifallax.

IES-LA is a short Internal Eliminated Sequence interrupting LA-MSC, a protein-coding gene of the 81 locus of Oxytricha fallax and O. trifallax. IES-LA is precisely excised from the gene during development of the macronucleus. The internal eliminated sequence is bounded by CAAT ... AATG, and thereby resembles a TBE1 transposon internal eliminated sequence insertion that is grossly shortened (4.1 kbp to 52-64 bp), consistent with the hypothesis that short IESs are degenerated ancient transposons. The pattern of sequence conservation between five alleles of IES-LA shows that it differs from previously characterized classes of ciliate short IESs: while many short IESs have conserved ends and diverged centers, IES-LA is more conserved in its center and its ends are diverged. This implies a excision mechanism for IES-LA that is distinct from those for other known Oxytricha IESs.

Animals↗
PubMed1987

A 230kb cosmid walk in the Duchenne muscular dystrophy gene: detection of a conserved sequence and of a possible deletion prone region.

A 230 kb genomic region from the Duchenne muscular dystrophy gene has been cloned in a cosmid walk, using an improved vector and by screening the same unamplified library for all steps. The region cloned surrounds the translocation breakpoint characterized by Worton et al and Ray et al, and overlaps by 70 kb the Pert region cloned by Monaco et al. We have identified a region of strong sequence conservation in mammals and chicken, and comparison of the homologous sequences in chicken and man has indicated the presence of two putative protein coding exons. Comparison with the sequence recently published by Koenig et al shows that only one is present in the Duchenne cDNA, and this raises the question of the functional significance of the other conserved sequence. Single copy probes and whole cosmids generated during this work have been used to analyse the corresponding region in Duchenne patients. Of five independant patients shown to be deleted for a probe 30 kb in 3' of the translocation breakpoint, three have the 5' endpoint of the deletion within a region of less than 20 kb, 100 kb away from the probe used to ascertain the deletion. This might suggest the presence of a region where deletions occur preferentially.

Amino Acid Sequence↗
PubMed1996

Conserved sequence elements involved in regulation of ribosomal protein gene expression in halophilic archaea.

A region of the Haloferax volcanii genome encoding ribosomal proteins L11e, L1e, L10e, and L12e was cloned and sequenced, and the transcripts derived from the cluster were characterized. Flanking and noncoding regions of the sequence were analyzed phylogenetically by comparison with the homologous sequences from two other halophilic archaea, i.e., Halobacterium cutirubrum and Haloarcula marismortui. Motifs, identified by high-level sequence conservation, include both transcriptional and translational regulatory elements and other elements of unknown function.

Archaea↗
PubMed2002

Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors.

The recently described inhibitor of cysteine proteinases from Trypanosoma cruzi, chagasin, was found to have close homologs in several eukaryotes, bacteria and archaea, the first protein inhibitors of cysteine proteases in prokaryotes. These previously uncharacterized 110-130 residue-long proteins share a well-conserved sequence motif that corresponds to two adjacent beta-strands and the short loop connecting them. Chagasin-like proteins also have other conserved, mostly aromatic, residues, and share the same predicted secondary structure. These proteins adopt an all-beta fold with eight predicted beta-strands of the immunoglobulin type. The phylogenetic distribution of the chagasins generally correlates with the presence of papain-like cysteine proteases. Previous studies have uncovered similar trends in cysteine proteinase binding by two unrelated inhibitors, stefin and p41, that belong to the cystatin and thyroglobulin families, respectively. A hypothetical model of chagasin-cruzipain interaction suggests that chagasin may dock to the cruzipain active site in a similar manner with the conserved NPTTG motif of chagasin forming a loop that is similar to the wedge structures formed at the active sites of papain and cathepsin L by stefin and p41.

Amino Acid Sequence↗
PubMed2001

Evolutionarily conserved sequences on human chromosome 21.

Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide arrays as a rapid approach for comparing human sequences with the DNA of multiple species whose sequences are not presently available. High-density arrays representing approximately 22.5 Mb of nonrepetitive human chromosome 21 sequence were synthesized and then hybridized with mouse and dog DNA to identify sequences conserved between humans and mice (human-mouse elements) and between humans and dogs (human-dog elements). Our data show that sequence comparison of multiple species provides a powerful empiric method for identifying actively conserved elements in the human genome. A large fraction of these evolutionarily conserved elements are present in regions on chromosome 21 that do not encode known genes.

Animals↗
PubMed1989

The 3'terminus of lactate dehydrogenase-elevating virus genome RNA does not contain togavirus or flavivirus conserved sequences.

Lactate dehydrogenase-elevating virus (LDV) is currently considered to be an unclassified togavirus. The 3' terminus of the genome RNA of the C-strain of LDV was cloned and sequenced. A synthetic DNA oligomer complementary to the 3' portion of this cloned sequence was then used to prime dideoxy sequencing from the LDV-C genome RNA as well as from the genome RNAs of three additional LDV isolates. A high degree of sequence conservation was observed in the 3' terminal region among the four LDV isolates analyzed. Comparison of the LDV 3' sequence with those of the alpha togaviruses, rubella virus, and the flaviviruses showed that the LDV genome does not contain conserved 3' sequences characteristic of these viruses.

Animals↗
PubMed1991

Laser microdissection of the fragile X region: identification of cosmid clones and of conserved sequences in this region.

Laser microdissection has been used to dissect material from the X-chromosome region involved in fragile-X-linked mental retardation. After dissection, single chromosome slices corresponding to this fragile site were subjected to DNA amplification using either a vector ligation method (to provide known anchor sequences) or primer oligonucleotides corresponding to the ubiquitous Alu sequences. Amplified material was then cloned or, alternately, used to screen a gridded cosmid library. Eight cosmid clones identified in this way were regionally mapped using a panel of hybrid cell lines and shown to originate from a narrow interval centered on the fragile X site. Two clones are included in the approximately 6-cM interval defined by probes RNI (DXS369, 5 cM proximal) and VK21 (DXS 296, 1-2 cM distal) and which includes the fragile site, and at least one clone contains sequences conserved across species suggestive of a gene. This method combines the focused approach of microdissection and the convenience of obtaining cosmid (rather than small-insert) clones; it may be useful for studies of other defined chromosomal regions.

Animals↗
PubMed1985

Highly conserved sequences in the 3' untranslated region of mRNAs coding for homologous proteins in distantly related species.

Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in their function or tissue specificity. A similar pattern of sequence conservation in the 3' UTR is also found in several other genes. Furthermore, while there is a great variation in the size of the 3' UTR of mRNAs coding for different proteins, mRNA coding for isotypic proteins in distantly related organisms often have 3' UTR of similar size. The data suggest that the 3' UTR may play an important role in the regulation of expression of at least some genes at the transcriptional or posttranscriptional level.

Actins↗
PubMed1996

Monoclonal anti-human aldolase C antibodies that react to the isozyme group-specific sequences and generally conserved sequences of human aldolase C1.

Nine monoclonal mouse anti-human aldolase C antibodies, mAbs A4, A8, B4, B7, B8, C1, D9, E10, and H1, were isolated and characterized. These mAbs fall substantially into four groups according to their reactivity with antigens. (i) Human aldolase C-specific mAbs (B8, D9, and H1). (ii) Type C aldolase-specific mAbs (B4 and E10). (iii) Ubiquitous mAbs, which react with vertebrate aldolases irrespective of type of isozyme and species (A4 and B7). (iv) Sub-ubiquitous mAbs, which are closely similar to the ubiquitous mAbs but differ slightly in terms of antigenic specificity (A8 and C1). Aldolase C-specific mAbs B8, H1, B4, and E10, but not D9, have their epitopes on a region within amino acid positions 79-193 of antigens, where the type-C isozyme group-specific sequence-3 (IGS-3) is situated. In contrast, ubiquitous mAbs A4 and B7 and sub-ubiquitous mAb A8 may have their epitopes on the commonly conserved regions of the three isozyme groups. The epitope of sub-ubiquitous mAb C1 appears to be on the IGS-2/3 but this is yet to be resolved. These nine mAbs can be classified into two groups based on the mode of epitope recognition, which was determined by ELISA, immunoblotting, and immunoprecipitation assays: (i) primary sequence-epitope mAbs such as B4, E10, and B7; and (ii) conformation-epitope mAbs (B8, D9, H1, A4, A8, and C1). Among these mAbs, aldolase C-specific mAbs H1 and E10 appear to be useful as probes for detection of conformational change around the type-C IGS-3 motif of human aldolase C because, when assessed by immunoprecipitation assay, mAb H1 reacts only with human aldolase C but not with CA250 and CA306, while mAb E10 reacts with CA250 and CA306 but not with aldolase C, even though these antigens have a common type-C IGS-3 motif. Similarly, the ubiquitous mAb B7 should serve as a probe for general use to detect vertebrate aldolases irrespective of isozyme groups and species.

Amino Acid Sequence↗
PubMed1980

The 3'-terminal primary structure of five eukaryotic 18S rRNAs determined by the direct chemical method of sequencing. The highly conserved sequences include an invariant region complementary to eukaryotic 5S rRNA.

The 3'-terminal sequences of 18S rRNA from chicken reticulocyte, mouse sarcoma, rat liver, rabbit reticulocyte and barley embryo were determined by the direct chemical sequencing method. The regions sequenced show complete homology for the first 73 nucleotides. A sequence 5'-proximal to the m6(2)Am6(2)A residues that is complementary to eukaryotic 5S RNAs is totally conserved. This supports the hypothesis that base-paired interaction between 5S and 18S rRNA, which are present in the large and small ribosomal subunits respectively, may be involved in the reversible association of ribosomal subunits during protein synthesis.

Animals↗
PubMed1989

Concerted evolution of alpha satellite DNA: evidence for species specificity and a general lack of sequence conservation among alphoid sequences of higher primates.

We investigated relationships among alpha satellite DNA families in the human, gorilla, chimpanzee, and orangutan genomes by filter hybridization with cloned probes which correspond to chromosome-specific alpha satellite DNAs from at least 12 different human chromosomes. These include representatives of both the dimer-based and pentamer-based subfamilies, the two major subfamilies of human alpha satellite. In addition, we evaluated several high-copy dimer-based probes isolated from gorilla genomic DNA. Under low stringency conditions, all human probes tested hybridized extensively with gorilla and chimpanzee alpha satellite sequences. However, only pentameric and other non-dimeric human alphoid probes hybridized with orangutan alpha satellite sequences; probes belonging to the dimer subfamily did not cross-hybridize detectably with orangutan DNA. Moreover, under high stringency conditions, each of the human probes hybridized extensively only with human genomic DNA; none of the probes cross-hybridized effectively with other primate DNAs. Dimer-based gorilla alpha satellite probes hybridized with human and chimpanzee, but not orangutan, sequences under low stringency hybridization conditions, yet were specific for gorilla DNA under high stringency conditions. These results indicate that the alpha satellite DNA family has evolved in a concerted manner, such that considerable sequence divergence is now evident among the alphoid sequences of closely related primate species.

Animals↗
PubMed1987

Sequence-specific interactions of nuclear factors with conserved sequences of human class II major histocompatibility complex genes.

All class II major histocompatibility complex genes contain two highly conserved sequences, termed X and Y, within the promoter regions(s), which may have a role in regulation of expression. To study trans-acting factors that interact with these sequences, sequence-specific DNA binding activity has been examined by the gel electrophoresis retardation assay using the HLA-DQ2 beta gene 5' flanking DNA and nuclear extracts derived from various cell types. Several specific protein-binding activities were found using a 45-base-pair (bp) HinfI/Sau96I (-142 to -98 bp) and a 38-bp Sau96I/Sau96I (-97 to -60 bp) fragment, which include conserved sequence X (-113 to -100 bp) and conserved sequence Y (-80 to -71 bp), respectively. Competition experiments, methylation interference analysis, and DNase I foot-printing demonstrated that distinct proteins in a nuclear extract of Raji cells (a human B lymphoma line) bind to sequence X, to sequence Y, and to DNA 5' of the X sequence (termed sequence W). The factor binding site in the W sequence is also found to be conserved among beta-chain genes and is suggested to be a gamma-interferon control region.

B-Lymphocytes↗
PubMed1995

Close evolutionary relatedness among functionally distantly related members of the (alpha/beta)8-barrel glycosyl hydrolases suggested by the similarity of their fifth conserved sequence region.

A short conserved sequence equivalent to the fifth conserved sequence region of alpha-amylases (173_LPDLD, Aspergillus oryzae alpha-amylase) comprising the calcium-ligand aspartate, Asp-175, was identified in the amino acid sequences of several members of the family of (alpha/beta)8-barrel glycosyl hydrolases. Despite the fact that the aspartate is not invariantly conserved, the stretch can be easily recognised in all sequences to be positioned 26-28 amino acid residues in front of the well-known catalytic aspartate (Asp-206, A. oryzae alpha-amylase) located in the beta 4-strand of the barrel. The identification of this region revealed remarkable similarities between some alpha-amylases (those from Bacillus megaterium, Bacillus subtilis and Dictyoglomus thermophilum) on the one hand and several different enzyme specificities (such as oligo-1,6-glucosidase, amylomaltase and neopullulanase, respectively) on the other hand. The most interesting example was offered by B. subtilis alpha-amylase and potato amylomaltase with the regions LYDWN and LYDWK, respectively. These observations support the idea that all members of the family of glycosyl hydrolases adopting the structure of the alpha-amylase-type (alpha/beta)8-barrel are mutually closely related and the strict evolutionary borders separating the individual enzyme specificities can be hardly defined.

Amino Acid Sequence↗
PubMed2004

A search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoter.

We describe a web-based resource to identify, search and analyze sequence patterns conserved in the multiple sequence alignments of orthologous promoters from closely related / distant Saccharomyces spp. The webtool interfaces with a database where conserved sequence patterns (greater than 4 bp) have been previously extracted from genome-wide promoter alignments, allowing one to carry out user-defined genome-wide searches for conserved sequences to assist in the discovery of novel promoter elements based on comparative genomics. The web-based server can be accessed at http://www2.imtech.res.in/ anand/sacch_prom_pat.html.

Base Sequence↗
PubMed2007

Occurrence of protein structure elements in conserved sequence regions.

BACKGROUND: Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. RESULTS: Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. CONCLUSION: These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function.

Amino Acid Sequence↗
PubMed1986

Conservation of kinetoplastid minicircle characteristics without nucleotide sequence conservation.

The nucleotide sequence and restriction fragment electrophoretic mobility of four minicircles from the kinetoplast DNA of Trypanosoma brucei were determined. Each minicircle possesses an approximately 130 base pair conserved sequence which occurs in other African trypanosome minicircles and contains a 13 base pair sequence that is conserved among kinetoplastid genera [Kidane et al. (1984) Gene 27, 265-277]. A sequence located adjacent to the conserved sequence conserves purine versus pyrimidine strand bias, but not nucleotide sequence, and contains periodic oligo(dA) tracts. Minicircle fragments containing the conserved sequence and adjacent segment exhibited anomalous electrophoretic mobility in polyacrylamide gels. The position of the oligo(dA) tracts in the fragments appears to influence this anomalous mobility. The presence of conserved features independent of conserved nucleotide sequence and the lack of conserved open reading frames among these minicircles suggests that minicircles may have a function other than encoding protein.

Animals↗