Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “cDNA sequencing”

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 271 records · Page 15Linked to original sources
PubMed1994

cDNA sequence of zebrafish (Brachydanio rerio) translation elongation factor-1 alpha: molecular phylogeny of eukaryotes based on elongation factor-1 alpha protein sequences.

We have isolated and determined the nucleotide sequence of a cDNA clone containing the complete coding region for elongation factor-1 alpha (EF-1 alpha) from an embryonic zebrafish cDNA library. A secondary structure model based on all known EF-1 alpha and EF-Tu protein sequences is presented and the presence of conserved putative protein kinase C phosphorylation sites in loop regions of eukaryotic EF-1 alpha is demonstrated. Using distance matrix and maximum parsimony methods we constructed multi-kingdom phylogenetic trees containing 22 different eukaryotic sequences. Strikingly, both tree constructions show Fungi to be the closest relative of Animalia among eukaryotic kingdoms. A 12 amino acid stretch present in all animal and fungal sequences known to date was found to be absent from all plant, protist an archaebacterial EF-1 alpha sequences suggesting that this sequence was inserted following the separation of plants from the lineage leading to fungi and animals. In contrast to our results, molecular phylogenies based on small subunit ribosomal RNA sequences as well as other protein sequences have failed to yield consistent results regarding the branching order among the kingdoms Plantae, Fungi and Animalia. The slow evolutionary rate and universal occurrence of EF-1 alpha (EF-Tu in eubacteria) makes this protein a particularly interesting tool for probing distant evolutionary relationships.

Animals↗
PubMed1986

Complete cDNA sequence for rabbit muscle glycogen phosphorylase.

The cDNA for the nearly full-length rabbit muscle glycogen phosphorylase mRNA has been isolated and sequenced. The cDNA is rich in G and C nucleotides. This feature is especially striking at the 3rd position of codons, where 86% of the 843 amino acid codons terminate with G or C. Methionine, presumably the initiation residue, is found at position-1, suggesting that the removal of only a single methionine residue precedes the amino-terminal acetylation at serine. Eight differences between the deduced amino acid sequence and the previously determined protein sequence are discussed.

Amino Acid Sequence↗
PubMed1995

Completion of a cDNA sequence from a tobamovirus pathogenic to crucifers.

Turnip vein-clearing virus (TVCV) is a tobamovirus related to ribgrass mosaic virus. We report the nucleotide (nt) sequences of the 5'-untranslated region (UTR) and the 3'-half of the TVCV genome (the 3' region of the 182-kDa protein-encoding gene, as well as the movement protein and coat protein genes and the 3'-UTR). The determination completes the nt sequence of the cDNA of TVCV.

Amino Acid Sequence↗
PubMed2003

A cellular retinoic acid-binding protein from zebrafish (Danio rerio): cDNA sequence, phylogenetic analysis, mRNA expression, and gene linkage mapping.

We report the sequence of a cDNA clone coding for a cellular retinoic acid-binding protein (CRABP) in zebrafish. The encoded polypeptide is 142 amino acids in length with an estimated molecular mass of 15.8 kDa and a calculated isoelectric point of 5.2. The zebrafish CRABP exhibits highest sequence identity to the pufferfish CRABPIIa (83%) and CRABPIIb (79%), and human CRABPII (74%) than to any other member of the intracellular lipid-binding protein (ILBP) family. A phylogenetic tree for different members of the ILBP multigene family including fatty acid-binding proteins (FABPs), cellular retinol-binding proteins (CRBPs) and CRABPs shows that the cloned zebrafish cDNA encodes a protein that clusters with CRABPs from other species and not with CRBPs and FABPs. Reverse-transcription polymerase chain reactions (RT-PCR), using oligonucleotide primers specific to the zebrafish CRABP cDNA made from total RNA of embryos collected at various developmental stages, did not detect the CRABP mRNA until 12 h post-fertilization. In adult zebrafish, CRABP mRNA was detected by RT-PCR in total RNA extracted from muscle, testes and skin, barely detectable in heart, ovary and brain and undetectable in liver, kidney and intestine. Quantitative RT-PCR (qRT-PCR) revealed a similar tissue-specific distribution for zebrafish CRABP mRNA with highest levels of CRABP mRNA in muscle followed by testes, skin, ovary and much lower levels in heart. Radiation hybrid mapping assigned the CRABP gene to linkage group 16 in the zebrafish genome. Comparison of the mapped zebrafish CRABP and human CRABPII genes revealed that zebrafish linkage group 16 has a syntenic relationship with human chromosome 1. Based on phylogenetic analysis and the syntenic relationship to the CRABPII gene in human, the zebrafish cDNA clone appears to code for a type II CRABP.

Amino Acid Sequence↗
PubMed1984

Comparative analysis of the cDNA sequences derived from the larval and the adult alpha 1-globin mRNAs of Xenopus laevis.

The complete nucleotide sequences of cloned cDNA segments derived from the larval and the adult alpha 1-globin mRNA of Xenopus laevis have been determined. These sequences comprise part of the 5' noncoding region, the entire coding region and the 3' noncoding region, including the polyadenylation site. The larval sequence differs from the adult one by a much longer 3' noncoding region. The sequences diverge by 47%, but codon usage is similar. Comparison of the amino acid sequences of vertebrates shows that the sites of heme contact are highly conserved, whereas the alpha 1/beta 1- and the alpha 1/beta 11-interfaces diverge to different degrees. In these regions the larval alpha 1-globin diverges less from embryonic than from adult alpha-like globins of vertebrates. This suggests that these sites are mainly responsible for the functional peculiarities of the larval amphibian hemoglobins.

Animals↗
PubMed1986

Complete cDNA sequence of human preceruloplasmin.

A cDNA for human ceruloplasmin (EC 1.16.3.1) was identified in a human liver cDNA library by screening with two mixtures of synthetic oligodeoxyribonucleotides that were complementary to two regions of ceruloplasmin mRNA as predicted from the amino acid sequence of plasma ceruloplasmin. The resulting clone (phCP1) contained DNA coding for amino acid residues 202-1046 of the protein, followed by a stop codon, a 3' untranslated region of 123 base pairs, and a poly(A) tail. To isolate cDNAs encoding the 5' end of ceruloplasmin mRNA, a cDNA library was constructed in lambda gt10. The cDNA for this library was synthesized by reverse transcription of human liver poly(A)+ RNA, using random oligonucleotides as primers. When this cDNA library was screened by using a 5' fragment of phCP1 as a hybridization probe, several positive clones were identified. One of these clones (lambda hCP1) contained DNA coding for a probable signal peptide of 19 amino acid residues followed by DNA coding for residues 1-380 of plasma ceruloplasmin. Blot hybridization analysis showed that ceruloplasmin mRNA from human liver and the human hepatoma cell line HepG2 is 3700 nucleotides in size. Liver contained an additional mRNA species that is like ceruloplasmin mRNA and is 4500 nucleotides in size. Comparison of the complete nucleotide sequences of human ceruloplasmin cDNA and human clotting factor VIII cDNA showed regions of sequence homology, suggesting that these two proteins have evolved from a common ancestor.

Base Sequence↗
PubMed1998

Isolation of mhc class II DMA and DMB cDNA sequences in a marsupial: the gray short-tailed opossum (Monodelphis domestica).

We report the cDNA sequences for the DMA and DMB family of Mhc genes of the gray short-tailed opossum. Until now DM sequences were available only in eutherian mammals. The marsupial sequences indicate that both members of the family are old and probably diverged from other classical class II families about the time of the radiation of jawed vertebrates some 450 million years ago. We examine the evolutionary rates of equivalent sets of classical and nonclassical genes to check for rate heterogeneity. We find the alpha-1 domain of the DR genes to be untypically conservative in its evolutionary mode. The DM genes appear to evolve at rates typical of other class II genes, indicating that their placement at the root of class II gene evolutionary trees may be justified.

Amino Acid Sequence↗
PubMed1997

Primary structure of the smallest (6.4-kDa) subunit of human and bovine ubiquinol-cytochrome c reductase deduced from cDNA sequences.

Amino acid sequences of the smallest subunit of human and bovine ubiquinol-cytochrome c reductase were deduced from nucleotide sequence of recombinant cDNA clones isolated by screening the corresponding cDNA libraries. Both proteins were composed of 56 amino acids. They were 84% homologous to each other in the coding nucleotide sequences and 88% homologous in the amino acid sequences. Southern blot analysis with human DNA suggested the presence of a single gene coding for the protein. Northern blot of human mRNAs from different tissues confirmed the existence of a single species of transcript among the tissues but the human gene is highly expressed in bioenergetically active tissues like heart and skeletal muscle.

Amino Acid Sequence↗
PubMedDate not supplied

Complete primary structure of a heterodimeric T-cell receptor deduced from cDNA sequences.

Two related, but distinct, cDNA clones have been isolated and sequenced from a functional murine cytotoxic T-lymphocyte clone. The genes corresponding to these cDNA are expressed and rearranged specifically in T cells and both have similarities to immunoglobulin variable and constant region genes. It is concluded that these genes code for the two subunits of the heterodimeric antigen receptor on the surface of the T cell; its complete deduced primary structure is presented.

Amino Acid Sequence↗
PubMed1991

NADH:ubiquinone oxidoreductase from bovine heart mitochondria. cDNA sequences of the import precursors of the nuclear-encoded 39 kDa and 42 kDa subunits.

The 39 kDa and 42 kDa subunits of NADH:ubiquinone oxidoreductase from bovine heart mitochondria are nuclear-coded components of the hydrophobic protein fraction of the enzyme. Their amino acid sequences have been deduced from the sequences of overlapping cDNA clones. These clones were amplified from total bovine heart cDNA by means of the polymerase chain reaction, with the use of complex mixtures of oligonucleotide primers based upon fragments of protein sequence determined at the N-terminals of the proteins and at internal sites. The protein sequences of the 39 kDa and 42 kDa subunits are 345 and 320 amino acid residues long respectively, and their calculated molecular masses are 39,115 Da and 36,693 Da. Both proteins are predominantly hydrophilic, but each contains one or two hydrophobic segments that could possibly be folded into transmembrane alpha-helices. The bovine 39 kDa protein sequence is related to that of a 40 kDa subunit from complex I from Neurospora crassa mitochondria; otherwise, it is not related significantly to any known sequence, including redox proteins and two polypeptides involved in import of proteins into mitochondria, known as the mitochondrial processing peptidase and the processing-enhancing protein. Therefore the functions of the 39 kDa and 42 kDa subunits of complex I are unknown. The mitochondrial gene product, ND4, a hydrophobic component of complex I with an apparent molecular mass of about 39 kDa, has been identified in preparations of the enzyme. This subunit stains faintly with Coomassie Blue dye, and in many gel systems it is not resolved from the nuclearcoded 36 kDa subunit.

Amino Acid Sequence↗
PubMed1995

Purification, characterization and cDNA sequence of an alkaline chymotrypsin from the midgut of Manduca sexta.

The chymotrypsin in the midgut of Manduca sexta has been purified, characterized and the cDNA encoding the protein has been cloned. The enzyme exists as a monomer of approx. 24 kDa and shows maximal activity between pH 10.5 and 11.0. Kinetic studies reveal that the Michaelis constant (Km) for the synthetic substrate N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide varies only slightly between pH 7.5 and 11.5 and the Dixon plot shows a kinetically significant pKa at 9.2. The specificity of the purified enzyme was determined to be the peptide bond on the carboxyl side of tyrosine, phenylalanine, tryptophan, histidine, leucine, threonine and glycine. The protease is inhibited by TPCK, PMSF, chymostatin and DFP. A 1 kilobase chymotrypsin cDNA clone was isolated and sequenced. The cDNA sequence encodes a preproenzyme with a putative 17 amino acid signal sequence, a 41 amino acid activation peptide and a mature enzyme of 235 amino acids. The isolated clone encodes the highly conserved active site residues (His, Asp, Ser) and specificity pocket residues present in bovine chymotrypsinogen B. Northern analysis localizes the mRNA for the chymotrypsin to the anterior and middle third of the midgut.

Amino Acid Sequence↗
PubMed1992

The complete cDNA sequence for dihydrolipoyl transacylase (E2) of human branched-chain alpha-keto acid dehydrogenase complex.

We have determined the complete nucleotide sequence for the cDNA encoding human dihydrolipoyl transacylase (E2) using the rapid amplification of cDNA ends (RACE) procedure. The full-length E2 cDNA is 3535 nucleotides in length. The coding region spans 1446 bp and the 3'-noncoding region spans 2074 bp. The latter contains three Alu repetitive sequences and two transcription termination sites.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗
PubMed1989

The primary sequence of the PFK-1 inactivating zinc-binding protein as deduced from cDNA sequencing. Identity of the zinc-binding protein with rat parathymosin.

We have recently described the sequence of the Zn2+-binding domain (43 amino acid residues) of a newly detected Zn2+-binding protein which reversibly inactivates phosphofructokinase-1 in a Zn2+-dependent manner [(1986) J. Biol. Chem. 269, 5895-5900; (1988) Eur. J. Biochem. 177, 561-568]. Here, we describe the primary sequence of this protein based on a full-length cDNA. A sequence comparison reveals the identity of the Zn2+-binding protein with a protein called parathymosin-alpha.

Amino Acid Sequence↗
PubMed1994

Baboon and cotton-top tamarin B2m cDNA sequences and the evolution of primate beta 2-microglobulin.

Nonhuman primates represent phylogenetic intermediates for studying the divergence of human and murine beta 2Ms. We report the nucleotide sequences of B2m cDNA clones from a baboon cell line, 26CB-1 (Papio hamadryas; primates: Cercopithecoidea), and a cotton-top tamarin cell line, 1605L (Saguinus oedipus; primates: Ceboidea). The baboon and tamarin B2m sequences indicate a very slow rate of B2m evolution in primates relative to that in murid rodents. Phenotypic evolution of beta 2M has also been very conservative in primates, with only 9-14 substitutions separating baboon or tamarin beta 2Ms from those of humans or orangutans. Analyses of silent and amino-acid-altering nucleotide substitutions provide evidence that negative selection has acted to limit variability in beta strands of primate beta 2Ms, while positive selection has promoted diversity in non-beta-strand regions of murine beta 2Ms. No evidence for the action of selection upon beta 2M residues that contact the class I heavy chain was found in primates or mice. The finding that different selective forces have operated upon primate and murine beta 2Ms suggests that beta 2M may have evolved to serve distinct functions in primates and mice.

Amino Acid Sequence↗
PubMed2003

A rapid method for detecting mutations of the human LDL receptor gene by complete cDNA sequencing.

We have developed and clinically tested a rapid and largely automated procedure to detect mutations in the coding region of a gene of interest. Our method relies on the automated sequencing of the complete cDNA, followed by an advanced mutation search-and-verification routine using an integrated set of computer analysis tools. We have applied our automated procedure to the diagnosis of familial hypercholesterolemia (FH) in 52 unrelated FH families, by sequencing the whole cDNA coding region of the LDLR gene. Here we report the procedures and performance of our method in the identification of the most common types of LDLR mutations: short deletions or insertions and point mutations. Our method can provide a standard procedure for the 'overnight' unequivocal identification of mutations in those genetic diseases where several different mutations, none clearly prominent, may affect a given gene.

Base Sequence↗
PubMed2005

Sphingomyelinase D from venoms of Loxosceles spiders: evolutionary insights from cDNA sequences and gene structure.

Loxosceles spider venoms cause dermonecrosis in mammalian tissues. The toxin sphingomyelinase D (SMaseD) is a sufficient causative agent in lesion formation and is only known in these spiders and a few pathogenic bacteria. Similarities between spider and bacterial SMaseD in molecular weights, pIs and N-terminal amino acid sequence suggest an evolutionary relationship between these molecules. We report three cDNA sequences from venom-expressed mRNAs, analyses of amino acid sequences, and partial characterization of gene structure of SMaseD homologs from Loxosceles arizonica with the goal of better understanding the evolution of this toxin. Sequence analyses indicate SMaseD is a single domain protein and a divergent member of the ubitiquous, broadly conserved glycerophosphoryl diester phosphodiesterase family (GDPD). Bacterial SMaseDs are not identifiable as homologs of spider SMaseD or GDPD family members. Amino acid sequence similarities do not afford clear distinction between independent origin of toxic SMaseD activity in spiders and bacteria and origin in one lineage by ancient horizontal transfer from the other. The SMaseD genes span at least 6500bp and contain at least 5 introns. Together, these data indicate L. arizonica SMaseD has been evolving within a eukaryotic genome for a long time ruling out origin by recent transfer from bacteria.

Amino Acid Sequence↗
PubMed1999

The cDNA sequences of equine antioxidative enzyme genes Cu/Zn-SOD and Mn-SOD, and these expressions in equine tissues.

The entire cDNA sequences were determined by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) techniques for equine copper/zinc superoxide dismutase (Cu/Zn-SOD) and manganese superoxide dismutase (Mn-SOD) through the use of total RNA extracted from the testis of an adult Thoroughbred. The results revealed a protein coding region for equine Cu/Zn-SOD with bases totaling 465 bp, accompanied by an estimated 154 residues of amino acids. As for equine Mn-SOD, its coding region contained a total of 669 bp and an estimated 222 residues of amino acids. Further, the expression of Cu/Zn-SOD and Mn-SOD genes were confirmed in the equine tissues by RT-PCR and in situ hybridization.

Amino Acid Sequence↗
PubMed1994

cDNA sequence analysis of the main olive allergen, Ole e I.

Olea europaea (Ole e) I-specific cDNA sequences were amplified by 3'-RACE-PCR, using specific primers based on the N-terminal sequence of the allergen, and cloned into appropriate vectors. The nucleotide sequence data obtained revealed the presence of isogenic variation in Ole e I gene(s). The molecular mass, pI, amino acid composition and sequence of the predicted polypeptides agree with data previously obtained by analysis of purified Ole e I from pollen. Furthermore, by treatment of purified Ole e I with specific glycopeptide hydrolases it has been demonstrated the presence of N-glycosylation in the allergen, and there is a unique concensus site for N-linked glycosylation at positions 111-113 of the deduced amino acid sequence. The Ole e I predicted sequence shows a significant homology with three putative proteins encoded respectively by the another-specific LAT52 gene from tomato and the pollen specific genes Zmc13 from maize and OSPSG from rice, suggesting that these proteins could have a role in one of the development processes unique to male gametophytes.

Allergens↗