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.

SourceResearch connectionFrom yearThrough year

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

At least 1,315 records · Page 73Linked to original sources

PubMed1994

Cloning and sequence analysis of cDNA encoding rabbit vitamin D-binding protein (Gc globulin).

The cDNA sequence of rabbit vitamin D-binding protein (DBP) was determined by sequencing clones isolated by immuno-screening and PCR amplification from a rabbit liver cDNA library. The 1641-nucleotide sequence included the 5' untranslated region and extended to the poly(A) tail. It encoded a protein of 460 amino acid residues in addition to a signal sequence of 16 residues, and had 84%, 79% and 78% sequence identities with human, rat and mouse DBP cDNA, respectively. In comparison with DBP amino acid sequences of other species, there are at least four heterogeneous regions. In contrast, a putative actin binding domain was conserved in the evolution process.

Amino Acid Sequence↗

PubMed1986

Nucleotide sequence of cDNA containing the complete coding sequence for human lysosomal glucocerebrosidase.

Complementary DNA clones for human glucocerebrosidase were isolated from a human hepatoma library in lambda gt11. The complete nucleotide sequence of the 1805-base pair cDNA insert has been determined. In addition to 5' and 3' untranslated regions (51 and 206 base pairs, respectively), the cDNA insert contains 1548 base pairs that completely encode human glucocerebrosidase. All possible N-linked glycosylation sites are identified. Examination of the 19 amino acids of the leader polypeptide beginning with the ATG at position 52 revealed a hydrophobic core and a carboxyl-terminal glycine at the peptidase cleavage site, features consistent with the leader sequences described for other human translocated proteins. The Mr of 57,000 calculated from the 516 amino acids deduced from cDNA sequence is in good agreement with that identified by immunoprecipitation following in vitro translation of human placental mRNA.

Amino Acid Sequence↗

PubMed1991

Cloning and sequence of a cDNA encoding human carbamyl phosphate synthetase I: molecular analysis of hyperammonemia.

Carbamyl phosphate synthetase I (CPSI) is the first enzyme involved in urea synthesis. CPSI deficiency is an autosomal recessive disorder characterized by hyperammonemic coma in the neonatal period. To analyze the enzyme and gene structures, and to elucidate the nature of mutations in CPSI deficiency, we isolated cDNA clones encoding human liver CPSI. Oligo(dT)-primed and random primer human liver cDNA libraries in lambda gt11 were screened using 5', middle, and 3' fragments of the rat CPSI cDNA as probes. Seven positive clones covered the full-length cDNA sequence with an open reading frame encoding a precursor polypeptide of 1500 amino acids (aa) (deduced Mr, 164,828) with a putative N-terminal presequence of 38 or 39 aa, a 5'-untranslated sequence of 118 bp and a 3'-untranslated sequence of 597 bp. Comparison with the rat CPSI cDNA showed that the deduced aa sequence of the human liver CPSI precursor is 94.4% identical to the rat enzyme precursor. A molecular analysis was made of the genomic DNA from three patients with CPSI deficiency. Heterogeneity of hybridized fragments that may or may not be the cause of the deficiency was apparent on the DNA blots from tissues from one patient.

Amino Acid Metabolism, Inborn Errors↗

PubMed2000

Molecular cloning and sequencing of the cDNA encoding the feline FcgammaRIIIA (CD16) homologue.

We amplified the cDNA encoding the feline FcgammaRIIIA (CD16) homologue from peripheral blood mononuclear cells by polymerase chain reaction and cloned two forms of FCGR3A cDNA. Sequencing analysis revealed that the open reading frame of feline FCGR3A cDNA consists of 750 or 747 base pairs encoding 250 or 249 amino acid residues, respectively. Comparison of the predicted amino acid sequence of feline FCGR3A cDNA with those of other mammalians' homologues revealed that the extracellular domain has a relatively low homology. However, the cytoplasmic domain contained an 8-amino acid motif, Leu-Phe-Val-Val-Asp-Thr-Gly-Leu, which was considered to interact with an accessory molecule such as the gamma chain of Fc receptors for IgE to form heterodimeric complexes.

Amino Acid Sequence↗

PubMed1996

Identification, cloning, and sequencing of a cDNA coding for rat gamma-glutamyl hydrolase.

Purified gamma-glutamyl hydrolase secreted from rat H35 hepatoma cells has been characterized as a diffuse band of 55 kDa on SDS-polyacrylamide gel electrophoresis that is converted to bands of 35 and 33 kDa after enzymatic removal of N-linked carbohydrate. Polyclonal antibodies against 55-kDa gamma-glutamyl hydrolase captured the enzyme activity and recognized the glycosylated and both deglycosylated forms of gamma-glutamyl hydrolase. A complete cDNA sequence of gamma-glutamyl hydrolase was obtained using degenerate oligonucleotides derived from peptide sequences, screening of a rat hepatoma cDNA library, and reverse transcription polymerase chain reaction. Based upon the deduced amino acid sequence the peptide component of gamma-glutamyl hydrolase had a molecular weight of 33,400. The results of amino acid analysis of the purified protein agreed with the deduced amino acid sequence in which there are seven potential asparagine-containing glycosylation sites.

Amino Acid Sequence↗

PubMed1994

Human cysteine dioxygenase type I: primary structure derived from base sequencing of cDNA.

The base sequence of cDNA encoding the complete human liver cysteine dioxygenase type I (CDO-I; EC 1.13.11.20) message, and the derived amino-acid sequence are reported. CDO-I is encoded on a single mRNA species (approx. 1.5 kb). Human CDO-I clones were identified by screening a liver cDNA library, and inserts were isolated and sequenced. In addition, human liver total RNA was reverse-transcribed and CDO-I cDNA amplified by PCR using a modified poly-T primer and specific CDO-I primers to give a second source of sequencing template. The CDO-I message encodes a 200 amino-acid residue protein, the sequence of which has greater than 90% homology with the equivalent rat enzyme. The message was not expressed in a human hepatoma cell line (Hep G2).

Amino Acid Sequence↗

PubMed1990

Molecular cloning and sequence analysis of cDNA encoding the macrophage lectin specific for galactose and N-acetylgalactosamine.

The primary structure of the macrophage lectin specific for galactose and N-acetylgalactosamine (macrophage asialoglycoprotein-binding protein, M-ASGP-BP) has been deduced from its cDNA sequence. The M-ASGP-BP cDNA encoded a protein consisting of 306 amino acid residues with a molecular mass of 34,242 daltons. The sequence was highly homologous with that of the rat liver asialoglycoprotein receptor (rat hepatic lectin, RHL), particularly that of RHL-1 (the major form of RHL), throughout its whole length, and especially so in its putative membrane-spanning region and carbohydrate recognition domain. There were two N-glycosylation sites in M-ASGP-BP, the location of which were identical to those in RHL-1. However, M-ASGP-BP was characteristic in having a shorter cytoplasmic tail, and an inserted segment of 24 amino acids containing an Arg-Gly-Asp sequence between the membrane-spanning region and carbohydrate recognition domain.

Acetylgalactosamine↗

PubMed1988

Nucleotide sequence of cDNA and predicted amino acid sequence of rat liver uricase.

A cDNA clone for rat liver uricase (EC 1.7.3.3), which is localized in the core of peroxisomes, was isolated from a rat liver cDNA library in lambda gt11. The clone, referred to as lambda rURC-1, induced formation of a fusion protein (molecular mass 140 kDa) in the presence of isopropyl beta-D-thiogalactoside. Immunoglobulin G reactive with the fusion protein recognized only a protein with molecular mass of 33 kDa, corresponding to the molecular mass of uricase. The nucleotide sequence of the isolated cDNA was determined and the amino acid sequence was predicted. An open reading frame was identified and found to encode a polypeptide of 280 amino acids with a molecular mass of 32226 Da. The cDNA contained 14 base pairs of 5'-untranslated sequence and 192 base pairs of 3'-untranslated sequence. The sequences of four internal peptide fragments, determined by Edman degradation, were identical to parts of the sequence predicted from the cDNA. The complete amino acid sequence predicted for rat liver uricase was compared with that of soybean nodulin uricase and nine highly homologous regions of the two enzymes were found.

Amino Acid Sequence↗

PubMed1992

Protein structure of pig liver 4-aminobutyrate aminotransferase and comparison with a cDNA-deduced sequence.

The amino acid sequence of pig liver 4-aminobutyrate aminotransferase has been determined by gas-phase sequencing of proteolytically derived peptide fragments. The sequence differs substantially from that predicted for the same enzyme on the basis of the sequence of cDNA derived from pig brain in recently published work [Kwon, O., Park, J. & Churchich, J. E. (1992) J. Biol. Chem. 267, 7215-7216]. Apart from a few minor differences, the two sequences are completely different in the segment of protein comprising the 36 residues at positions 107-142. Insertion of a cytosine between bases 402 and 403 in the cDNA sequence, together with deletion of the guanine at position 510, results in a DNA sequence which predicts exactly the amino acid sequence determined by peptide analysis in the present work. The mammalian enzyme has approximately 44% sequence identity with the same enzyme from two unicellular eukaryotes (Saccharomyces cerevisiae, Aspergillus nidulans) and 22% identity with that from Escherichia coli.

4-Aminobutyrate Transaminase↗

PubMed1987

Complete nucleotide sequence of cDNA and deduced amino acid sequence of rat liver arginase.

Arginase (EC 3.5.3.1) catalyzes the last step of urea synthesis in the liver of ureotelic animals. The nucleotide sequence of rat liver arginase cDNA, which was isolated previously (Kawamoto, S., Amaya, Y., Oda, T., Kuzumi, T., Saheki, T., Kimura, S., and Mori, M. (1986) Biochem. Biophys. Res. Commun. 136, 955-961) was determined. An open reading frame was identified and was found to encode a polypeptide of 323 amino acid residues with a predicted molecular weight of 34,925. The cDNA included 26 base pairs of 5'-untranslated sequence and 403 base pairs of 3'-untranslated sequence, including 12 base pairs of poly(A) tract. The NH2-terminal amino acid sequence, and the sequences of two internal peptide fragments, determined by amino acid sequencing, were identical to the sequences predicted from the cDNA. Comparison of the deduced amino acid sequence of the rat liver arginase with that of the yeast enzyme revealed a 40% homology.

Amino Acid Sequence↗

PubMed1993

Isolation and sequence determination of cDNA encoding human T-protein of the glycine cleavage system.

We present the full-length cDNA sequence of human T-protein of the glycine cleavage system. Overlapping cDNA clones were isolated by screening human liver cDNA libraries with bovine T-protein cDNA. The 1209 base pair open reading frame encodes 403 amino acid precursor protein, and the deduced amino acid sequence of the mature peptide shows 90 and 68% homology to that of bovine and chicken counterpart, respectively. RNA blot analysis of human liver transcripts and Southern blot analysis of human genomic DNA confirm that human T-protein is encoded by a single gene.

Adult↗

PubMed1997

Sequencing of cDNA clones that encode bovine ferritin H and L chains.

The molecular weight of the liver-type subunit (L) of bovine ferritin is much larger than that of the heart-type subunit (H) as determined by SDS-PAGE (L, 20.5 kDa; H, 18.4 kDa). The migration of these two subunits on SDS-PAGE gels, relative to each other, is opposite to that reported for ferritin L and H subunits in other mammalian species (L, 19 kDa; H, 21 kDa). To determine the cause of this anomaly, full-length cDNA clones of the bovine L and H chains were isolated from a bovine spleen gamma gt11 cDNA library and sequenced. The amino acid sequences of the L and H chains of bovine ferritin, deduced from their cDNA sequences, contained open reading frames coding for 174 and 180 amino acid residues with calculated molecular weights of 19,856 and 20,920 Da, respectively. The deduced amino acid sequence of the L chain shows 86%, 84%, 87%, 83% and 83% homology with the amino acid sequences of horse, human, rabbit, rat and mouse L chains, respectively. The H chain displays a higher homology with the human, rat and mouse H chains (91%, 92% and 93%, respectively). In addition, the bovine L chain did not contain the extra octapeptide present in rodent L chains, and bovine, L and H chains did not react with concanavalin A. The bovine L and H chains expressed using a baculovirus expression system showed almost the same mobilities as those of bovine spleen ferritin, respectively, by SDS-PAGE. These results suggest that the much slower mobility of the bovine L chain compared with other mammalian L chains on SDS-PAGE cannot be attributed to insertion(s) of amino acid(s) or peptide(s) into the L chain, to the deletion(s) of them of it or to the addition of carbohydrate chains(s) but may result from significant differences in the binding affinity of SDS for bovine ferritin L chains.

Amino Acid Sequence↗

PubMed1985

Structure of mouse interferon-beta cDNA clones: sequence rearrangements in a cloned cDNA.

A fraction enriched in interferon (IFN) mRNA was prepared from mouse C243-3 induced cells and was used for the construction of a cDNA library. Two plasmids were obtained after screening by differential colony hybridization and IFN mRNA hybridization-selection and translation. The nucleotide sequences of the cDNA inserts revealed that both were partial copies of IFN-beta mRNA. The cDNA 861 corresponds to the entire 3' nontranslated region of the mRNA while the cDNA 2939 consists of rearranged translated regions of IFN mRNA. A mechanism for the rearrangement events during cDNA synthesis is proposed. A chromosomal DNA fragment hybridizing to cDNA 2939 was identified by screening a mouse genomic library.

Animals↗

PubMed1984

Nucleotide sequence of cDNA and derived amino acid sequence of human complement component C9.

The nucleotide sequence coding for the ninth component of human complement (C9) has been determined and the corresponding amino acid sequence has been derived. A human liver cDNA library was screened by the colony-hybridization technique using two radiolabeled oligonucleotide probes that correspond to known regions of the C9 amino acid sequence. Two recombinant plasmids were isolated and their cDNA inserts were sequenced. The derived protein sequence consists of 537 amino acids in a single polypeptide chain. A profile of the hydropathic index versus sequence number indicates that the amino-terminal half of C9 is predominantly hydrophilic in character whereas the carboxyl-terminal section of this protein is more hydrophobic. The amphipathic organization of the primary structure of C9 is consistent with the known potential of polymerized C9 to penetrate lipid bilayers, causing the formation of transmembrane channels.

Amino Acid Sequence↗

PubMedDate not supplied

Cloning and sequencing of a cDNA for a ligninase from Phanerochaete chrysosporium.

Lignin is a complex polymer of phenylpropanoid subunits. It is an essential component of woody tissue, to which it imparts structural rigidity. Lignin is remarkably resistant to degradation by most microbes; nevertheless, a few species of white-rot fungi are able to catalyse its oxidation to CO2. Its biodegradation is of great ecological significance because, next to cellulose, lignin is the most abundant renewable polymer on Earth. The first step in lignin degradation is depolymerization, catalysed by the lignin peroxidase isozymes (ligninases). These isozymes are secreted, along with hydrogen peroxide (H2O2) by the fungus Phanerochaete chrysosporium Burds, under conditions of nutrient (nitrogen) limitation. Ligninases are not only important in lignin biodegradation, but are also potentially valuable in chemical waste disposal because of their ability to degrade environmental pollutants. We have undertaken the cloning of the ligninase genes to understand further their regulation and enzymology. We report here the isolation and characterization of a ligninase complementary DNA clone with a full-length insert. The cDNA sequence shows that the sequence of the mature ligninase is preceded by a 28-residue leader, and the mature protein is predicted to have a relative molecular mass of 37,000 (Mr 37K). Consistent with the classification of ligninase as a peroxidase certain residues thought to be essential for peroxidase activity can be identified and near these residues the ligninase shows homology with other known peroxidases. Our cDNA clone has also allowed us to show that expression of ligninase is regulated at the messenger RNA level.

Agaricales↗

PubMed1993

Studies of the hyperthermophile Thermotoga maritima by random sequencing of cDNA and genomic libraries. Identification and sequencing of the trpEG (D) operon.

Random sequencing of cDNA and genomic libraries has been used to study the genome of the hyperthermophile Thermotoga maritima. To date, 175 unique clones have been analyzed by comparing short sequence tags with known proteins in the PIR and GenBank databases. We find that a significant proportion of sequences can be matched to previously identified protein from non-Thermotoga sources. A high match rate was obtained from an oligo(dT)-primed cDNA library, where one-third of all unique sequences analyzed (21/65) shared high amino acid sequence similarity with proteins in the PIR and GenBank databases. Also, approximately one-third of the unique sequences from a second cDNA library (28/89), constructed with random oligo primers, could be matched to sequences in PIR and GenBank. Identification of genes from the oligo(dT)-primed cDNA library indicates that some Thermotoga mRNAs are polyadenylated. Genes have also been identified from a 1 to 2 kb genomic DNA library. Here, (3/21) of genomic sequences analyzed could be matched to protein in PIR and GenBank. One of the genomic clones had high sequence similarity to the tryptophan synthesis gene anthranilate synthase component I (trpE). Using this sequence tag, the Thermotoga trp operon was isolated and sequenced. The Thermotoga maritima trp operon is arranged with trpE forming an overlapping transcript with a second protein consisting of a fusion of anthranilate synthase component II (trpG) and anthranilate phosphoribosyltransferse (trpD). With regard to the fusion, the operon organization is similar to Escherichia coli and Salmonella typhimurium, but lacks the classic attenuation system of enteric bacteria. Amino acid sequence comparison with 19 trpE, 18 trpG and 14 trpD genes from other organisms suggest that the Thermotoga trp genes resemble corresponding genes from other thermophiles more closely than expected.

Amino Acid Sequence↗

PubMed2004

Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have been conducting a mouse cDNA project to predict protein-coding sequences of mouse homologues of human KIAA and FLJ genes since 2001. As an extension of these projects, we herein present the entire sequences of 500 mKIAA cDNA clones and 4 novel cDNA clones that were incidentally identified during this project. We have isolated cDNA clones from the size-fractionated mouse cDNA libraries derived from 7 tissues and 3 types of cultured cells. The average size of the 504 cDNA sequences reached 4.3 kb and that of the deduced amino acid sequences from these cDNAs was 807 amino acid residues. We assigned the integrity of CDSs from the comparison with the corresponding human KIAA cDNA sequences. The comparison of mouse and human sequences revealed that two different human KIAA cDNAs are derived from single genes. Furthermore, 3 out of 4 proteins encoded in the novel cDNA clones showed moderate sequence similarity with human KIAA proteins, thus we could obtain new members of KIAA protein families through our mouse cDNA projects.

Animals↗

PubMed1986

Complete nucleotide sequence of cDNA and deduced amino acid sequence of rat liver catalase.

We have isolated five cDNA clones for rat liver catalase (hydrogen peroxide:hydrogen peroxide oxidoreductase, EC 1.11.1.6). These clones overlapped with each other and covered the entire length of the mRNA, which had been estimated to be 2.4 kilobases long by blot hybridization analysis of electrophoretically fractionated RNA. Nucleotide sequencing was carried out on these five clones and the composite nucleotide sequence of catalase cDNA was determined. The 5' noncoding region contained 83 bases and was followed by 1581 bases of an open reading frame that encoded 527 amino acids. The 3' noncoding region was 831 bases long and contained long repeats of the unit AC. The amino acid sequence deduced from the nucleotide sequence of the cDNAs showed about 90% homology with the reported primary structure of bovine liver catalase. The molecular weight of rat liver catalase was calculated to be 59,758 from the predicted amino acid sequence. The amino acid residues in contact with the heme group are completely identical for bovine liver and rat liver catalases. The amino acid sequence at the COOH terminus was confirmed by the results of carboxypeptidase P treatment of the protein purified from rat liver in the presence of leupeptin. Rat liver catalase has no cleavable signal peptide for translocation of the enzyme into peroxisomes.

Amino Acid Sequence↗