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 217 records · Page 12Linked to original sources
PubMed1993

Characterization of two full-length cDNA sequences encoding for apoproteins of peridinin-chlorophyll a-protein (PCP) complexes.

Characterizations are presented for RNA, 2 cDNA libraries, and 2 full-length cDNA sequences encoding for photosynthetic light-harvesting peridinin-chlorophyll a-protein (PCP) in the dinoflagellate Heterocapsa pygmaea. Subsequent analyses of the PCP system also indicate that (1) it is represented by multiple nuclear encoded genes, (2) a subset of mRNAs encoding for PCP apoproteins are regulated by growth irradiance, (3) PCP preproteins are larger than the mature apoproteins, and (4) PCP cDNA clones sequenced thus far contain a conserved region but are not identical. Results are discussed in the context of photoadaptation in dinoflagellates.

Amino Acid Sequence↗
PubMed1994

The cDNA sequence of the flavoprotein subunit of human heart succinate dehydrogenase.

We report the full-length cDNA sequence for the flavoprotein subunit of human heart succinate dehydrogenase (succinate: (acceptor) oxidoreductase EC 1.3.99.1). Identical sequence was obtained for part of the cDNA of the human placental flavoprotein, in contrast to a previously published sequence. The human sequence, like the bovine one, contains a cysteine triplet and at the active site there is an additional cysteine when compared with yeast or prokaryotes.

Amino Acid Sequence↗
PubMed1992

Selective amplification of cDNA sequence from total RNA by cassette-ligation mediated polymerase chain reaction (PCR): application to sequencing 6.5 kb genome segment of hantavirus strain B-1.

A method, referred to as cassette-ligation mediated polymerase chain reaction (PCR), has been developed to permit selective and specific amplification of cDNA sequence from total cellular RNA. This technique comprises (i) digestion of cDNA with multiple restriction enzymes, (ii) ligation of cleavage products to double-stranded DNA cassettes possessing a corresponding restriction site and (iii) amplification of cassette-ligated restriction fragments containing a short, known sequence (but not all the other ligation products) by PCR using the specific and cassette primers; the specific primer is designed to prime synthesis from the known sequence of the cDNA whereas the cassette primer anneals to one strand of the cassette. Sequencing from the cassette primer provides information to design a new primer for the next walking step. The amplified cDNA fragments are often larger than the maximum DNA fragments (500-600 bp) that can be sequenced without the need of synthesizing internal sequencing primer. Each of such large cDNA fragments is dissected into smaller DNA fragments by repeating cassette-ligation mediated PCR exploiting different restriction sites and different sets of cassette primers. This dissection process reduces the number of specific primers to a minimum, thereby increasing the speed of sequencing and minimizing the overall cost. We have successfully applied this cDNA walking and sequencing by the cassette-ligation mediated PCR to the sequencing of an entire 6.5 kb genome segment of hantavirus strain B-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1986

Complete amino acid sequence of rat liver alcohol dehydrogenase deduced from the cDNA sequence.

Alcohol dehydrogenase (ADH) catalyzes the rate-determining reaction in the metabolism of ethanol. We report here the complete nucleotide sequence of a cDNA encoding rat liver ADH, and the deduced amino acid (aa) sequence of the protein. The rat enzyme contains a cluster of aa substitutions and an aa insertion in the region between aa residues 111 and 118, which is near the intron-exon junction reported for the human ADH gene. It also contains an additional cysteine in the highly variable region from aa residues 108-125 which may account for the unusual lability of rat ADH compared with ADH from other species.

Alcohol Dehydrogenase↗
PubMed2003

CDS annotation in full-length cDNA sequence.

The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance of intergenic sequence in the genome, and provides little information about how different parts of potential CDS regions are expressed. In contrast, mammalian gene CDS prediction from cDNA sequence offers obvious advantages, yet encounters a different set of complexities when performed on high-throughput cDNA (HTC) sequences, such as the set of 60,770 cDNAs isolated from full-length enriched libraries of the FANTOM2 project. We developed a CDS annotation strategy that uses a variety of different CDS prediction programs to annotate the CDS regions of FANTOM2 cDNAs. These include rsCDS, which uses sequence similarity to known proteins; ProCrest; Longest-ORF and Truncated-ORF, which are ab initio based predictors; and finally, DECODER and NCBI CDS predictor, which use a combination of both principles. Aided by graphical displays of these CDS prediction results in the context of other sequence similarity results for each cDNA, FANTOM2 CDS inspection by curators and follow-up quality control procedures resulted in high quality CDS predictions for a total of 14,345 FANTOM2 clones.

Animals↗
PubMed1983

Isolation of cDNA sequences coding for a part of human tissue plasminogen activator.

We have isolated a cDNA sequence coding for a part of human tissue plasminogen activator. mRNA coding for tissue plasminogen activator was partially purified, copied into double-stranded cDNA, and cloned into Escherichia coli. Two sets of partially overlapping oligodeoxynucleotide mixtures corresponding to all possible coding sequences for a known portion of the tissue plasminogen activator gene were prepared. One set was used as a probe to screen cDNA containing bacterial clones and both were used as probes in hybridization against purified plasmid DNA. Of 4,200 bacterial clones examined, 1 carried a plasmid that hybridized to both sets of oligonucleotides. This plasmid contained a 370-base-pair cDNA insert, which was shown by nucleotide sequence analysis to code for the cleavage site region in the one-chain form of the human tissue plasminogen activator.

Amino Acid Sequence↗
PubMed2001

Cloning of a metallothionein gene and characterization of two other cDNA sequences in the Pacific oyster Crassostrea gigas (CgMT1).

Metallothionein (MT) genes encode essential metal-binding proteins involved in metallic homeostasis and detoxification in living organisms. Here, we describe the structure of the first Pacific oyster Crassostrea gigas metallothionein (CgMT1) gene and the sequences of two other MT cDNA. The CgMT1 gene sequence contains three coding exons plus a 5' entirely non-coding exon, and the predicted protein contains 21 cysteine residues organized in Cys-X-Cys motifs as classically described for MTs. The three cDNA sequences present few substitutions in either coding sequence or UTRs. Induction of these MT-mRNA in heavy metal-treated oysters (i.e. cadmium) was confirmed by Northern blot analysis and RT-PCR and suggests a potential specific tissue expression rate. Southern blot analysis suggested the presence of multiple CgMT genes, and allowed the detection of restriction fragment length polymorphisms (RFLPs). Although the CgMT1 coding sequence showed 30-73% nucleotide identities with known sequences in other mollusks, it included the specific motif Cys-X-Cys-X(3)-Cys-Thr-Gly-X-X-X-Cys-X-Cys-X(5)-Cys-X-Cys-Lys found in Mollusk family 2. Marine bivalves are commonly used as pollution bioindicators, thus the development of genetic markers based on CgMT1 polymorphism will allow a monitoring of heavy metal exposure in anthropogenically disturbed ecosystems.

Amino Acid Sequence↗
PubMed1990

The cDNA sequence of mouse LAMP-2. Evidence for two classes of lysosomal membrane glycoproteins.

We describe the isolation and sequencing of a cDNA encoding the mouse lysosomal membrane glycoprotein mLAMP-2 and the sequence differences that distinguish this molecule from the LAMP-1 class of proteins. An oligonucleotide probe corresponding to the NH2-terminal amino acid sequence of purified mLAMP-2 was synthesized by the polymerase chain reaction and used to screen several cDNA libraries. cDNA clones with an insert of 1,700 nucleotides were identified and sequenced. The deduced amino acid sequence of mLAMP-2 comprises a signal sequence of 25 residues and a 390-amino acid polypeptide (Mr 43,017) with the following putative domains: a large intraluminal region (residues 1-354) with 17 N-linked glycosylation sites (Asn-X-Ser/Thr), a hydrophobic transmembrane-spanning region of 24 residues (355-378), and a COOH-terminal cytoplasmic tail of 12 residues (379-390). When this sequence is compared with those of other lysosomal membrane glycoproteins, it is apparent that mouse LAMP-2 and human LAMP-2 form one homology class (LAMP-2) that is separated from the LAMP-1 class of proteins. The sequence differences in these two classes provide a basis for comparing the structure of the proteins with their biochemical and biological properties.

Amino Acid Sequence↗
PubMed1994

Drosophila ribosomal protein L18a: cDNA sequence, expression and chromosomal localization of the gene.

We describe the cDNA sequence of the Drosophila homologue of the rat ribosomal protein L18a. The protein sequence predicted has identical or conservatively substituted amino acids in 80% of positions. It is distinctly basic in character with an overall net positive charge of + 20. Analysis of L18a RNA with the Northern blot technique shows it to be expressed both during embryonic development and in the adult fly. In situ hybridisation to polytene chromosomes reveals that the L18a gene(s) is located at 54B on the second chromosome.

Amino Acid Sequence↗
PubMed2001

Partial cDNA sequence analysis of the boar proacrosin-binding protein.

A partial cDNA sequence of the boar 28, 29-kDa proacrosin-binding protein was determined. The desired sequence was amplified and obtained by RT-PCR followed by nested PCR. The oligonucleotide primers for RT-PCR were designed by deduction from the internal amino acid sequence of the boar proacrosin-binding protein. An approximately 1-kbp DNA fragment was analysed by agarose gel electrophoresis, in which the boar testicular total RNA or poly(A)+ RNA was used as a template for RT-PCR followed by nested PCR. This PCR product was inserted into a TA vector. The DNA sequence of the inserted PCR product was then determined by the chain termination method.

Amino Acid Sequence↗
PubMedDate not supplied

[Computer program recognition of a cDNA sequence specifying signal peptides].

An application of a computational analysis of cDNA sequences is presented in this paper. The goal is the identification of functional domains on sequence data. The results show the capability of this technique to identify a zone of DNA associated with the signal peptide coding region, whose biological function at DNA or RNA level is still unknown.

Base Sequence↗
PubMed1996

A liver-specific isoform of the betaine/GABA transporter in the rat: cDNA sequence and organ distribution.

We report the cloning of a 2.2 kb cDNA encoding a Na(+)-and Cl- dependent betaine/GABA (gamma-aminobutyric acid) transporter from rat liver poly(A+) RNA. 5'-RACE revealed an additional 355 bases 5' to the 2.2 kb cDNA sequence. Northern analysis demonstrated two (2.2 kb and 2.6 kb) mRNA isoforms in rat liver. Betaine transporter mRNA was also detected in the brain, spleen, lung, and kidney using the 2.2 kb cDNA clone as a probe. Only the 2.6 kb mRNA from the liver hybridized with the 5'-RACE product.

Amino Acid Sequence↗
PubMed1998

[Primary study of differentially expressed cDNA sequences in cell line HNE1 of human nasopharyngeal carcinoma by cDNA representational difference analysis].

OBJECTIVE: To search differentially expressed sequences correlated with pathogenesis of human nasopharyngeal carcinoma (NPC), including the candidates of tumor suppressor genes. METHODS: cDNA representational difference analysis (RDA) was performed to isolate differentially expressed sequences between cDNA from normal human primary cultures of nasopharyngeal epithelial cells and cDNA from NPC cell line HNE1. The sources of differentially expressed products were proved by Southern blot and Northern blot. The fragments were cloned with pGEM-T easy kit and sequenced by the chain termination reaction. RESULTS: Four differentially expressed cDNA fragments were isolated in the fourth subtractive hybridization using cDNA from normal human primary cultures of nasopharyngeal epithelial cells as tester amplicon and cDNA from NPC cell line HNE1 as driver amplicon by cDNA RDA. These differential cDNA fragments revealed that they really came from the tester amplicon and were not expressed or down-regulated in the NPC HNE1 cells. Of these obtained clones, some are the fragments of the human known genes including house-keeping genes, the others are novel genes. CONCLUSION: NPC involves alteration of multiple genes. Some of known genes matched with the differentially expressed sequences have an effective suppressive ability on the carcinoma.

Base Sequence↗
PubMed1983

Carp preproinsulin cDNA sequence and evolution of insulin genes.

The nucleic acid sequence of the preproinsulin cDNA of carp (Cyprinus carpio), cloned in the PstI-site of pBR322 (1), has been determined. The sequenced insert of 439 bp includes the complete coding information for carp preproinsulin (108 amino acids), 10 nucleotides of the 5'-and 105 nucleotides of the 3'-nontranslated regions. The nucleotide sequence confirms the previously established amino acid sequence of carp insulin (2) and determines those of the signal (21 aa 1) and C-peptide (35 aa 1). The observed shortness of the signal peptide of carp preproinsulin and the N-terminal addition of 2 amino acids to the carp insulin B-chain suggest that the cleavage site of the signal peptidase has moved. Calculations based on the comparison of known preproinsulin cDNA sequences showed that the evolutionary distance between fresh water and salt water teleostians is not smaller than between man and chicken.

Amino Acid Sequence↗
PubMed1984

Carp preproinsulin cDNA sequence and evolution of insulin genes.

The nucleic acid sequence of the preproinsulin cDNA of carp (Cyprinus carpio), cloned in the PstI site of pBR322 ( Liebscher et al. 1980), has been determined. The sequenced insert of 439 bp includes the complete coding information for carp preproinsulin (108 amino acids), 10 nucleotides of the 5'-and 105 nucleotides of the 3'-nontranslated regions. The nucleotide sequence confirms the previously established amino acid sequence of carp insulin ( Makower et al. 1982) and determines those of the signal 21 amino acids and C peptide (35 amino acids). The observed shortness of the signal peptide of carp preproinsulin and the N-terminal addition of 2 amino acids to the carp insulin B chain suggest that the cleavage site of the signal peptidase has moved. Calculations based on the comparison of known preproinsulin cDNA sequences showed that the evolutionary distance between fresh water and salt water teleostians is not smaller than that between man and chicken.

Amino Acid Sequence↗
PubMed1992

Amino acid and cDNA sequences of a neutral phospholipase A2 from the long-nosed viper (Vipera ammodytes ammodytes) venom.

The amino acid sequence of a non-toxic phospholipase A2, ammodytin I2, from the venom of the long-nosed viper (Vipera ammodytes ammodytes) and its cDNA sequence have been determined. The protein sequence was elucidated by sequencing the peptides generated by CNBr cleavage, mild acid hydrolysis and tryptic digestion of maleylated and non-maleylated protein. Sequencing of the cDNA showed that the protein is synthesized as an 137-amino-acid-residue precursor molecule consisting of a 16-residue signal peptide, followed by a 121-residue mature enzyme. Ammodytin I2 cDNA shows 73% nucleotide and 59% amino acid identities in the mature protein region in comparison to that of ammodytoxin A, the most presynaptically neurotoxic phospholipase A2 from the long-nosed viper. Identities in the signal-peptide region are considerably higher, 96% and 100%, respectively.

Amino Acid Sequence↗
PubMed1988

Primary structure of chicken skeletal muscle and fibroblast alpha-actinins deduced from cDNA sequences.

The complete 897-amino-acid sequence of chicken skeletal muscle alpha-actinin and the 856-amino-acid sequence (97% of the entire sequence) of chicken fibroblast alpha-actinin have been determined by cloning and sequencing the cDNAs. Genomic Southern analysis with the cDNA sequences shows that skeletal and fibroblast alpha-actinins are encoded by separate single-copy genes. RNA blot analyzes show that the skeletal alpha-actinin gene is expressed in the pectoralis muscle and that the fibroblast gene is expressed in the gizzard smooth muscle as well as in the fibroblast. The deduced skeletal alpha-actinin molecule has a calculated Mr of 104 x 10(3), and each alpha-actinin can be divided into three domains: (1) the NH2-terminal highly conserved actin-binding domain, which shows similarity to the product of the Duchenne's muscular dystrophy locus; (2) the middle rod-shaped dimer-forming domain, which contains the spectrin-type repeat units; and (3) the COOH-terminal two EF-hand consensus regions. Comparison of the skeletal alpha-actinin sequence with the fibroblast and smooth muscle alpha-actinin sequences demonstrated that the EF-hand structure was conserved in all of these alpha-actinin sequences, despite the reported variability of the Ca2+ sensitivities of the actin-gelation by various alpha-actinin isoforms.

Actinin↗
PubMed1986

Protein and cDNA sequence of a glycine-rich, dimethylarginine-containing region located near the carboxyl-terminal end of nucleolin (C23 and 100 kDa).

By a combination of protein chemistry and recombinant DNA methods a glycine-rich region was found to be located near the carboxyl terminus of the nucleolar specific phosphoprotein, nucleolin, from Novikoff hepatoma (protein C23) and Chinese hamster ovary cells (100-kDa nucleolar protein). A sequence of 192 amino acid residues was derived from partial sequences of cyanogen bromide and N-bromosuccinimide fragments of protein C23 and deduced protein sequence from Chinese hamster ovary cell 100-kDa cDNA sequences. The 66 residues sequenced by protein methods were identical to the corresponding residues deduced by DNA sequencing. The multiple residues of NG,NG-dimethylarginine (DMA) contained in the nucleolin polypeptide were found to be limited to a segment of less than 10 kDa near the carboxyl-terminal end of the protein. This segment also contained internally repeated sequences (e.g. 7 copies of the sequence Gly-Gly-Arg-Gly-Gly were found) which were unrelated to sequences closer to the amino-terminal end. Most arginine residues in this region were surrounded by 2 or 3 glycine residues and were relatively close in sequence to phenylalanine residues.

Amino Acid Sequence↗