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At least 325 records · Page 18Linked to original sources
PubMed1989

Avian adipose lipoprotein lipase: cDNA sequence and reciprocal regulation of mRNA levels in adipose and heart.

cDNA clones for chicken adipose lipoprotein lipase were isolated from an expression library in lambda gt11 by antibody screening and characterized by hybridization selection and nucleotide sequencing. Based on the cDNA sequence and on N-terminal sequence analysis of the purified enzyme, chicken adipose lipoprotein lipase is a mature protein of 465 amino acids with a signal peptide of 19 or 25 amino acids, depending on which of two methionine residues is used for translation initiation. The predicted amino-acid sequence was found to be 73-77% identical to the four known mammalian adipose lipoprotein lipase sequences, with conservation of position of cysteine residues and putative functional domains, and number of potential N-glycosylation sites. Chicken lipoprotein lipase differs from mammalian lipoprotein lipases with respect to the position of one N-glycosylation site and the presence of an additional 15-17 C-terminal amino acids. 32P-labeled cDNA clones hybridized to mRNA species of 3.7 and 4.0 kb in Northern blots of heart and adipose, but not of liver RNA. In chickens that were fasted for 48 h and then refed, lipoprotein lipase mRNA levels in adipose increased to a maximal level of 350% that of controls at 10 h, whereas heart lipoprotein lipase mRNA levels fell to 40% of controls at 14 h. Concomitantly, no changes in total RNA were observed. Thus, avian lipoprotein lipase is subject to reciprocal pretranslational regulation in adipose and heart.

Adipose Tissue↗
PubMed1988

DR and DQ beta cDNA sequences associated with a DR2 haplotype.

Three cDNA clones encoding a DQ beta and two DR beta polypeptides have been isolated and sequenced from an American black individual expressing a DR2,DQw1 haplotype. The sequences of the cDNA clones are identical to previously described DR and DQ sequences from a DR2,Dw2 cell. The differences between DQw1-associated beta chains from DR2 and DR1 haplotypes is substantial, although a DQw1-specific sequence can be identified. The identical DQ and DR beta sequences found in unrelated individuals from different racial backgrounds suggests that class II structural polymorphism within the human population will be limited.

Amino Acid Sequence↗
PubMed1994

Chromosomal assignment of short cDNA sequences by PCR using overlapping and tailed short primers.

Overlapping primers and tailed short primers are effective agents for mapping very short cDNA sequences. By using such primers, human cDNAs as short as 32 nucleotides in length can produce PCR bands. Using these and other primers of ordinary size, 44 cDNAs were assigned to chromosomes, of which 24 were assigned to single chromosomes, and 2 were assigned to two chromosomes and two were assigned to three chromosomes, respectively. Among the 24 cDNAs, all of which matched GenBank entries, 6 cDNAs were observed to map to the same chromosomes as reported previously.

Animals↗
PubMed1989

Primary structure of chicken pituitary prolactin deduced from the cDNA sequence. Conserved and specific amino acid residues in the domains of the prolactins.

The perform of chicken prolactin (PRL) deduced from the cDNA sequence contains a signal peptide of 30 amino acid residues followed by a mature PRL of 199 residues. Chicken PRL shows 77, 68, 67, 58, and 31% identity of amino acid sequence with whale, human, ovine, rat, and salmon PRLs, respectively. Elucidation of the primary structure of avian PRL enabled extended analysis of the specific and conserved amino acid residues and domains of the PRL molecules. The mammalian, teleostean, and avian PRLs share 32 common residues, and these conserved residues are observed to cluster in four distinct domains (PD1 to PD4), corresponding to four of five conserved domains of the growth hormones. Of the 32 residues, 8 residues in the PD2 and PD4 domains, including 4 cysteines, are conserved by other members of the growth hormone family, which indicates that these 8 residues may be essential for common structural features of the gene family. On the other hand, 13 other residues distributed among all four domains are conserved almost exclusively in the PRLs, suggesting that these residues are indispensable for specific binding of the PRLs to their receptors.

Amino Acid Sequence↗
PubMed1995

Rapid cDNA sequencing in combination with RNA expression studies in mice identifies a large number of male germ cell-specific sequence tags.

A large number of cDNA clones were isolated from an adult mouse testis cDNA library and partially sequenced. Sequence comparisons revealed that many of them displayed similarities to genes previously identified only in invertebrates and lower eukaryotes, including, e.g., one cDNA clone related to the Drosophila melanogaster suppressor of forked gene. Other cDNA clones were found to be related, but not identical, to rodent genes involved in a variety of cellular activities, e.g., signal transduction and tumor development. The RNA expression patterns of 258 cDNA clones were analyzed through use of Northern blot methodology. Forty-two novel cDNA clones were found to be expressed only in male germ cells, the majority of them during spermiogenesis. One male germ cell-specific mouse cDNA clone was found to be similar to tektin A1, a protein known to interact with the flagellar microtubules of sea urchin sperm.

Amino Acid Sequence↗
PubMed2002

Complete cDNA sequences of the HLA-DRB1*0402 and DRB1*11041 alleles.

Since the development of the polymerase chain reaction, most HLA class II allele sequencing has been exclusively focused on the highly polymorphic exon 2. We present here the full cDNA sequences of two HLA-DRB1 alleles, DRB1*0402 and DRB1*11041, both of which were previously only available as partial sequences. HLA-DRB1*11041 was found to be completely homologous to DRB1*11011 in exons 1, 3, 4, 5 and 6 and HLA-DRB1*0402 was found to be identical to DRB1*04011 in exons 1, 3, 4, 5 and 6.

Alleles↗
PubMed2000

The cDNA sequences of three tetrins, the structural proteins of the Tetrahymena oral filaments, show that they are novel cytoskeletal proteins.

The oral filaments of the ciliate Tetrahymena consist of the tetrins, insoluble polypeptides with molecular masses of around 85 kD. We characterised the tetrins of T. thermophila by two-dimensional gels and derived a large number of peptide sequences by in gel digestion. Using RT-PCR techniques and RACE-PCR, the complete cDNA sequences of tetrins A, B and C were established. Although tetrins differ strikingly in protein sequence they show a common structural principle. A N-terminal domain of 60 to 100 residues contains most of the proline residues of the tetrins and is probably globular. It is followed by a long alpha-helical domain of 620 to 640 residues which either lacks prolines or in tetrin A contains a single proline residue. Although this long domain has coiled coil forming ability, the individual heptad repeats are not extensive. Tetrins are novel cytoskeletal proteins unique to ciliates. Since the three tetrin sequences account for all 900 amino acid residues obtained by microsequencing of peptides, an additional major tetrin seems excluded. A minor component D is related to tetrin B by peptide sequences. The isoelectric variants, particularly obvious for tetrin A, most likely reflect post-translational modifications. These could arise by phosphorylation of serines and threonines in the proline rich N-terminal domain.

Acrylic Resins↗
PubMed2000

Isolation and characterization of plant N-acetyl glucosaminyltransferase I (GntI) cDNA sequences. Functional analyses in the Arabidopsis cgl mutant and in antisense plants.

We report on the isolation and characterization of full-length cDNA sequences coding for N-acetylglucosaminyltransferase I (GnTI) from potato (Solanum tuberosum L.), tobacco (Nicotiana tabacum L.), and Arabidopsis. The deduced polypeptide sequences show highest homology among the solanaceous species (93% identity between potato and tobacco compared with about 75% with Arabidopsis) but share only weak homology with human GnTI (35% identity). In contrast to the corresponding enzymes from animals, all plant GnTI sequences identified are characterized by a much shorter hydrophobic membrane anchor and contain one putative N-glycosylation site that is conserved in potato and tobacco, but differs in Arabidopsis. Southern-blot analyses revealed that GntI behaves as a single-copy gene. Northern-blot analyses showed that GntI-mRNA expression is largely constitutive. Arabidopsis cgl mutants deficient in GnTI activity also possess GntI mRNA, indicating that they result from point mutations. GntI-expression constructs were tested for the ability to relieve the GnTI block in protoplasts of the Arabidopsis cgl mutant and used to obtain transgenic potato and tobacco plants that display a substantial reduction of complex glycan patterns. The latter observation indicates that production of heterologous glycoproteins with little or no antigenic glycans can be achieved in whole plants, and not in just Arabidopsis, using antisense technology.

Amino Acid Sequence↗
PubMed1989

Murine transforming growth factor-beta 2 cDNA sequence and expression in adult tissues and embryos.

Murine transforming growth factor-beta 2 (TGF-beta 2) cDNAs were isolated from cDNA libraries derived from a differentiated murine embryonic carcinoma cell line, PCC3. The composite cDNA sequence is 4267 nucleotides long, including a 1217 nucleotides 5'-untranslated sequence, and encodes a murine TGF-beta 2 precursor of 414 amino acids with 96% identity to its human counterpart. Several consensus polyadenylation sequences are present in the 1807 nucleotides 3'-untranslated sequence. Five TGF-beta 2 mRNA species are observed in the developing mouse fetus and they show different patterns of expression during development. TGF-beta 2 mRNA expression was also examined in adult mouse tissues, in which four of the five RNA species were observed. TGF-beta 2 mRNAs were present in all adult mouse tissues examined, except liver, and was most abundant in placenta, the male submaxillary gland and lung. The patterns of expression suggest a physiological role for TGF-beta 2 both in embryonic development and in the maintenance of adult tissues.

Amino Acid Sequence↗
PubMed2000

Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences.

MOTIVATION: In the previous works, we developed ATGpr, a computer program for predicting the fullness of a cDNA, i.e. whether it contains an initiation codon or not. Statistical information of short nucleotide fragments was fully exploited in the prediction algorithm. However, sequence similarities to known proteins, which are becoming increasingly available due to recent rapid growth of protein database, were not used in the prediction. In this work, we present a new prediction algorithm based on both statistical and similarity information, which provides better performance in sensitivity and specificity. RESULTS: We evaluated the accuracy of ATGpr for predicting fullness of cDNA sequences from human clustered ESTs of UniGene, and we obtained specificity, sensitivity, and correlation coefficient of this prediction. Specificity and sensitivity crossed at 46% over the ATGpr score threshold of 0.33 and the maximum correlation coefficient of 0.34 was obtained at this threshold. Without ATGpr we found it effective to use alignments with known proteins for predicting the fullness of cDNA sequences. That is, specificity increased monotonously as similarity (identity of the alignments) increased. Specificity was achieved greater than 80% if identity was greater than 40%. For more effective prediction of fullness of cDNA sequences we combined the similarity (identity of query sequence) with known proteins and ATGpr score. As a result, specificity became greater than 80% if identity was greater than 20%. AVAILABILITY: The prediction program, called ATGpr_ sim, is available at http://www.hri.co.jp/atgpr/ATGpr_sim.html CONTACT: nisikawa@crl.hitachi.co.jp

Amino Acid Sequence↗
PubMed1984

Kappa-chain allotypes and isotypes in the rabbit: cDNA sequences of clones encoding b9 suggest an evolutionary pathway and possible role of the interdomain disulfide bond in quantitative allotype expression.

The constant regions of rabbit kappa light chains are unusual because the sequences of the allotypic forms can differ more from each other than do some variable regions with which they associate. We report the nucleic acid sequence of a full-length cDNA clone of b9 allotype and show comparisons to available sequences of the rabbit kappa allotypes b4, b5, and bas-N4. Our analyses suggest that the primordial rabbit kappa gene encoded a bas-like sequence. They also reveal a surprising difference in the position of the variable region cysteine that forms the interdomain disulfide bond that is unique to most rabbit kappa chains. One b9 cDNA sequence lacks the usual cysteine-80 and instead encodes cysteine-108, which in three-dimensional models appears capable of forming the interdomain disulfide bond with cysteine-171 in the constant region. A partial sequence of a second b9 clone encodes both cysteine-80 and cysteine-108; the translation product of this clone could have a free reactive sulfhydryl group that might lead to an unstable nonfunctional Ig molecule. The fact that pre-B cells with b9 kappa chains do not differentiate and expand into productive Ig-producing cells with frequencies comparable to the other allotypes may be explained if a substantial proportion of the gene products have a free sulfhydryl group. Our sequence results suggest that in cells differentiating to produce kappa light chains of b9 allotype the number and location of the cysteines influence immunoglobulin expression.

Animals↗
PubMed2006

A cDNA sequence coding for a glutamic acid-rich protein is differentially expressed in cassava storage roots.

We report the isolation and characterization of a cDNA sequence (Mec1) coding for a glutamic acid-rich protein (Pt2L4) from cassava storage roots. Comparative sequence analysis showed a high identity of Pt2L4 with cassava protein C54, which is expressed in vascular tissues of storage roots. Northern blot analysis showed that the Mec1 transcript expression pattern might be related to the maturation of the storage parenchyma cells.

Amino Acid Sequence↗
PubMed1993

Genomic structure, cDNA sequence, and expression of gly96, a growth factor-inducible immediate-early gene encoding a short-lived glycosylated protein.

We report the cDNA sequence and genomic structure of gly96, an immediate early gene inducible by serum growth factors in mouse fibroblasts. It encodes a 153-amino acid protein that does not share significant sequence similarity with any known protein. In the adult mouse, gly96 is expressed predominantly in the lung, testes and the uterus. We have identified the Gly96 protein in Balb/c 3T3 cells using affinity-purified antibodies recognizing the Gly96 polypeptide. We show that Gly96 is glycosylated and has a short half-life in serum stimulated fibroblasts.

3T3 Cells↗
PubMed1993

Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library.

A human infant brain cDNA library, made specifically for production of expressed sequence tags (ESTs) was evaluated by partial sequencing of over 1,600 clones. Advantages of this library, constructed for EST sequencing, include the use of directional cloning, size selection, very low numbers of mitochondrial and ribosomal transcripts, short polyA tails, few non-recombinants and a broad representation of transcripts. 37% of the clones were identified, based on matches to over 320 different genes in the public databases. Of these, two proteins similar to the Alzheimer's disease amyloid precursor protein were identified.

Amino Acid Sequence↗
PubMed2004

Equine beta-defensin-1: full-length cDNA sequence and tissue expression.

beta-Defensins are cysteine-rich endogenously produced antimicrobial peptides that play an important role in innate immune defense. Although, previous investigations have identified beta-defensins in several mammalian species, no reports have identified equine beta-defensins. Using a strategy of database searching for expressed sequence tags (EST) we identified putative expression of equine beta-defensins in hepatic tissue. Based on this information, sequence specific primers were designed for the equine gene enabling the identification of the full-length cDNA sequence of equine beta-defensin-1. Comparative analyses showed that equine beta-defensin-1 has 46-52% amino-acid identity with other beta-defensins, sharing the greatest identity with porcine beta-defensin-1. Complete conservation of cysteine residues was maintained between the species evaluated, and RT-PCR analysis revealed diverse mRNA tissue expression for equine beta-defensin-1. These data extend the repertoire of equine antimicrobial peptides and expand our understanding of equine innate immunity.

Amino Acid Sequence↗
PubMed2001

Bovine melanocortin receptor 4: cDNA sequence, polymorphisms and mapping.

A cDNA encoding the bovine melanocortin receptor 4 (MC4R) was cloned and sequenced. Comparing human, pig and rat homologues showed a 87, 85 and 89% identity on the DNA level, respectively, and over 90% on the protein level. The bovine MC4R gene was mapped to BTU 24 by radiation hybrid mapping. Two nucleotide changes were identified by single stranded conformation polymorphism (SSCP) and sequencing. The substitutions proved to be a T to C and G (allele B) to A (allele A) resulting, respectively, in a conservative valine to alanine substitution (Val 145 Ala) and an alanine to threonine (Ala 172 Thr). Using PCR-RFLP, 13 different cattle breeds were screened for the presence of the Ala 172 Thr substitution. With the exception of one Red Pied animal, allele A could only be detected in Red Holstein animals.

Amino Acid Sequence↗
PubMed2003

Identification of a new laccase gene and confirmation of genomic predictions by cDNA sequences of Trametes sp. I-62 laccase family.

The strain Trametes sp. I-62 (CECT 20197) is a white-rot fungus with great potential for biotechnological applications in the fields of industrial waste water decolorization and clean up. Three laccase genes: lcc1, lcc2 and lcc3 have been cloned and sequenced from this basidiomycete. In this work, the coding regions of the corresponding cDNAs have been synthesized, cloned, and sequenced. They are 1563, 1563 and 1575 bp in length, respectively. Former putative intron/exon structures from genomic DNA are fully confirmed by match analysis with our cDNA sequences. Using Polymerase Chain Reaction--Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, an additional laccase cDNA was also identified, corresponding to a new gene, lcc1A, which displayed 99.6% identity with lcc1 at protein level. Such high similarity between lcc1 and lcc1A sequences, and the comparison with reports from other basidiomycete laccases, suggest that in this strain these two genes are allelic variants.

Amino Acid Sequence↗