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PubMed2006

PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences.

We formerly released the porcine expressed sequence tag (EST) database Pig EST Data Explorer (PEDE; http://pede.dna.affrc.go.jp/), which comprised 68,076 high-quality ESTs obtained by using full-length-enriched cDNA libraries derived from seven tissues. We have added eight tissues and cell types to the EST analysis and have integrated 94,555 additional high-quality ESTs into the database. We also fully sequenced the inserts of 10,147 of the cDNA clones that had undergone EST analysis; the sequences and annotation of the cDNA clones were stored in the database. Further, we constructed an interface that can be used to perform various searches in the database. The PEDE database is the primary resource of expressed pig genes that are supported by full-length cDNA sequences. This resource not only enables us to pick cDNA clones of interest for a particular analysis, but it also confirms and thus contributes to the sequencing integrity of the pig genome, which is now being compiled by an international consortium (http://www.piggenome.org/). PEDE has therefore evolved into what we now call 'Pig Expression Data Explorer'.

Animals↗
PubMed1984

The human transferrin receptor gene: genomic organization, and the complete primary structure of the receptor deduced from a cDNA sequence.

Heteroduplex analysis shows that the transferrin receptor gene contains at least 19 distinct coding sequences distributed over 31 kb of genomic DNA. The nucleotide sequence of these coding regions has been determined from a cDNA clone. The sequence contains a single complete open reading frame of 2280 bases which specifies a 760 residue polypeptide with a molecular weight of 85K daltons. The deduced amino acid sequence of the receptor shows that it does not contain an N-terminal hydrophobic signal peptide. We have found a single region of sufficient length and hydrophobicity to span the membrane, located 61 amino acids from the N-terminus. This leads to the prediction that the receptor is oriented in the membrane with a cytoplasmic N-terminus and an extracellular C-terminus. The receptor has no significant homology with transferrin, or with any receptor for which a sequence is available.

Amino Acid Sequence↗
PubMed1995

Construction of a gene expression profile of a human fetal liver by single-pass cDNA sequencing.

We have obtained an overall gene expression profile of a human fetal liver by sequencing the 5' ends of random cDNA clones from an unbiased cDNA library. As a result, many novel genes that might be related to liver growth and hemopoiesis have been identified. Poly (A)+ RNA was purified from the liver of a human fetus obtained at the 22nd week of gestation, and a directional library was constructed with oligo d(T)-primed cDNAs synthesized without any normalizing procedures. The 5' end of each randomly chosen clone was sequenced by the dideoxy-chain termination methods, and each sequence was used for homology search in the public databases such as GenBank, SWISS-PROT, and PIR. Of 1231 random cDNA clones analyzed, 697 clones representing 204 different transcripts (57%), were identical to previously known human genes. The spectrum of the genes in this category reflected well the physiological characteristics of the fetal liver, a combination of hepatic and hemopoietic functions. About 4% of the clones represented novel gene transcripts with significant homologies to known genes of human or other organisms. These included several genes that are known to be involved in cellular differentiation and/or proliferation. About 25% of the clones had no statistically significant match to any known genes. In summary, we have identified 546 different gene transcripts consisting of 204 known human genes, 42 homologous genes, and 300 unknown genes. Thus, this approach appears to be a highly efficient way to identify novel genes of biological interest.

Base Sequence↗
PubMed1996

The cDNA sequence of porcine vitronectin and its expression in liver and skeletal muscle of GH-supplemented pigs.

A cDNA (1555 bp) (DNA database accession number, D61396) having a homology with human vitronectin (Vn) was isolated from a porcine liver cDNA library, and its sequence was determined. The open reading frame in the cDNA was found to code a protein with 388 amino acids, then the amino acid sequence of the protein (porcine putative Vn) was aligned to the other mammalian (mouse, rabbit, and human) Vns previously reported. The alignment revealed that the functional amino acid sequences reported as the cell attachment site, the heparin binding site, the region involved in glycosylation, and plasminogen activator inhibitor I-binding domain were conserved in the porcine putative Vn. These findings together with the fact that the calculated molecular weight and the N-terminal amino acid sequence of the putative Vn agreed with those reported by biochemical analysis on porcine Vn, led us to conclude that the cDNA isolated in the present study coded for the porcine Vn. Then, a time course study was performed to examine whether the administration of growth hormone (GH) affects Vn mRNA expression in liver and skeletal muscle, since the level of Vn mRNA was reported to be affected by inflammation, and since GH was reported to be involved in inflammation. This revealed that GH has no effect on the level of liver Vn mRNA, and that Vn mRNA level in skeletal muscle seemed to be affected following GH-injection.

Amino Acid Sequence↗
PubMed1996

The cDNA sequence and infectious transcripts of peanut stripe virus.

A full-length cDNA clone of the blotch isolate of the peanut stripe potyvirus (PStV) RNA genome was constructed downstream from the bacteriophage SP6 RNA polymerase promoter. The full-length PStV cDNA clone (PStVSF9) was sequenced and compared to the previously published sequence of PStV-B. In vitro-synthesized PStV transcripts capped with m7GpppG were infectious in Nicotiana benthamiana plants, and the progeny virus was aphid transmissible. To confirm the origin of infection, a mutant PStV (PStVDAE), with a Gly14 to Glu mutation in the coat protein-encoding gene, was constructed. Transcripts from PStVDAE produced symptoms indistinguishable from native or PStVSF9 virus, but was not transmitted by aphids.

Arachis↗
PubMed1990

Cloning and cDNA sequence of a bovine submaxillary gland mucin-like protein containing two distinct domains.

A lambda gt11 cDNA library prepared from bovine submaxillary gland mRNA was screened with polyclonal anti-apo-bovine submaxillary mucin antibodies with the aim of obtaining the deduced amino acid sequence of the mucin core protein. One of the positive clones had a 1.8 kilobase (kb) cDNA insert and coded for an incomplete protein. A 2.0-kb cDNA clone was isolated by rescreening the library with the 1.8-kb cDNA. Nucleotide sequencing of the full-length 2.0-kb cDNA revealed an open reading frame that coded for a 563-amino acid protein. A striking feature of the cloned protein is the skewed distribution of the amino acids, most notably that of the hydroxy amino acids and cysteine. The amino-terminal domain of 339 residues is very rich in threonine, serine, and glycine and poor in cysteine, aspartic acid, tyrosine, phenylalanine, and tryptophan. In contrast, the carboxyl-terminal domain of 224 residues is rich in cysteine, aspartic acid, tyrosine, lysine, and asparagine and relatively poor in threonine, serine, and glycine. A search of the protein data bank for homologies to the deduced amino acid sequence revealed statistically significant matches to several proteins, including the porcine submaxillary apomucin fragment. The cysteine-rich domain by itself was not statistically homologous with any of the registered polypeptide sequences. RNA blot analysis using DNA probes corresponding to the mucin-like and cysteine-rich regions detected a nearly identical pattern of transcripts, demonstrating that the characterized clones are not artifacts of cDNA library construction. The blots also showed the presence of polydisperse transcripts in bovine submaxillary gland but no detectable hybridization signals in liver or brain RNA.

Amino Acid Sequence↗
PubMed1992

A lung type prostaglandin F synthase is expressed in bovine liver: cDNA sequence and expression in E. coli.

Using the cDNA of bovine lung prostaglandin F synthase (EC 1.1.1.2) as a probe, we isolated a clone from a bovine liver cDNA library which differed in only eleven nucleotides from the probe. The corresponding protein contained three amino acid substitutions, including a leucine residue which is conserved throughout all aldo-keto reductases. We inserted the liver cDNA into expression vector pUC19 and expressed the recombinant liver enzyme in E.coli. The purified liver enzyme reduced prostaglandin H2 as well as prostaglandin D2 and various carbonyl compounds. The high relative activity against prostaglandin H2 in combination with a high Km value for prostaglandin D2 identified this liver enzyme as a lung type prostaglandin F synthase. However, the binding constant for NADPH of the liver enzyme was 3.5 fold higher than that of lung prostaglandin F synthase.

Amino Acid Sequence↗
PubMed1992

cDNA sequence of human p11 calpactin I light chain.

The cDNA encoding full-length human p11 calpactin I light chain has been cloned and subjected to DNA sequencing. The open reading frame specifies a 97-amino-acid residue protein that surprisingly is identical to the p11 sequences of two mammalian ungulate species, cow and pig. However, the previously reported p11 polypeptide sequences of mouse and rat exhibited 8-9% nonidentity to human p11. These mammalian sequence comparison results are unexpected in view of current molecular cladistic theories that suggest a closer relationship between primates and rodents, rather than primates and ungulates. The mouse p11 gene has been previously mapped to chromosome 3 at a position syntenic with a centromeric-proximal region on human chromosome 1, and the human p11 cDNA clone is likely to be useful in physical mapping on chromosome 1.

Amino Acid Sequence↗
PubMed1997

Cloning of the human cDNA sequence encoding the NADH:ubiquinone oxidoreductase MLRQ subunit.

A cDNA clone encoding human NADH:ubiquinone oxidoreductase (complex I of mitochondrial respiratory chain) MLRQ subunit was isolated from human fetal liver cDNA library. The clone contained an open reading frame of 246 by which predicted a protein comprising 81 amino acids with a calculated molecular weight of 9,370 Da. The deduced amino acid sequence exhibited 95% homology (88% identity and 7% favored substitution) to that of bovine MLRQ subunit. Northern analysis revealed that the cDNA clone hybridized with a 0.7 kb mRNA species which was present in all tissues examined. The expression level of the 0.7 kb mRNA in heart, skeletal muscle, and brain was higher than in other organs. Human MLRQ cDNA could cross-hybridize with the genomic DNAs from various species.

Amino Acid Sequence↗
PubMed1996

Porcine S-antigen: cDNA sequence and expression in retina, ciliary epithelium and iris.

cDNA clones encoding S-antigen (arrestin) were isolated from the expression library constructed from porcine retina and sequenced. The 1490 base pair fragment contained a 1215 base pair open reading frame. From the nucleotide sequence, an amino acid sequence consisting of 405 residues was deduced and a molecular mass of 45,102 daltons was calculated. In order to determine whether the S-antigen mRNA transcript was expressed in anterior eye tissues, mRNA from ciliary non-pigmented epithelial cells and pigmented epithelial cells and iris was analysed by the reverse transcription polymerase chain reaction (PCR) using primers taken from sequences flanking the coding and non-coding regions of retinal S-antigen. Sequence analysis of the expected 611 base pairs in the 5' region and 672 base pairs in the 3' region of DNA fragments indicated that an identical mRNA for S-antigen was expressed in the anterior tissues examined. To investigate the in situ expression of S-antigen mRNA, 35S-labeled sense and antisense RNA probes were synthesized from the cDNA to label frozen sections of retina, ciliary body and iris and the treated sections were examined by autoradiography. The antisense probe labeled the layer between retinal pigmented epithelium and the outer nuclear layer of the retina, ciliary epithelium, and iris epithelium. From the results of sequencing PCR products and in situ hybridization, we concluded that, in porcine eye, the mRNA for S-antigen is expressed not only in the retina but also in the anterior tissues such as the ciliary epithelium and iris epithelium.

Animals↗
PubMed1996

Full-length cDNA sequence of a progesterone membrane-binding protein from porcine vascular smooth muscle cells.

A full-length cDNA clone for a progesterone membrane binding protein from porcine vascular smooth muscle cells was isolated and the complete nucleotide sequence determined. The cDNA encodes a protein of 194 amino acids with a transmembrane segment. This protein is likely to represent the first steroid membrane receptor or a part of it for which sequence information is available.

Amino Acid Sequence↗
PubMed1995

Translation initiation factor eIF-4E from Drosophila: cDNA sequence and expression of the gene.

A Drosophila melanogaster cDNA clone encoding the translation initiation factor eIF-4E was isolated and sequenced. The deduced polypeptide consists of 259 amino acids with a predicted molecular weight of 29,223. It shares 48%, 37% and 35% identity to its mammalian, yeast and wheat counterparts, respectively. Several residues (including eight tryptophans), which were shown to be critical for the function of mammalian and yeast eIF-4Es, are conserved in the Drosophila protein. Three transcripts of the eIF-4E gene were detected throughout Drosophila development.

Amino Acid Sequence↗
PubMed1998

G alpha q cDNA sequence from human platelets.

G-proteins play a major role in cell signaling and specific abnormalities in these proteins have been implicated in some diseases. Although, two human G alpha q coding sequences are published, they differ at functionally important regions. We have sequenced the human G alpha q cDNA synthesized from normal platelet mRNA by reverse transcription. Our results showed that the penultimate amino acid leucine is conserved in the human G alpha q sequence which has 94.4% identity in nucleotide sequence and 99.2% homology in amino acid sequence with murine sequence.

Amino Acid Sequence↗
PubMed1985

Human p53 cellular tumor antigen: cDNA sequence and expression in COS cells.

A 2.5-kb cDNA clone for human p53 tumor antigen has been isolated. This clone contains the entire coding region including 135 bp upstream of the first ATG. Comparison of the nucleotide sequence of human p53 and mouse p53 demonstrates that the first ATG in human p53 corresponds to the second ATG (codon No. 4) in mouse p53. The human p53 comprises 393 residues and is longer than the mouse p53 due to six additional codons present at the region corresponding to exon 4 of the mouse p53 gene. The DNA sequence homology between the coding regions of mouse and human p53 is 81% and the conservation of homology is not equally distributed along the molecule. When inserted into SV40-based expression vectors the human p53 cDNA successfully directs the production of a polypeptide with an apparent mol. wt. of 55 kd which can be precipitated by monoclonal antibodies to p53.

Animals↗
PubMed1987

Cloning and identification of lupin nodule specific cDNA sequences.

Yellow lupin nodule specific sequences were selected by screening of cDNA library prepared from lupin nodule poly(A)+RNA. From about 3,000 clones containing fragments of lupin DNA 150-1,500 base pair long, 7% of clones carrying nodule specific sequences were identified. Among them the most abundant sequence species, represented by 32% clones, encodes leghemoglobin. Another abundant species designated pLN13 is represented by 13% clones. The Northern blot analysis of lupin mRNA confirmed nodule specificity of the cloned sequences. The nucleotide sequence of one clone, pLN281 of 225 bp, is presented.

Base Sequence↗
PubMed1990

Mouse asialoglycoprotein receptor cDNA sequence: conservation of receptor genes during mammalian evolution.

The asialoglycoprotein receptor internalizes galactose-terminated glycoproteins into mammalian hepatocytes for degradation in lysosomes. We report the cloning and sequencing of one murine asialoglycoprotein receptor cDNA which exhibits homology with rat and human receptor forms. Conserved regions may correlate with functional domains. The membrane-bound M (mouse) HL polypeptide does not contain a cleavable N-terminal signal sequence and is probably anchored to the membrane via an internal insertion sequence.

Amino Acid Sequence↗