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At least 1,063 records · Page 59Linked to original sources
PubMed1986

The developmentally regulated type X collagen gene contains a long open reading frame without introns.

Type X collagen is a recently discovered product of hypertrophic chondrocytes that is localized to presumptive mineralization zones of hyaline cartilage. Thus, in the epiphyseal growth plate of long bones it is present only in the zone of hypertrophic chondrocytes and absent in the resting and rapidly growing cartilage and in bone. Type X collagen represents, therefore, a transient and developmentally regulated collagen which is synthesized by a subpopulation of chondrocytes. We report here the isolation and characterization of cDNA and genomic clones specific for the chicken protein. The results demonstrate that the polypeptide chains of this collagen contain three distinct domains: a short non-collagenous, amino-terminal region, a collagenous domain of 460 amino acid residues, and a non-collagenous, carboxyl-terminal domain of 170 amino acid residues. The nucleotide sequence of the gene shows that these domains are encoded by a long open reading frame that is not interrupted by introns. Examination of the amino acid sequence derived from this nucleotide sequence reveals the presence of a hydrophobic segment localized 10 amino acid residues upstream from the translational stop codon. The length and sequence characteristics of this segment raise the intriguing possibility that Type X collagen polypeptides may contain a transmembrane segment.

Amino Acid Sequence↗
PubMed2004

Instability of the restriction fragment length polymorphism pattern of open reading frame 5 of porcine reproductive and respiratory syndrome virus during sequential pig-to-pig passages.

Restriction fragment length polymorphism (RFLP) analysis is one of the tools commonly used to study the molecular epidemiology of porcine reproductive and respiratory syndrome viruses (PRRSVs). As PRRSVs are genetically variable, the stability of the RFLP pattern of a PRRSV during in vivo replication was evaluated by carrying out 13 sequential pig-to-pig passages (P1 to P13) of PRRSV ATCC VR-2332 in three independent pig lines for a total of 727 days. During P1 the pigs were inoculated with a homogeneous inoculum (CC-01) prepared through a series of plaque purifications, and during P2 to P13 the pigs were inoculated with a tissue filtrate from the corresponding pig in the previous passage. Fifteen viral plaque clones were directly isolated from CC-01 and the day 7 serum of each pig of each passage, open reading frame 5 of the clones was sequenced, and the clones were compared to CC-01 to assess the mutation rates and RFLP patterns (obtained by digestion with MluI, HincII, and SacII) over time. Among the 495 viral clones recovered during the passages, 398 clones, including CC-01, had pattern 2-5-2 (MluI-HincII-SacII); however, the remaining 97 viral clones showed different patterns (2-6-2 [P2], 1-5-2 [P3], 2-5-4 [P7], and 2-1-2 [P10]). Importantly, the MluI site that was reported to be present in only one of the PRRS modified live virus vaccine strains (Ingelvac) and its parental strain (ATCC VR-2332) can disappear during in vivo replication. Furthermore, sequence homology between CC-01 and clones with pattern 2-5-2 or clones with other patterns differed by 0.05 to 1.58% and 0.5 to 1.45%, respectively, suggesting that RFLP analysis cannot accurately predict genetic relatedness between PRRSVs. Collectively, precaution should be taken when the molecular epidemiology of PRRSVs is evaluated by RFLP analysis.

Animals↗
PubMed1986

Nucleotide sequence analysis of TL-DNA of Agrobacterium rhizogenes agropine type plasmid. Identification of open reading frames.

We have determined the nucleotide sequence of the Ri TL-DNA region from an Agrobacterium rhizogenes agropine-type plasmid using subcloned regions from the essentially identical Ri TL-DNAs from strains A4 and HRI. This sequenced region of 21,126 base pairs (bp) contains the complete TL-DNA region of the Ri plasmid as determined by analysis of TL-DNA borders in the genome of infected, clonal, Convolvulus arvensis plants. The left and right borders of the TL-DNA are flanked by 25-bp sequences which match the 25-bp terminal sequences found near the borders of T-DNA regions of Agrobacterium tumefaciens Ti plasmids. Other DNA sequences similar to these 25-bp terminal sequences are found within the TL region, and some of these sequences appear to be associated with Ri TL-DNA structures found in transformed tobacco plants. The TL-DNA region contains 18 open reading frames, many of which have 5' and 3' regulatory elements similar to those found in eukaryotic genes. In many cases, CCAAT and TATA elements were found upstream from putative transcriptional initiation codons, and poly(A) addition (AATAAA) elements were observed in presumed 3'-noncoding regions. Comparison of Ri TL-DNA coding and noncoding sequence regions with T-DNA sequence regions from octopine type Ti plasmid pTi15955 reveals no extensive sequence homologies.

Base Sequence↗
PubMed1982

18S coding sequences in amplified ribosomal DNA from Xenopus laevis oocytes are highly homogeneous, unmethylated, and lack major open reading frames.

We have used two approaches to search for sequence variants in the 18S coding region of amplified ribosomal DNA (rDNA) from Xenopus laevis oocytes. First, using clones derived from amplified rDNA, we compared the equivalent of a complete 18S coding region from two clones and short regions from two other clones with the 18S sequence previously determined from a "reference" clone. The respective sequences in all the clones were identical. Secondly, we examined greater than 60% of the 18S sequence in "pooled 18S genes" in uncloned amplified rDNA. The predominant sequence corresponded to that in the reference clone and no heterogeneities were apparent. Since many chromosomal rDNA units contribute to rDNA amplification the findings indicate that 18S coding sequences in X. laevis are largely homogeneous. The previously established sequence is the predominant one, thus providing a reliable basis for studies on 18S rRNA. Sequencing gels on uncloned amplified rDNA confirmed the absence of methylated cytosine in this DNA. The 18S sequence lacks major open reading frames.

Animals↗
PubMed1984

Sequences of six genes and several open reading frames in the kinetoplast maxicircle DNA of Leishmania tarentolae.

The DNA sequence of approximately 80% of the transcribed region of the kinetoplast maxicircle DNA of Leishmania tarentolae was obtained, and structural genes were localized by comparison of the translated amino acid sequences with those of known mitochondrial genes from other organisms. By this method, the genes for cytochrome oxidase subunits I, II, and III, cytochrome b, and human mitochondrial unidentified reading frames 4 and 5 were identified. By comparing the amino acid sequences of the putative L. tarentolae genes with those of known genes, we conclude that TGA codes for tryptophan, as in most other mitochondrial systems. This is the only apparent change from the universal genetic code. The six identified structural genes show various degrees of divergence from the homologous genes in other species, with cytochrome oxidase subunit I being the most conserved and cytochrome oxidase subunit III being the least conserved. A comparison of the cytochrome b genes from L. tarentolae and Trypanosoma brucei showed that the ratio of transversions to transitions is 1:1, suggesting that these species diverged from each other more than 80 X 10(6) years ago. Several as yet unidentified open reading frames were also present in the maxicircle sequence. These data confirm that maxicircle DNA has a coding potential which typifies other mitochondrial systems.

Amino Acid Sequence↗
PubMed1989

The L1 family of long interspersed repetitive DNA in rabbits: sequence, copy number, conserved open reading frames, and similarity to keratin.

The L1 family of long interspersed repetitive DNA in the rabbit genome (L1Oc) has been studied by determining the sequence of the five L1 repeats in the rabbit beta-like globin gene cluster and by hybridization analysis of other L1 repeats in the genome. L1Oc repeats have a common 3' end that terminates in a poly A addition signal and an A-rich tract, but individual repeats have different 5' ends, indicating a polar truncation from the 5' end during their synthesis or propagation. As a result of the polar truncations, the 5' end of L1Oc is present in about 11,000 copies per haploid genome, whereas the 3' end is present in at least 66,000 copies per haploid genome. One type of L1Oc repeat has internal direct repeats of 78 bp in the 3' untranslated region, whereas other L1Oc repeats have only one copy of this sequence. The longest repeat sequenced, L1Oc5, is 6.5 kb long, and genomic blot-hybridization data using probes from the 5' end of L1Oc5 indicate that a full length L1Oc repeat is about 7.5 kb long, extending about 1 kb 5' to the sequenced region. The L1Oc5 sequence has long open reading frames (ORFs) that correspond to ORF-1 and ORF-2 described in the mouse L1 sequence. In contrast to the overlapping reading frames seen for mouse L1, ORF-1 and ORF-2 are in the same reading frame in rabbit and human L1s, resulting in a discistronic structure. The region between the likely stop codon for ORF-1 and the proposed start codon for ORF-2 is not conserved in interspecies comparisons, which is further evidence that this short region does not encode part of a protein. ORF-1 appears to be a hybrid of sequences, of which the 3' half is unique to and conserved in mammalian L1 repeats. The 5' half of ORF-1 is not conserved between mammalian L1 repeats, but this segment of L1Oc is related significantly to type II cytoskeletal keratin.

Animals↗
PubMed1988

Fine mapping of the latency-related gene of herpes simplex virus type 1: alternative splicing produces distinct latency-related RNAs containing open reading frames.

The latency-related (LR) gene of herpes simplex virus type 1 (HSV-1) is transcriptionally active during HSV-1 latency, producing at least two LR-RNAs. The LR gene partially overlaps the immediate-early gene ICP0 and is transcribed in the opposite direction from ICP0, producing LR-RNAs that are complementary (antisense) to ICP0 mRNA. The LR gene is thought to be involved in HSV-1 latency. We report here the fine mapping and partial sequence analysis of this HSV-1 LR gene. 32P-labeled genomic DNA restriction fragments and synthetic oligonucleotides were used as probes for in situ hybridizations and Northern (RNA) blot hybridizations of RNA from trigeminal ganglia of rabbits latently infected with HSV-1. The two most abundant LR-RNAs appeared to share their 5' and 3' ends and to be produced by alternative splicing. These LR-RNAs were approximately 2 and 1.3 to 1.5 kilobases in length and were designated LR-RNA 1 and LR-RNA 2, respectively. Their 5' ends started approximately 1,210 nucleotides downstream from the 3' end of the ICP0 mRNA. Their 3' ends overlapped ICP0 by nearly 1,000 nucleotides. LR-RNA 1 appeared to have at least one intron removed, while LR-RNA 2 appeared to have at least two introns removed. The LR-RNAs contained two potential long open reading frames, suggesting the possibility that one or more of the LR-RNAs may be a functional mRNA.

Animals↗
PubMed1987

Expression of a cDNA clone corresponding to the long open reading frame (XBL-I) of the bovine leukemia virus.

Nucleotide sequence analysis of a cDNA clone corresponding to the XBL-I open reading-frame of bovine leukemia virus (BLV) revealed that the AUG initiation codon was located 44 bases downstream from that of the env gene and was part of the p34x mRNA splice donor. . .ATGG/GTAA at the end of the pol gene sequence. RNA from this clone was synthesized in vitro by the SP6 RNA polymerase and translated into a 34,000 mol wt protein in rabbit reticulocyte lysates. The protein (p34x) is recognized in Western blots by most sera of BLV-infected sheep and tumor-bearing cattle, by an anti-synthetic peptide rabbit serum, and by the serum of a rabbit immunized by XBL-I RNA programmed reticulocyte lysates. Both sera react with a 34,000 mol wt protein present in nuclei of BLV-infected cells.

Base Sequence↗