Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans

10.1038/85913 ◽  
2001 ◽  
Vol 27 (3) ◽  
pp. 332-336 ◽  
Author(s):  
Jérôme Reboul ◽  
Philippe Vaglio ◽  
Nia Tzellas ◽  
Nicolas Thierry-Mieg ◽  
Troy Moore ◽  
...  
Keyword(s):  
Open Reading Frame ◽  
Reading Frame ◽  
C Elegans ◽  
Open Reading Frame Sequence ◽  
Frame Sequence

scholarly journals Genome Sequence of an Unknown Subtype of Hepatitis C Virus Genotype 6: Another Piece for the Taxonomic Puzzle

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Martin Schou Pedersen ◽  
Sarah Mollerup ◽  
Lone Gilmor Nielsen ◽  
Håvard Jenssen ◽  
Jens Bukh ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Genome Sequence ◽  
Open Reading Frame ◽  
Virus Genotype ◽  
Reading Frame ◽  
Open Reading Frame Sequence ◽  
Frame Sequence ◽  
Reference Genomes ◽  
Virus Strains

The surveillance and correct subtyping of hepatitis C virus strains require available and up-to-date publicly available reference genomes. Here, we present the complete open reading frame sequence of a hepatitis C virus genotype 6 strain of an unknown subtype that was discovered during routine subtyping of patients in the clinic.

scholarly journals Open reading frame sequence of an Asian enterovirus 73 strain reveals that the prototype from California is recombinant

2002 ◽  
Vol 83 (7) ◽  
pp. 1721-1728 ◽  
Author(s):  
Helene Norder ◽  
Lotte Bjerregaard ◽  
Lars O. Magnius
Keyword(s):  
Molecular Typing ◽  
Open Reading Frame ◽  
North India ◽  
Human Enterovirus ◽  
Reading Frame ◽  
Open Reading Frame Sequence ◽  
Frame Sequence ◽  
Recombination Point ◽  
The Usa ◽  
Structural Region

Phylogenetic analysis within the VP1 region now enables molecular typing of enteroviruses consistent with neutralization results. Three untypable isolates, 2776/82, 57/99 and 22/00, from Korea, North India and Bangladesh, respectively, showed within this region 98·0–99·0% amino acid identities. These were less than 77% to the previous enterovirus prototypes, but 91·5–92·5% to CA55-1988, the recently identified enterovirus 73 (EV73) prototype from California. All three strains were, however, most similar to CA64-4454, an EV73 prime strain, to which they shared 96·5–98·5% identity. Seven compared EV73 strains formed two clusters in the VP1 dendrogram, one cluster with strains from South and East Asia and CA64-4454, and the other with strains from Oman and California including the prototype. When sequencing the complete open reading frame of 2776/82, its non-structural region was found to be divergent from all human enterovirus B (HEV-B) strains, including CA55-1988, indicating that one or other strain was recombinant. Boot scanning of the genomes showed a recombination point within the P2 region. Therefore, part of this was sequenced for 57/99 and 22/00 and was found similar to 2776/82, while CA55-1988 was similar to coxsackievirus B3, demonstrating that CA55-1988 was the recombinant. Since all strains of EV73 isolated so far outside California originate from Asia, where it has a broad geographical distribution, it seems that EV73 may have been introduced to California from Asia. Further analysis of EV73 strains will reveal if the recombination occurred in the USA or in Asia and will help to elucidate the origin of this virus.

Human cytomegalovirus (HCMV) UL139 open reading frame: Sequence variants are clustered into three major genotypes

2006 ◽  
Vol 78 (4) ◽  
pp. 517-522 ◽  
Author(s):  
Ying Qi ◽  
Zhi-Qin Mao ◽  
Qiang Ruan ◽  
Rong He ◽  
Yan-Ping Ma ◽  
...  
Keyword(s):  
Human Cytomegalovirus ◽  
Open Reading Frame ◽  
Sequence Variants ◽  
Reading Frame ◽  
Open Reading Frame Sequence ◽  
Frame Sequence

scholarly journals A novel member of the GCN5-related N-acetyltransferase superfamily from Caenorhabditis elegans preferentially catalyses the N-acetylation of thialysine [S-(2-aminoethyl)-L-cysteine]

2004 ◽  
Vol 384 (1) ◽  
pp. 129-137 ◽  
Author(s):  
Benjamin ABO-DALO ◽  
Dieudonne NDJONKA ◽  
Francesco PINNEN ◽  
Eva LIEBAU ◽  
Kai LÜERSEN
Keyword(s):  
Caenorhabditis Elegans ◽  
Reversed Phase ◽  
Open Reading Frame ◽  
Side Chain ◽  
Homologous Gene ◽  
Reversed Phase Hplc ◽  
Nematode Caenorhabditis Elegans ◽  
Reading Frame ◽  
Considerable Similarity ◽  
C Elegans

The putative diamine N-acetyltransferase D2023.4 has been cloned from the model nematode Caenorhabditis elegans. The 483 bp open reading frame of the cDNA encodes a deduced polypeptide of 18.6 kDa. Accordingly, the recombinantly expressed His6-tagged protein forms an enzymically active homodimer with a molecular mass of approx. 44000 Da. The protein belongs to the GNAT (GCN5-related N-acetyltransferase) superfamily, and its amino acid sequence exhibits considerable similarity to mammalian spermidine/spermine-N1-acetyltransferases. However, neither the polyamines spermidine and spermine nor the diamines putrescine and cadaverine were efficiently acetylated by the protein. The smaller diamines diaminopropane and ethylenediamine, as well as L-lysine, represent better substrates, but, surprisingly, the enzyme most efficiently catalyses the N-acetylation of amino acids analogous with L-lysine. As determined by the kcat/Km values, the C. elegans N-acetyltransferase prefers thialysine [S-(2-aminoethyl)-L-cysteine], followed by O-(2-aminoethyl)-L-serine and S-(2-aminoethyl)-D,L-homocysteine. Reversed-phase HPLC and mass spectrometric analyses revealed that N-acetylation of L-lysine and L-thialysine occurs exclusively at the amino moiety of the side chain. Remarkably, heterologous expression of C. elegans N-acetyltransferase D2023.4 in Escherichia coli, which does not possess a homologous gene, results in a pronounced resistance against the anti-metabolite thialysine. Furthermore, C. elegans N-acetyltransferase D2023.4 exhibits the highest homology with a number of GNATs found in numerous genomes from bacteria to mammals that have not been biochemically characterized so far, suggesting a novel group of GNAT enzymes closely related to spermidine/spermine-N1-acetyltransferase, but with a distinct substrate specificity. Taken together, we propose to name the enzyme ‘thialysine Nε-acetyltransferase’.

scholarly journals CSCD2: an integrated interactional database of cancer-specific circular RNAs

2021 ◽  
Author(s):  
Jing Feng ◽  
Wenbo Chen ◽  
Xin Dong ◽  
Jun Wang ◽  
Xiangfei Mei ◽  
...  
Keyword(s):  
Cell Lines ◽  
Rna Binding ◽  
Human Cancer ◽  
Circular Rnas ◽  
Binding Motifs ◽  
Reading Frame ◽  
Normal Tissues ◽  
Open Reading Frame Sequence ◽  
Significant Function ◽  
Frame Sequence

Abstract The significant function of circRNAs in cancer was recognized in recent work, so a well-organized resource is required for characterizing the interactions between circRNAs and other functional molecules (such as microRNA and RNA-binding protein) in cancer. We previously developed cancer-specific circRNA database (CSCD), a comprehensive database for cancer-specific circRNAs, which is widely used in circRNA research. Here, we updated CSCD to CSCD2 (http://geneyun.net/CSCD2 or http://gb.whu.edu.cn/CSCD2), which includes significantly more cancer-specific circRNAs identified from a large number of human cancer and normal tissues/cell lines. CSCD2 contains >1000 samples (825 tissues and 288 cell lines) and identifies a large number of circRNAs: 1 013 461 cancer-specific circRNAs, 1 533 704 circRNAs from only normal samples and 354 422 circRNAs from both cancer and normal samples. In addition, CSCD2 predicts potential miRNA–circRNA and RBP–circRNA interactions using binding motifs from >200 RBPs and 2000 microRNAs. Furthermore, the potential full-length and open reading frame sequence of these circRNAs were also predicted. Collectively, CSCD2 provides a significantly enhanced resource for exploring the function and regulation of circRNAs in cancer.

scholarly journals The cDNA for rat selenoprotein P contains 10 TGA codons in the open reading frame

1991 ◽  
Vol 266 (16) ◽  
pp. 10050-10053
Author(s):  
K.E. Hill ◽  
R.S. Lloyd ◽  
J.G. Yang ◽  
R. Read ◽  
R.F. Burk
Keyword(s):  
Open Reading Frame ◽  
Selenoprotein P ◽  
Reading Frame
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