scholarly journals Felis domesticus papillomavirus, isolated from a skin lesion, is related to canine oral papillomavirus and contains a 1·3 kb non-coding region between the E2 and L2 open reading frames

2002 ◽  
Vol 83 (9) ◽  
pp. 2303-2307 ◽  
Author(s):  
Masanori Terai ◽  
Robert D. Burk
Keyword(s):  
Phylogenetic Analysis ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Domestic Cat ◽  
Homology Search ◽  
Coding Region ◽  
Reading Frame ◽  
Blast Homology Search ◽  
Reading Frames ◽  
Felis Domesticus

We have characterized the complete genome (8300 bp) of an isolate of Felis domesticus papillomavirus (FdPV) from a domestic cat with cutaneous papillomatosis. A BLAST homology search using the nucleotide sequence of the L1 open reading frame demonstrated that the FdPV genome was most closely related to canine oral papillomavirus (COPV). A 384 bp non-coding region (NCR) was found between the end of L1 and the beginning of E6, and a 1·3 kbp NCR was located between the end of E2 and the beginning of L2. Phylogenetic analysis placed FdPV in the E3 clade with COPV. Both viruses contain the atypical second NCR, which has no homology with sequences in existing databases.

SOME HINTS ON OPEN READING FRAME STATISTICS — HOW ORF LENGTH DEPENDS ON SELECTION

1999 ◽  
Vol 10 (04) ◽  
pp. 635-643 ◽  
Author(s):  
AGNIESZKA GIERLIK ◽  
PAWEŁ MACKIEWICZ ◽  
MARIA KOWALCZUK ◽  
STANISŁAW CEBRAT ◽  
MIROSŁAW R. DUDEK
Keyword(s):  
Genetic Code ◽  
Dna Sequences ◽  
Nucleotide Composition ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Antisense Strand ◽  
Coding Sequences ◽  
Reading Frame ◽  
Intergenic Sequences ◽  
Reading Frames

Coding sequences of DNA generate Open Reading Frames (ORFs) inside them with much higher frequency than random DNA sequences do, especially in the antisense strand. This is a specific feature of the genetic code. Since coding sequences are selected for their length, the generated ORFs are indirect results of this selection and their length is also influenced by selection. That is why ORFs found in any genome, even much longer ones than those spontaneously generated in random DNA sequences, should be considered as two different sets of ORFs: The first one coding for proteins, the second one generated by the coding ORFs. Even intergenic sequences possess greater capacity for generating ORFs than random DNA sequences of the same nucleotide composition, which seems to be a premise that intergenic sequences were generated from coding sequences by recombinational mechanisms.

scholarly journals Translation Termination Reinitiation between Open Reading Frame 1 (ORF1) and ORF2 Enables Capsid Expression in a Bovine Norovirus without the Need for Production of Viral Subgenomic RNA

2008 ◽  
Vol 82 (17) ◽  
pp. 8917-8921 ◽  
Author(s):  
Christopher J. McCormick ◽  
Omar Salim ◽  
Paul R. Lambden ◽  
Ian N. Clarke
Keyword(s):  
Hepg2 Cells ◽  
Nonstructural Protein ◽  
Translation Termination ◽  
Surrogate Marker ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Subgenomic Rna ◽  
Reading Frame ◽  
Reading Frames ◽  
Open Reading Frame 1

ABSTRACT A generally accepted view of norovirus replication is that capsid expression requires production of a subgenomic transcript, the presence of capsid often being used as a surrogate marker to indicate the occurrence of viral replication. Using a polymerase II-based baculovirus delivery system, we observed capsid expression following introduction of a full-length genogroup 3 norovirus genome into HepG2 cells. However, capsid expression occurred as a result of a novel translation termination/reinitiation event between the nonstructural-protein and capsid open reading frames, a feature that may be unique to genogroup 3 noroviruses.

scholarly journals Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader.

1987 ◽  
Vol 7 (8) ◽  
pp. 2728-2734 ◽  
Author(s):  
C A Strick ◽  
T D Fox
Keyword(s):  
Amino Acids ◽  
Regulatory Gene ◽  
Mitochondrial Protein ◽  
Nuclear Gene ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Amino Terminal ◽  
Interesting Pattern ◽  
Reading Frames

The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader

1987 ◽  
Vol 7 (8) ◽  
pp. 2728-2734
Author(s):  
C A Strick ◽  
T D Fox
Keyword(s):  
Amino Acids ◽  
Regulatory Gene ◽  
Mitochondrial Protein ◽  
Nuclear Gene ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Amino Terminal ◽  
Interesting Pattern ◽  
Reading Frames

The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

scholarly journals Small open reading frames and cellular stress responses

2019 ◽  
Vol 15 (2) ◽  
pp. 108-116 ◽  
Author(s):  
Alexandra Khitun ◽  
Travis J. Ness ◽  
Sarah A. Slavoff
Keyword(s):  
Stress Responses ◽  
Cellular Stress ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Cellular Stress Responses ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Increasing evidence suggests that some small open reading frame-encoded polypeptides (SEPs) function in prokaryotic and eukaryotic cellular stress responses.

scholarly journals smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

2020 ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at http://www.cuilab.cn/smorfunction.

scholarly journals smORFunction: a tool for predicting functions of small open reading frames and microproteins

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at https://www.cuilab.cn/smorfunction.

scholarly journals smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

2020 ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at http://www.cuilab.cn/smorfunction.

scholarly journals Genes Specific for the Biosynthesis of Clavam Metabolites Antipodal to Clavulanic Acid Are Clustered with the Gene for Clavaminate Synthase 1 in Streptomyces clavuligerus

1999 ◽  
Vol 43 (5) ◽  
pp. 1215-1224 ◽  
Author(s):  
Roy H. Mosher ◽  
Ashish S. Paradkar ◽  
Cecilia Anders ◽  
Barry Barton ◽  
Susan E. Jensen
Keyword(s):  
Clavulanic Acid ◽  
Double Mutant ◽  
Streptomyces Clavuligerus ◽  
Gene Replacement ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Common Pool ◽  
Replacement Procedure ◽  
Reading Frames

ABSTRACT Portions of the Streptomyces clavuligerus chromosome flanking cas1, which encodes the clavaminate synthase 1 isoenzyme (CAS1), have been cloned and sequenced. Mutants of S. clavuligerus disrupted in cvm1, the open reading frame located immediately upstream of cas1, were constructed by a gene replacement procedure. Similar techniques were used to generate S. clavuligerus mutants carrying a deletion that encompassed portions of the two open reading frames,cvm4 and cvm5, located directly downstream ofcas1. Both classes of mutants still produced clavulanic acid and cephamycin C but lost the ability to synthesize the antipodal clavam metabolites clavam-2-carboxylate, 2-hydroxymethyl-clavam, and 2-alanylclavam. These results suggested that cas1 is clustered with genes essential and specific for clavam metabolite biosynthesis. When a cas1 mutant of S. clavuligerus was constructed by gene replacement, it produced lower levels of both clavulanic acid and most of the antipodal clavams except for 2-alanylclavam. However, a double mutant of S. clavuligerus disrupted in both cas1 andcas2 produced neither clavulanic acid nor any of the antipodal clavams, including 2-alanylclavam. This outcome was consistent with the contribution of both CAS1 and CAS2 to a common pool of clavaminic acid that is shunted toward clavulanic acid and clavam metabolite biosynthesis.

scholarly journals smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

2020 ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at http://www.cuilab.cn/smorfunction.

Sign in / Sign up

Export Citation Format

Share Document