Read Rat cytomegalovirus open reading frame R44 is an early-late gene that encodes a nuclear protein, Archives of Virology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
TY - JOUR. T1 - Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomaviruses. AU - Chen, Zigui. AU - Schiffman, Mark. AU - Herrero, Rolando. AU - DeSalle, Rob. AU - Burk, Robert D.. PY - 2007/4/10. Y1 - 2007/4/10. N2 - Complete genomes of HPV101 and HPV103 were PCR amplified and cloned from cervicovaginal cells of a 34-year-old female with cervical intraepithelial neoplasia grade 3 (CIN 3) and a 30-year-old female with a normal Pap test, respectively. HPV101 and HPV103 contain 4 early genes (E7, E1, E2, and E4) and 2 late genes (L2 and L1), but both lack the canonical E6 ORF. Pairwise alignment similarity of the L1 ORF nucleotide sequences of HPV101 and HPV103 indicated that they are at least 30% dissimilar to each other and all known PVs. However, similarities of the other ORFs (E7, E1, E2, and L2) indicated that HPV101 and HPV103 are most related to each other. Phylogenetic analyses revealed that ...
TY - JOUR. T1 - Identification of a novel 23 kDa protein encoded by putative open reading frame 2 of TT virus (TTV) genotype 1 different from the other genotypes. AU - Tanaka, Y.. AU - Orito, E.. AU - Ohno, T.. AU - Nakano, T.. AU - Hayashi, K.. AU - Kato, T.. AU - Mukaide, M.. AU - Iida, S.. AU - Mizokami, M.. PY - 2000/1/1. Y1 - 2000/1/1. N2 - We report the entire open reading frames (ORFs) sequences of four TT virus (TTV) isolates, one genotype 2 (G2) and three G4 isolates. Despite a DNA virus, TTV possesses high rate of amino acid (aa) substitution: the aa sequence homology of ORF1 and 2 is lower than the nucleotide homology. The partial N22 region of ORF1 is suitable for genotyping of prototype TTV isolates, because the phylogenetic tree from partial N22 sequence is consistent with that from the entire ORF1. Based on our sequence data, ORF2 from most isolates excluding G1 encode truncated 49 aa (pORF2a) because of an in-frame stop codon, although ORF2s from most G1 isolates encode 202 ...
Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants. We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs. This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (|150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved
TY - JOUR. T1 - Genes within genes. T2 - independent expression of phage T4 intron open reading frames and the genes in which they reside.. AU - Gott, J. M.. AU - Zeeh, A.. AU - Bell-Pedersen, D.. AU - Ehrenman, Karen. AU - Belfort, M.. AU - Shub, D. A.. PY - 1988/1/1. Y1 - 1988/1/1. N2 - The td, nrdB, and sunY introns of bacteriophage T4 each contain a long open reading frame (ORF). These ORFs are preceded by functional T4 late promoters and, in the case of the nrdB intron ORF, a functional middle promoter. Expression of phage-encoded intron ORF-lacZ fusions indicates that these T4 genes are highly regulated. The lack of translation of these ORFs from early pre-mRNAs can be accounted for by the presence of secondary structures that are absent from the late RNAs. Because translation of the intron ORFs could disrupt core structural elements required for pre-mRNA splicing, such regulation may be necessary to allow expression of the genes in which they reside.. AB - The td, nrdB, and sunY introns ...
Background Within the scanning model of translation initiation, reinitiation is a non-canonical mechanism that operates on mRNAs harboring upstream open reading frames. The h subunit of eukaryotic initiation factor 3 (eIF3) boosts translation reinitiation on the uORF-containing mRNA coding for the Arabidopsis bZip transcription factor, AtbZip11, among others. The RPL24B protein of the large ribosomal subunit, which is encoded by SHORT VALVE1, likewise fosters translation of uORF-containing mRNAs, for example mRNAs for auxin response transcription factors (ARFs). Results Here we tested the hypothesis that RPL24B and eIF3h affect translation reinitiation in a similar fashion. First, like eif3h mutants, rpl24b mutants under-translate the AtbZip11 mRNA, and the detailed spectrum of translational defects in rpl24b is remarkably similar to that of eif3h. Second, eif3h mutants display defects in auxin mediated organogenesis and gene expression, similar to rpl24b. Like AtbZip11, the uORF-containing ARF mRNAs
TY - JOUR. T1 - Conservation of the influenza virus membrane protein (M1) amino acid sequence and an open reading frame of RNA segment 7 encoding a second protein (M2) in H1N1 and H3N2 strains. AU - Lamb, Robert A.. AU - Lai, Ching Juh. PY - 1981/7/30. Y1 - 1981/7/30. N2 - The complete sequence of a full-length cloned DNA copy of the influenza virus A/Udorn/72 (H3N2) RNA segment 7 has been determined. A second open reading frame has been found which overlaps the membrane protein (M1) sequence by 68 nucleotides. This second reading frame could code, in the +1 reading frame, for a protein (M2) with a maximum of 97 amino acids depending on whether there is splicing of the mRNA and the methionine residue used for initiation of protein synthesis. Comparison of the present H3N2 sequence with the previously published sequence (G. Winter and S. Fields, Nucleic Acids Res., 8, 1965-1975, 1980; H. Allen, J. McCauley, M. Waterfield, and M.-J. Gething, Virology, 107, 548-551, 1980) of RNA segment 7 of ...
Theres a great guide regarding how to ensure that the automated gene annotator that identified the gene youre working on chose the proper start location for translation. The guide is in Dropbox (you dont need an account in Dropbox to get these, but its handy free cloud storage.) The guide can be downloaded here ...
Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, Blangero J, Bowden DW, Brandslund I, Brosnan J, Burslem F, Chambers J, Cho YS, Christensen C, Douglas DA, Duggirala R, Dymek Z, Farjoun Y, Fennell T, Fontanillas P, Forsén T, Gabriel S, Glaser B, Gudbjartsson DF, Hanis C, Hansen T, Hreidarsson AB, Hveem K, Ingelsson E, Isomaa B, Johansson S, Jørgensen T, Jørgensen ME, Kathiresan S, Kong A, Kooner J, Kravic J, Laakso M, Lee JY, Lind L, Lindgren CM, Linneberg A, Masson G, Meitinger T, Mohlke KL, Molven A, Morris AP, Potluri S, Rauramaa R, Ribel-Madsen R, Richard AM, Rolph T, Salomaa V, Segrè AV, Skärstrand H, Steinthorsdottir V, Stringham HM, Sulem P, Tai ES, Teo YY, Teslovich T, Thorsteinsdottir U, Trimmer JK, Tuomi T, Tuomilehto J, Vaziri-Sani F, Voight BF, Wilson JG, Boehnke M, McCarthy MI, Njølstad PR, Pedersen O, Groop L, Cox DR, Stefansson K, Altshuler D. Loss-of-function mutations in SLC30A8 protect against type 2 ...
Research groupsGene regulation and morphogenesis Genetics and functional genomics of genes with small open reading frames Dr Juan Pablo ..
Research groupsGene regulation and morphogenesis Genetics and functional genomics of genes with small open reading frames Dr Juan Pablo ..
Genome map of SSV1. Open reading frames are shown as block arrows and labeled as in Palm et al. (1991). Virus structural protein genes (Reiter et al., 1987a) an
Virions are constructed from a major capsid protein (CP) encoded by the second open reading frame (ORF2). The CP binds to surface heparin sulfate proteoglycans (HSPGs) on liver cells (Kalia et al., 2009) and may be proteolytically processed. A small immunoreactive protein (113-114 amino acids, 12.5 kDa) encoded by the third ORF (ORF3) has been identified and shown to exhibit multiple functions associated with virion morphogenesis, egress and viral pathogenesis. Recently, the ORF3 polypeptide has been shown to share several structural features with class I viroporins (Ding et al., 2017). Non-structural proteins encoded by the first major ORF (ORF1) have limited similarity with the alpha-like supergroup of viruses and contain domains consistent with a methyltransferase, papain-like cysteine protease, macro domain, RNA helicase and RNA-dependent RNA polymerase (Cao and Meng 2012). Some of these predicted enzymatic properties have been confirmed experimentally (Karpe and Lole 2010, Parvez 2015, ...
Upstream open reading frames (uORFs) are small open reading frames found in the 5 UTR of a mature mRNA, and can potentially mediate translational regulation of the largest, or major, ORF (mORF). CPuORF30 represents a conserved upstream opening reading frame relative to major ORF AT3G18000.1 ...
Codons consist of six bases and there are six reading frames for each DNA strand, so ... so researchers must evaluate six open reading frames.
(KudoZ) English to Polish translation of complete open reading frame of a cDNA molecule: otwarta ramka odczytu (cząsteczki cDNA) [Medical].
Stern-Ginossar and the other researchers suspected that existing maps of HCMVs protein-coding potential, based largely on computational methods, were far from complete. So, they began mapping the positions of ribosomes-the cellular organelles in which proteins are synthesized-during an HCMV infection of human fibroblast cells. With the resulting map, Stern-Ginossar and her colleagues discovered templates for hundreds of previously unidentified proteins that were encoded in corresponding DNA segments of the viral genome, known as open reading frames.. Surprisingly, the researchers found that many of these open reading frames encode for exceptionally short protein sequences (fewer than 100 amino acids). And some of the newly identified open reading frames were even hiding inside other open reading frames, they say.. A key finding of our work is that each of these templates can encode more than one protein, said Annette Michalski from the Max Planck Institute of Biochemistry in Martinsried, ...
Myc-DDK-tagged ORF clone of Homo sapiens chromosome 5 open reading frame 13 (C5orf13), transcript variant 3 as transfection-ready DNA - 10 µg - OriGene - cdna clones
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and
Myc-DDK-tagged ORF clone of Homo sapiens chromosome 16 open reading frame 52 (C16orf52) as transfection-ready DNA - 10 µg - OriGene - cdna clones
TY - JOUR. T1 - Yeast CAL1 is a structural and functional homologue to the DPR1 (RAM) gene involved in ras processing. AU - Ohya, Yoshikazu. AU - Goebl, Mark. AU - Goodman, Laurie E.. AU - Petersen-Bjørn, Sara. AU - Friesen, James D.. AU - Tamanoi, Fuyuhiko. AU - Anraku, Yasuhiro. PY - 1991. Y1 - 1991. N2 - A 2.3-kilobase pair DNA fragment of the yeast CAL1 gene was cloned by complementation of the cal1-1 mutation, which causes a defect in nuclear division and bud formation (Ohya, Y., Ohsumi, Y., and Anraku, Y. (1984) Mol. & Gen. Genet. 193, 389-394). Nucleotide sequencing of this fragment revealed a single open reading frame (ORF) encoding a polypeptide of 376 amino acids. Comparative analysis of the predicted amino acid sequence has shown that the CAL1 product has similarity to two yeast proteins: the DPR1 (RAM) gene product that is involved in processing of ras protein at the farnesylation step, and the essential ORF2 protein whose structural gene has a head-to-head arrangement with PRP4, ...
The BY4741 strain used in (Nagalakshmi et al. 2008) was used in this study. RNA-Seq was performed using the protocol developed in (Nagalakshmi et al. 2008), further described in (Nagalakshmi et al. 2010) and (Waern et al. 2011), and using the modifications developed by (Parkhomchuk et al. 2009) to generate strand-specific reads.. Analysis was performed on custom software developed in-house using BowTie (Langmead et al. 2009) to map reads to the S288C reference genome available on SGD, downloaded on May 17, 2010. Python, NumPy, SciPy, and matplotlib were used to further process the data. The softwares source code is available (Saccharomyces Genome Database). Of note, to maximize the information gleaned, unmappable reads were trimmed by four bases from the 3′ end and remapping was attempted; this was done iteratively until only 28 bp remained, at which point the read was considered unmappable. This end trimming typically doubled or more the number of mappable reads.. Expression levels were ...
Sorts alternative splicing (AS) and discovers coding potential. spliceR simplifies downstream sequence analysis by allowing annotation of genomic coordinates of the differentially spliced elements. It is able to detect coding potential of transcripts, determines untranslated region (UTR) and open reading frame (ORF) lengths and predicts whether transcripts are nonsense mediated decay (NMD)-sensitive based on compatible annotated start codon positions and their downstream ORF.
C20orf203 is a de novo human gene that evolved from non-coding DNA after the split between human and chimp. In the human lineage 5 point mutations in the region resulted in the creation of an open reading frame which lead to the expression and translation of 194 amino acid (22kDa) protein. This protein is enriched in the brain and is up regulated in the brains of Alzheimers patients and thus has been hypothesized to play a role in the pathogenesis of this disease.. ...
Abstract: Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ambigrammatic and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be ...
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Recombinant Chromosome 10 Open Reading Frame 33 (C10ORF33) Protein (His tag). Spezies: Ratte (Rattus). Quelle: Hefe. Jetzt Produkt ABIN1635561 bestellen.
The structures of both eukaryotic and prokaryotic genes involve several nested sequence elements. Each element has a specific function in the multi-step process of gene expression. The sequences and lengths of these elements vary, but the same general functions are present in most genes.[2] Although DNA is a double-stranded molecule, typically only one of the strands encodes information that the RNA polymerase reads to produce protein-coding mRNA or non-coding RNA. This sense or coding strand, runs in the 5 to 3 direction where the numbers refer to the carbon atoms of the backbones ribose sugar. The open reading frame (ORF) of a gene is therefore usually represented as an arrow indicating the direction in which the sense strand is read.[10] Regulatory sequences are located at the extremities of genes. These sequence regions can be next to the transcribed region (the promoter) or separated by many kilobases (enhancers and silencers).[11] The promoter is located at the 5 end of the gene ...
Predicting open reading frames within genomic sequences is probably one of the most basic yet important hallmarks of bioinformatics and sequencing analysis. This is the process by which, given an organisms genomic sequence or a section of that genomic sequence, we predict what sections of that genome are potential genes. At its most basic level, this can be done by looking for sequence regions between start and stop codons (sequence signals for the beginning and end of a gene). While there are many programs for predicting open reading frames, I often use the common Glimmer3 toolkit. This program works great overall, but one drawback is that it can sometimes be hard to visualize your open reading frames on your genome or genomic region (using Geneious or the Integrated Genomics Viewer) because it does not give you a .gff3 formatted file, which is commonly used by these programs. In this technical post, I am going to focus on the file types you get from Glimmer3, I will explain the .gff3 file ...
LOC101241902 (chromosome 4 open reading frame 46 pseudogene), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
Compare chromosome 9 open reading frame 62 Biomolecules from leading suppliers on Biocompare. View specifications, prices, citations, reviews, and more.
These plasmids were used in Phoebe Lus paper: Lu PD, Harding HP and Ron D. 2004. Translation re-initiation at alternative open reading frames regulates gene expression in an integrated stress response. J Cell Biol. 167:27-33.. Important Note: These ...
p,Transcripts that dont contain an open reading frame (ORF) and cannot be placed in one of the other categories.,/p,Processed transcript ...
from Bio import SeqIO ,,,record = SeqIO.read(sequence.fasta, fasta) ,,, table = 1 ,,, min_pro_len = 100 ,,,for strand, nuc in [(+1, record.seq), (-1, record.seq.reverse_complement())]: for frame in range(3): length = 3 * ((len(record)-frame) // 3) #Multiple of three for pro in nuc[frame:frame+length].translate(table).split(*): if len(pro) ,= min_pro_len: print(%s...%s - length %i, strand %i, frame %i \ % (pro[:30], pro[-3:], len(pro), strand, frame)) YSDIDQINLNQISNLQRNLKYFITMGDSTG...NNV - length 554, strand 1, frame 2 SSPGDKGHNCKGGSASSLCPHREEHHSHNG...ILT - length 162, strand -1, frame 1 IEHQDSHDDVQPTGYKEGDPPGREGCGTAA...HNW - length 216, strand -1, frame 1 TKVTGNVQATIITPIHVSPCSVVKCEVEKK...SDA - length 122, strand -1, frame 2 ...
We have taken a first step towards learning which upstream Open Reading Frames (uORFs) regulate gene expression (i.e., which uORFs are functional) in the yeast Saccharomyces cerevisiae. We do this by integrating data from several resources and combining a bioinformatics tool, ORF Finder, with a machine learning technique, inductive logic programming (ILP). Here, we report the challenge of using ILP as part of this integrative system, in order to automatically generate a model that identifies functional uORFs. Our method makes searching for novel functional uORFs more efficient than random sampling. An attempt has been made to predict novel functional uORFs using our method. Some preliminary evidence that our model may be biologically meaningful is presented.
Current Research: 1. Angiotensin receptor signaling and trafficking: The angiotensin type 1 receptor is a peptide hormone G protein-coupled receptor that is widely targeted to treat hypertension. We previously discovered that RNA binding proteins regulate the function of the rat type 1a receptor (AT1aR) by selectively binding within exon 2 of the receptor 5′-leader sequence and that this translational regulation is mediated by a short open reading frame in exon 2. More recently, this research direction has led to the exciting discovery of a seven amino acid peptide (PEP7) encoded within a short open reading frame in exon 2, which is a selective inhibitor of AT1aR signaling; PEP7 inhibits the Erk1/2 but not the classic inositol trisphosphate pathway. PEP7 may also contribute to age-related impairments in urine-concentrating mechanisms and modulates AT1aR trafficking. We study AT1aR signal transduction by conducting enzyme and radioligand binding assays as well as by measuring signaling ...
Upstream open reading frames (uORFs) are open reading frames that occur within the 5′ UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes.... Read more ...
Upstream open reading frames (uORFs) are open reading frames that occur within the 5′ UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes.... Read more ...
Abnova Human EXT1 Full-length ORF (NP_000118.2, 1 a.a. - 746 a.a.) Recombinant Protein with GST-tag at N-terminal 2µg Life Sciences:Protein Biology:Proteins:Proteins
Abnova Human ERAS Full-length ORF (NP_853510.1, 1 a.a. - 233 a.a.) Recombinant Protein with GST-tag at N-terminal 25µg Life Sciences:Protein Biology:Proteins:Proteins
We show that cytotoxic T lymphocytes (CTLs) infiltrating a kidney tumor recognize a peptide encoded by an alternative open reading frame (ORF) of the macrophage colony-stimulating factor (M-CSF) gene. Remarkably, this alternative ORF, which is translated in many tumors concurrently with the major ORF, is also translated in some tissues that do not produce M-CSF, such as liver and kidney. Such a dissociation of the translation of two overlapping ORFs from the same gene is unexpected. The antigenic peptide encoded by the alternative ORF is presented by human histocompatibility leukocyte antigen (HLA)-B*3501 and has a length of 14 residues. Peptide elution indicated that tumor cells naturally present this 14 mer, which is the longest peptide known to be recognized by CTLs. Binding studies of peptide analogues suggest that it binds by its two extremities and bulges out of the HLA groove to compensate for its length.
Translation of the polycistronic 35S RNA of CaMV (cauliflower mosaic virus) occurs via a reinitiation mechanism, which requires TAV (transactivator/viroplasmin). To allow translation reinitiation of the major open reading frames on the polycistronic RNA, TAV interacts with the host translational machinery via eIF3 (eukaryotic initiation factor 3) and the 60S ribosome. Accumulation of TAV and eIF3 in the polysomal fraction isolated from CaMV-infected cells suggested that TAV prevents loss of eIF3 from the translating ribosomes during the first initiation event. The TAV-eIF3-80S complex could be detected in vitro by sucrose-gradient-sedimentation analysis. The question is whether TAV interacts directly with the 48S preinitiation complex or enters polysomes after the first initiation event. eIF4B, a component of the 48S initiation complex, can preclude formation of the TAV-eIF3 complex via competition with TAV for eIF3 binding; the eIF4B- and TAV-binding sites on eIF3g overlap. eIF4B out-competes ...
TY - JOUR. T1 - Cloning and expression of Xenopus laevis xSox12 cDNA. AU - Komatsu, Naoki. AU - Hiraoka, Yoshiki. AU - Shiozawa, Masahide. AU - Ogawa, Motoyuki. AU - Aiso, Sadakazu. PY - 1996/3/1. Y1 - 1996/3/1. N2 - A family of SRY-related genes has been termed SOX. We have isolated and sequenced a cDNA encoding xSox12 from Xenopus laevis ovary. The cDNA contained an open reading frame (ORF) coding for 470 amino acids encompassing an HMG box characteristic of the SOX family, a leucine zipper motif and glutamine-rich segments. The size of the xSox12 mRNA was determined to be 3.0 knt by Northern analysis. The ovary was the most prominent in the expression of the Sox mRNA among the various tissues of adult frog as far as examined.. AB - A family of SRY-related genes has been termed SOX. We have isolated and sequenced a cDNA encoding xSox12 from Xenopus laevis ovary. The cDNA contained an open reading frame (ORF) coding for 470 amino acids encompassing an HMG box characteristic of the SOX family, a ...
TY - JOUR. T1 - Inactivation of the open reading frame slr0399 in Synechocystis sp. PCC 6803 functionally complements mutations near the Q(A) niche of photosystem II. A possible role of Slr0399 as a chaperone for quinone binding. AU - Ermakova-Gerdes, Svetlana. AU - Vermaas, Willem. PY - 1999/10/22. Y1 - 1999/10/22. N2 - The Synechocystis sp. PCC 6803 triple mutant D2R8 with V247M/A249T/M329I mutations in the D2 subunit of the photosystem II is impaired in Q(A) function, has an apparently mobile Q(A), and is unable to grow photoautotrophically. Several photoautotrophic pseudorevertants of this mutant have been isolated, each of which retained the original psbDI mutations of D2R8. Using a newly developed mapping technique, the site of the secondary mutations has been located in the open reading frame slr0399. Two different nucleotide substitutions and a deletion of about 60% of slr0399 were each shown to restore photoautotrophy in different pseudorevertants of the mutant D2R8, suggesting that ...
A human cytomegalovirus early gene which possesses three temporally regulated promoters is located in the large unique component of the viral genome between 0.054 and 0.064 map units (C.-P. Chang, C.L. Malone, and M.F. Stinski, J. Virol. 63:281-290, 1989). This gene contains a major open reading frame (ORF) located 233 bases downstream of the cap site of an early unspliced RNA. The major ORF predicts a polypeptide of 17 kilodaltons (kDa) which contains a glycoproteinlike signal and anchor domains as well as potential N-glycosylation sites. Antisera were prepared against synthetic peptides derived from amino acid sequences within the major ORF. The antisera detected a viral glycoprotein of 48 kDa in infected cells and recognized the in vitro-translated 17-kDa protein early-gene product. The viral glycoprotein, designated gp48, was modified by N-linked glycans and possibly O-linked glycans. The synthesis of gp48 occurred in the absence of viral DNA replication but accumulated to the highest levels ...
It has been shown previously, by sequence analysis of the S RNA segment of snowshoe hare (SSH) bunyavirus, that two overlapping open reading frames in the viral complementary sequence code for proteins with molecular weights of 26.8 X 10(3) and 10.5 X 10(3) respectively. In addition to the viral nucleocapsid (N) protein, which is coded by the S RNA, analyses of parental and reassortant bunyavirus-infected cell extracts have shown that the viral S RNA and M RNA species each code for non-structural proteins (NSS and NSM, respectively). In the present report, in vitro translation analyses of the S mRNA species recovered from virus-infected cells indicate that a single size class of mRNA directs the synthesis of N and NSS. Compositional analyses of selected tryptic peptides of N and NSS have provided proof that N is the product of the first open reading frame, and NSS the product of the second.
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Peanut yellow spot virus (PYSV) represents a distinct tospovirus species based on serology and nucleic acid hybridization. The sequence of the S RNA was 2 970 nucleotides with 22 nucleotide long inverted repeats (with three mismatches) at the termini. The coding was ambisense with a long open reading frame (ORF) in each strand. The 5-large ORF (1 440 nucleotides in the viral sense (v) strand) encoded a protein with a predicted size of 53.2 kDa that was identified as the nonstructural (NSs) protein based on 16-21% sequence identity and 42- 48% sequence similarity with other tospoviruses. A 3 ORF (741 nucleotides) in the virus complementary (vc) sense encoded a 28.0 kDa protein that was identified as the nucleocapsid (N) gene based on immuno-blot analysis of the in vitro expressed protein with PYSV polyclonal antiserum. The predicted N protein had 24-28% amino acid sequence identity and 44-51% sequence similarity with the members of other serogroups. In contrast to other tospoviruses, a third ORF (204
The combined sequences encoding a partial and putative rpsI open reading frame (ORF), non-coding (NC) region, a putative ORF for the Campylobacter adhesin to fibronectin-like protein (cadF), a putative Cla_0387 ORF, NC region and a partial and putative Cla_0388 ORF, were identified in 16 Campylobacter lari isolates, using two novel degenerate primer pairs. Probable consensus sequence at the -35 and -10 regions were identified in all C. lari isolates, as a promoter. Thus, cadF (-like) gene is highly conserved among C. lari organisms. Transcription of the cadF (-like) gene in C. lari cells in vivo was also confirmed and the transcription initiation site was determined. A peptidoglycan-associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins was completely conserved amongst the putative cadF (-like) ORFs from the C. lari isolates. The putative cadF (-like) ORFs from all C. lari isolates were nine amino acid larger than those from C. jejuni, and showed amino acid
TY - JOUR. T1 - First report of a novel alphapartitivirus in the basidiomycete Rhizoctonia oryzae-sativae. AU - Das, Subha. AU - Das, Sampa. PY - 2019/3/1. Y1 - 2019/3/1. N2 - Rhizoctonia oryzae-sativae is a soil-borne basidiomycete fungus that causes aggregate sheath spot disease on rice worldwide. Here, we report the complete genome sequence of a partitivirus designated as Rhizoctonia oryzae-sativae partitivirus 1 (RosPV1) infecting this fungus. The genome of RosPV1 consists of two double-stranded RNA (dsRNA) segments. The larger segment, designated as dsRNA-1 (1,961 bp), contains a single open reading frame (ORF) that encodes a putative polypeptide with a conserved RNA-dependent RNA polymerase (RdRp) domain. The smaller segment, dsRNA-2 (1,819 bp), also has a single ORF, which is predicted to encode the capsid protein (CP). BLAST searches and phylogenetic analyses suggested that RosPV1 is a representative member of a new species within the genus Alphapartitivirus. This is the first report of ...
Flowering time of rice (Oryza sativa L.) is among the most important agronomic traits for region adaptation and grain yield. In the process of rice breeding, efficient and slightly modulating the flowering time of an elite cultivar would be more popular with breeder. Hence, we are interested in slightly increasing the expression of flowering repressors by CRISPR/Cas9 genome editing system. It was predicated there were three uORFs in 5 leader sequence of Hd2. In this study, through editing Hd2 uORFs, we got four homozygous mutant lines. Phenotypic analysis showed that the hd2 urf edited lines flowered later by 4.6-11.2 days relative to wild type SJ2. Supporting the later flowering phenotype, the expression of Ehd1, Hd3a, and RFT1 is significantly decreased in hd2 urf than that in wild type. Moreover, we found that the transcription level of Hd2 is not affected, whereas the Hd2 protein level was increased in hd2 urf compared with wild type, which indicated that Hd2 uORFs indeed affect the translation of
We have previously described sigma A and sigma B and their structural genes, mysA and mysB, respectively, in Mycobacterium smegmatis. We have now sequenced the corresponding regions in the M. tuberculosis and M. leprae chromosomes, and have found the two homologous genes. The chromosomal linkage and the deduced amino acid (aa) sequences of the two genes show very high similarity in the three species of mycobacteria. We also report the finding of two other open reading frames (ORF) in these clusters. orfX, which has an unknown function, is located between mysA and mysB. The other ORF, located downstream from mysB, encodes a homolog of DtxR, the iron regulatory protein from Corynebacterium diphtheriae (Cd). Doukhan, L; Predich, M; Nair, G; Dussurget, O; Mandic-Mulec, I; Cole, S T; Smith, D R; Smith, I
The E4 region of human adenovirus type 2 is predicted to encode seven proteins as judged from its nucleotide sequence and the pattern of differential splicing of its transcript. Two of the open reading frames (ORFs), ORF1 and ORF2, had been identified as being disrupted in the recently published sequence of the related serotype 5 virus. These ORFs were resequenced and found to be intact in the wt300 strain of adenovirus type 5.
FusionGDB is the Fusion Gene annotation DataBase, aiming to provide a resource or reference for functional annotation of fusion genes in cancer for better therapeutic targets. We first collected 48 117 FGs across pan-cancer from three representative fusion gene resources: the improved database of chimeric transcripts and RNA-seq data (ChiTaRS 3.1), an integrative resource for cancer-associated transcript fusions (TumorFusions), and The Cancer Genome Atlas (TCGA) fusions by Gao et al. For these ~48K FGs, we performed functional annotations including gene assessment across pan-cancer fusion genes, open reading frame (ORF) assignment, and protein domain retention search based on multiple isoform gene structure with multiple break points and finally provided the fusion transcript and amino acid sequences for each break point and gene isoforms. For each fusion partner gene, the user can access multiple annotations such as gene summary, assessment scores of each gene in pan-cancer, biological process ...
In innate immune system, the response to invading pathogens is initiated by pattern recognition receptor (PRRs) that bind pathogen-associated molecular patterns (PAMPs) and arise various immune response. Lectins are well-knows PRRs that recognize the carbohydrate molecules on surface of pathogens. Galectins, known as S-type lectin, have a carbohydrate recognition domain (CRD), specificity for β-galactosides and Ca2+- independent activity. In this study, we described the molecular cloning and characterization of a cDNA sequence of galectin 3 from big belly seahorse, Hippocampus abdominalis. The HaGal3 cDNA includes an open reading frame (ORF) of 1068 bp with 5 untranslated region (UTR) of 83 bp and a 3 UTR of 214 bp. The ORF encoded a putative protein of 356 amino acids with a theoretical isoelectric point of 8.49 and predicted molecular mass of 38.6 kDa. The deduced protein includes a carbohydrate-recognition domain and a galactoside-type carbohydrate-binding motif H-NPR/W-E-R. HaGal3 showed ...
From the cloning and characterization of cDNAs, we found that the Epstein-Barr virus (EBV) open reading frame (ORF) BMLF1-BSLF2 coding for the early protein EB2 is present in several mRNAs generated by alternative splicing and expressed in the leftward direction from two promoters PM and PM1. The PM promoter controls the expression of two abundant mRNA species of 1.9 and 2 kilobases (kb), whereas the PM1 promoter controls the expression of at least three mRNAs 3.6, 4.0, and 4.4 kb long. The PM promoter probably overlaps with the PS promoter which controls the transcription of a 3.6-kb mRNA expressed in the rightward direction and containing the ORF BSRF1. Although it increases the amount of chloramphenicol acetyltransferase enzyme expressed from the chimeric pMCAT gene, EB2 is not a promiscuous trans-activator of gene expression and does not positively regulate its own expression from promoter PM. The EB2 activation is not promoter dependent but could possibly act by stabilizing mRNAs and ...
We expressed the M2 gene in prokaryotic cells using the pAED4 expression vector system to produce native and purified M2 protein as a candidate for universal recombinant vaccine against influenza A subtypes. The open reading frame (ORF) of avian influenza A/chicken/Iran/101/1998 (H9N2) M2 gene was amplified by 2-step RT-PCR using specific primers and pfu DNA polymerase. pAED4 was used as expression vector, purified PCR product digested by Nde I and EcoR I restriction enzymes was ligated to the same digested site in the vector using T4 ligase to form pAED4-M2. The cloned M2 gene was confirmed by PCR and restriction enzymes pattern. M2 polypeptide was produced through the expression of this recombinant expression vector (pAED4+M2) in Escherichia coli BL21 (DE3) strain. The expressed M2 polypeptide was analyzed on SDS-PAGE and confirmed by western blotting assay. The level of 100% homology between the N-terminal domain of H5 and H9 isolates was considerable. It seems that recombinant vaccine based ...
Units 1, 2, and 3 will use high-throughput transcriptome analysis (RNA-seq) based on quantitative next-generation sequencing (NGS) technologies, with the aim to compare the transcript profiles of hyper-/hypo-pathogenic Leishmania strains. Mapping of reads to the L. donovani and L. major reference genomes will help to define (i) the density of reads associated to any open reading frame (ORF), (ii) transcripts generated by alternative trans-splicing events, (iii) the map of initiation sites of parasite-specific poly-cistronic transcription, and (iv) sense and antisense transcript abundance [3]. This analysis will allow revealing transcripts that are exclusively expressed in virulent Leishmania, and will thus allow important new insight into Leishmania pathogenicity mechanisms.. ...
Thioredoxin system plays an important role in antioxidative stress, thioredoxin 2 (Trx2) being one of the most important components in the thioredoxin system. The full-length cDNA sequence of thioredoxin 2 from Euphausia superba (EsTrx2) is 1276 bp and contain a 5′ untranslated region (UTR) of 94 bp, a 3′ UTR of 741 bp and an open reading frame (ORF) of 441 bp, encoding a putative protein of 146 a ...
Laborator Synevo. Informatii generale. Virusul hepatitei E (HEV), recent inclus in genul Hepevirus al familiei Hepeviridae, cauzeaza o infectie acuta, de obicei, autolimitanta. Este un virus sferic, lipsit de invelis, cu diametru de 27-34 nm, alcatuit dintr-un genom ARN monocatenar cu polaritate pozitiva. Sunt descrise 4 genotipuri majore si un singur serotip. Genomul prezinta 3 cadre de citire (open reading frames = ORF): ORF1 codifica metiltransferaza, proteaza, helicaza si replicaza; ORF 2 codifica proteina capsidei; ORF3 codifica o proteina a carei functie nu a fost definita4.. HEV se transmite pe cale fecal-orala; consumul de apa potabila contaminata cu fecale este responsabil de aparitia majoritatii epidemiilor. Transmiterea directa de la o persoana la alta este neobisnuita. Transmiterea pe cale sexuala sau prin transfuzii nu a fost dovedita1;4.. Hepatita cu virus hepatitic E este endemica in Asia de sud-est si centrala, cu mai multe focare in Orientul Mijlociu, Africa de nord si de vest ...
防御素(defensins)是一类在先天性免疫系统中起着重要作用的阳离子抗菌肽。因其在机体抵御病原入侵方面起着重要作用,固命名为防御素。防御素对许多病原微生物有着天然的抵抗活性,包括病毒和细菌。目前,几个跟防御素的转录调控相关的转录因子已经被鉴定,如NF-κB、NF-IL6等。在本论文中,我们主要就青鳉防御素的基因功能及转录调控进行研究。首先,我们运用3′, 5′末端快速扩增法 (Rapid Amplification of cDNA Ends techniques, RACE)在青鳉(Oryzias latipes)眼睛中克隆到一个新的β-防御素基因,命名为OlBD。该基因的cDNA全长480bp,其中5′端和3′端非翻译区(Untranslated region,UTR)分别为68bp和240bp,在3′ 末端还含有一个典型的加尾信号(ATTAA)和26bp的多聚腺嘌呤尾(poly A 尾)。在该cDNA中的189bp 的开放阅读框(open reading frame,ORF) 编码了63个氨基酸(aa)的多肽。Southern blot ...
Researchers from IBCh RAS together with their international collаborators discovered an evolutionary link between efficiency of start codons and the probability of AUG codon occurrence in the 5'-end parts of protein-coding sequences. When start codons are inefficient the next AUG codon is more likely to be found in the same reading frame. At the same time in case of highly efficient start codons, the next AUG codon is more likely to be found in alternative frames. They also have shown that weak initiation at the first starts is associated with the synthesis of shortened proteoforms as a result of initiation at the second starts.
Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate genome annotation is of paramount importance. However, increasing evidence indicates that currently annotated bacterial genomes have missed many genes encoding small proteins ≤60 aa (Wood et al. 2012; Warren et al. 2010). A small gene, or a small open reading frame (sORF), has previously been defined as one encoding proteins of ≤60 aa (Hemm et al. 2010); or alternatively, it accommodates those up to 100 aa (Andrews and Rothnagel 2014). While small proteins have been increasingly reported for their important cellular roles in bacteria (Alix and Blanc-Potard 2008; Martin et al. 2015; Hobbs et al. 2012), studies on small proteins are limited, partly because many small genes are unannotated in sequenced bacterial genomes (Alix and Blanc-Potard 2009; Storz et al. 2014). Despite much effort made to improve gene annotation, the accurate identification of small genes has been a persistent challenge ...
Plants respond to changes in sugar concentrations by altering their transcriptional profile and their metabolic processes. Sucrose triggers the translational repression of the transcription factor bZIP11 in Arabidopsis thaliana. Rahmani et al. show that this repression requires the 5′-leader sequence of bZIP11, which, when transferred to a reporter gene, decreased the expression of the reporter gene product (luciferase) in response to sucrose, consistent with sugar-induced translational repression. Deletion analysis revealed that the second upstream open reading frame (uORF2) was required. When the mRNA sequence of uORF2 was mutated without affecting the encoded peptide, sugar-induced translational repression occurred. Transplantation of the 82 nucleotides of the uORF2 sequence into the promoter of a gene not normally regulated by sucrose caused the production of the reporter gene to decrease in response to sucrose. Mutation of the encoded peptide, or changing the length of the encoded ...
The present invention relates to a method for transmitting a signal using a frame having a predetermined CP (Cyclic Prefix) length in a wireless communication system. The method includes receiving a signal from a base station using a first frame, and transmitting the signal to the base station using the first frame. Wherein the first frame is a frame supported by a first cell among the plurality of cells and the first frame is a frame different from a second frame supported by a second cell among the plurality of cells, An area where an uplink area of a first frame overlaps with a downlink area of the second frame or an area where a downlink area of the first frame overlaps with an uplink area of the second frame is punctured, The length of the CP of the first frame and the CP length of the second frame are different from each other. Frame, Cyclic Prefix, Interference
Gene expression during development is regulated both transcriptionally and translationally; however, relatively few examples of translational regulation are known. On p. 3575, Imai and colleagues describe for the first time how an upstream open reading frame (uORF) mediates translational control during plant development. Loss-of-function mutants of Arabidopsis ACAULIS 5 (ACL5), which encodes spermine synthase, have a dwarf phenotype because of a defect in stem elongation. To find out how ACL5 regulates stem elongation, the researchers isolated a dominant suppressor mutant of the acl5 phenotype - sac51-d. They show that sac51-d disrupts a short uORF of SAC51, which encodes a bHLH transcription factor. Other experiments indicate that this disruption might increase the translation of SAC51. Thus, the researchers suggest that the uORF-encoded protein normally prevents the initiation of SAC51 translation, and that ACL5 acts directly or indirectly (possibly through spermines effects on protein ...
This month the Open Knowledge Foundation is five years old.. Over those last five years weve done much to promote open access to information - from sonnets to stats, genes to geodata - not only in the form of specific projects like Open Shakespeare and Public Domain Works but also in the creation of tools such as KnowledgeForge and the Comprehensive Knowledge Archive Network, standards such as the Open Knowledge Definition, and events such as OKCon, designed to benefit the wider open knowledge community. (More about what weve been up just over the last year can be found in our latest annual report).. While we have achieved a lot, we believe we can do much, much more. We are therefore reaching out to our community and asking you to help us take our vision further.. Our aim: at least a 100 supporters committed to making regular, ongoing donations of £5 (EUR 6, $7.50) or more a month.. These funds will be essential in expanding and sustaining our work by allowing us to invest in infrastructure ...
This gene encodes an endonuclease that specifically degrades the RNA of RNA-DNA hybrids and is necessary for DNA replication and repair. This enzyme is present in both mitochondria and nuclei, which are resulted from translation of a single mRNA with two in-frame initiation start codons. The use of the first start codon produces the mitochondrial isoform and the use of the second start codon produces the nuclear isoform. The production of the mitochondrial isoform is modulated by an upstream open reading frame (uORF) which overlaps the first initiation start codon in human. An alternately spliced transcript variant has been found which encodes a shorter isoform. This gene has three pseudogenes; two of them are at different locations of chromosome 17 and one of them is on chromosome 1q32.2. [provided by RefSeq, Sep 2014 ...
Although nonsense mutations have been associated with the skipping of specific constitutively spliced exons in selected genes, notably the fibrillin gene, the basis for this association is unclear. Now, using chimaeric constructs in a model in vivo expression system, premature termination codons are …
A network system in which administrators of frame relay networks can recognize the quality of the ATM network suitably and manage the frame relay networks in accordance with the quality condition of the ATM network. When a frame F is transmitted from a frame relay network FR1 at a transmitting side to an IWF, a frame header in which a transmission number is stored is added to the frame F. Then, the frame F is received by a frame relay network FR2 at a transmitted side through the IWF and the ATM network. In the frame relay network FR2, a difference between the transmission number stored in the frame header of the frame F and a reception condition variable kept in the frame relay network FR2 is calculated, and the difference is stored in a quality information collection table as a number of discarded frames in the ATM network.
Greetings, faithful readers! Im sure you have both been wondering why the long hiatus - lots of reasons, mostly to do with laziness, but theres one in particular I need to get out of the way right away. I promised myself that I wouldnt say anything on the blog until Id corrected an error - and promptly stopped blogging for about two years!. But now I have things I want to talk about again, so its time (OK, way past time!) to do the necessary update.. In these two posts, I relied heavily on an NIH estimate of author-side charges, using it to calcluate page and colour charges on the basis of the assumption that most toll-access journals charge these.. On liblicense-L, Anthony Watkinson took me to task for that assumption, pointing out that it did not accord with his many years of experience as a publisher and going to the trouble of soliciting opinion from colleagues with similar backgrounds (all of whom agreed with him).. At the time, I could do no more than cede Anthonys point that my ...
The worlds first wiki where authorship really matters. Due credit and reputation for authors. Imagine a global collaborative knowledge base for original thoughts.
The worlds first wiki where authorship really matters. Due credit and reputation for authors. Imagine a global collaborative knowledge base for original thoughts.
sORFs.org datasets. This section provides detailed information about the datasets used. For more information about the dataset processing please consult the INFO page. navigate through the datasets on the left to acquire more information about the corresponding dataset. ...
We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each clusters gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq ...
It finally happened. Yesterday, Genentech announced that they made a go decision to advance T-DM1 into a phase III trial. Although no official announcement is out as of yet, Genentechs President of Product Development, Sue Hellmann, left no doubt in her prepared remarks: Additionally, we recently made a Phase III go decision for T-DM1 in…
Calculates entropy of the reads coverage over each grl group. The entropy value per group is a real number in the interval (0:1), where 0 indicates no variance in reads over group. For example c(0,0,0,0) has 0 entropy, since no reads overlap.
BiTE Antibodies A BiTE (Bispecific T Cell Engager) antibody is a bi-specific antibody (bsAb) which directs T-cells to attack cancer cells, by simultaneously binding the two cells. Upon binding, a physical link is created between the two cells, which in turn triggers the T cell to attack the target cell. Every BiTE antibody has two…