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The Tata-Less Promoter of VP1, A Plant Gene Controlling Seed Germination 控制种子萌发的植物基因VP1的无tata启动子
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109047563
F. Carrari, Nicolás Frankel, D. Lijavetzky, R. Benech-Arnold, R. Sánchez, N. Iusem
{"title":"The Tata-Less Promoter of VP1, A Plant Gene Controlling Seed Germination","authors":"F. Carrari, Nicolás Frankel, D. Lijavetzky, R. Benech-Arnold, R. Sánchez, N. Iusem","doi":"10.3109/10425170109047563","DOIUrl":"https://doi.org/10.3109/10425170109047563","url":null,"abstract":"Vp1 is a seed-specific gene involved in the control of dormancy and germination. We here present the complete sequence of the sorghum vp1 promoter/enhancer region highlighting its main features, especially the lack of canonical TATA and CAAT boxes and the presence of elements responsive to abscisic acid and light. The region closest to the start of transcription is highly homologous to the partial proximal sequence reported for the maize vp1 promoter. This region is interrupted by a 57-nt stretch containing 14 CT microsatellite repeats. We observed a poor overall homology to the promoter from abi3 gene, the Arabidopsis counterpart bearing a similar coding sequence. However, there exists a high degree of homology (89%) between a TATA-rich 103-bp stretch of the sorghum vp1 promoter located about 700 nt upstream of the startpoint and miniature inverted transposable elements (MITEs) interspersed within the sorghum seed-specific kafirin cluster. This sorghum MITE-like element displays considerable homology (68%) to the TATA-less promoter from the sorghum NADP-malate dehydrogenase gene and lesser similarity to the Tourist, Pilgrim and Batuta MITEs previously identified within the promoter from the maize Abp1 (auxin-binding protein) gene.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"36 1","pages":"107 - 114"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87553238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 13
Short Communication:Nucleotide Sequence of the Porcine 60S Ribosomal Protein L35 cDNA 短通讯:猪60S核糖体蛋白L35 cDNA的核苷酸序列
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109084472
T. Horibe, M. Kikuchi
{"title":"Short Communication:Nucleotide Sequence of the Porcine 60S Ribosomal Protein L35 cDNA","authors":"T. Horibe, M. Kikuchi","doi":"10.3109/10425170109084472","DOIUrl":"https://doi.org/10.3109/10425170109084472","url":null,"abstract":"The cDNA encoding the 60S ribosomal protein L35 was cloned from the porcine liver cDNA library using the N-terminal fragment coding region of human protein disulfide isomerase as the probe.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"30 1","pages":"443 - 445"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72999609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
M13 Cloning of Mung Bean Nuclease Digested PCR Fragments as a Means of Gap Closure Within A/T-rich, Genome Sequencing Projects 绿豆核酸酶酶切PCR片段的M13克隆及其在富含a / t基因组测序项目中的缺口闭合方法
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109084459
M. Quail
{"title":"M13 Cloning of Mung Bean Nuclease Digested PCR Fragments as a Means of Gap Closure Within A/T-rich, Genome Sequencing Projects","authors":"M. Quail","doi":"10.3109/10425170109084459","DOIUrl":"https://doi.org/10.3109/10425170109084459","url":null,"abstract":"Obtaining the complete DNA sequence of a genome is often not straightforward. After standard shotgun sequencing strategies have been employed there are often gaps remaining and these can be the most intractable regions, frequently containing repeat sequences, “uncloneable” sequences and/or regions of potential secondary structure or differential base composition. In genomes with a high A/T content, such as Plasmodium falciparum and Dictyostelium discoideum, solving these gaps is a particularly difficult problem as the sequences concerned are “fragile” and easily denatured, commonly uncloneable and have a paucity of good oligonucleotide priming sites. Reported here is a simple, yet reliable method for determining the sequence of A/T-rich gap-spanning PCR products. This method relies on the slippage of the specificity of mung bean nuclease so that it digests A/T-rich double-stranded DNA into a set of deletion fragments that can then be cloned into M13, sequenced and the original sequence assembled therefrom.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"111 1","pages":"355 - 359"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74486386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Molecular Cloning and Sequence Analysis of a Human Untranslated Alu-Containing RNA 人非翻译含铝RNA的分子克隆及序列分析
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109042055
S. Kwok, I. Daskal
{"title":"Molecular Cloning and Sequence Analysis of a Human Untranslated Alu-Containing RNA","authors":"S. Kwok, I. Daskal","doi":"10.3109/10425170109042055","DOIUrl":"https://doi.org/10.3109/10425170109042055","url":null,"abstract":"A cDNA, designated LNX1, has been identified by subtractive hybridization on the basis that it is expressed in normal human prostate but not in LNCaP cells. Sequence analysis revealed that it contained two Alu repetitive sequences but no long open reading frame. Hence, it belongs to a class of untranslated Alu-containing RNAs. LNX1 is expressed in most tissues. It is encoded by a single copy gene, which is localized on human chromosome 14.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"16 1","pages":"85 - 89"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74771700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparison of the Coding Sequence of the Platelet-activating Factor Receptor Gene in Three Species 三种动物血小板活化因子受体基因编码序列的比较
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109024998
Wensheng Yang, J. Diehl, W. Roudebush
{"title":"Comparison of the Coding Sequence of the Platelet-activating Factor Receptor Gene in Three Species","authors":"Wensheng Yang, J. Diehl, W. Roudebush","doi":"10.3109/10425170109024998","DOIUrl":"https://doi.org/10.3109/10425170109024998","url":null,"abstract":"The actions of platelet-activating factor (PAF, 1-0-alkyl-2-acetyl-sn-glycero-3-phosphocholine) are mediated through the PAF receptor (PAFr), which is a member of G-protein coupled superfamily of receptors. Our laboratory has data showing PAF has a role(s) in reproduction in domestic animals. Porcine, bovine and caprine PAFr genes cloned in BAC vectors were sequenced. Each PAFr coding sequence (cds) in these three species is 1029 nucleotides long and contains no intervening sequences. The deduced amino acid sequences (AAS) appear to contain seven putative transmembrane domains with an extracellular N-terminus in each species. There is a common glycosylation site at the fourth asparagine residue of N-terminus. In the tail of each deduced amino acid sequence, five to six serines and five threonine residues could act as phosphorylation sites, which play an important role in rapid receptor desensitization. The degree of homology of the three species is from 89 to 96% in nucleotide sequences (NtS), and 87–96% in identities (I) and 94–97% in positives (P) in amino acid sequences (AAS). The degree of homology with human, guinea pig, mouse and rat is 84–87, 82–88 and 83–88% in NtS, 77–84 (I) or 85–90 (P), 77–84 (I) or 85–90 (P) and 75–83 (I) or 87–90% (P) in AAS for caprine, bovine and pig, respectively. Southern blotting results suggested that the PAFr gene exists as a single copy in the genome of pig.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"1 1","pages":"239 - 251"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76164521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Characterization of a Processed Pseudogene of Human ΨHSP40 on Chromosome 2q32 人2q32染色体ΨHSP40加工假基因的鉴定
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109025006
M. Hata, K. Kagotani, K. Okumura, M. Seto, K. Ohtsuka
{"title":"Characterization of a Processed Pseudogene of Human ΨHSP40 on Chromosome 2q32","authors":"M. Hata, K. Kagotani, K. Okumura, M. Seto, K. Ohtsuka","doi":"10.3109/10425170109025006","DOIUrl":"https://doi.org/10.3109/10425170109025006","url":null,"abstract":"A pseudogene for the human Hsp40 gene has been characterized (ΨHSP40). The pseudogene sequence shows 90% similarity to the human Hsp40 mRNA at the nucleotide level. No introns were found in the region corresponding to the human Hsp40 cDNA, and two direct repeats flank this same region. Because of these features, the pseudogene can be classified as a processed pseudogene. ΨHSP40 was assigned to chromosome 2q32 by in situ hybridization. This is the first report of a pseudogene for a member of the DnaJ (Hsp40) family protein gene.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"1 1","pages":"293 - 297"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80076989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterisation of a cDNA Encoding Chick Eukaryotic Translation Initiation Factor-2β 鸡真核翻译起始因子-2β cDNA编码的鉴定
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109042051
Kyra J. Sneesby, D. Crane, W. Murrell
{"title":"Characterisation of a cDNA Encoding Chick Eukaryotic Translation Initiation Factor-2β","authors":"Kyra J. Sneesby, D. Crane, W. Murrell","doi":"10.3109/10425170109042051","DOIUrl":"https://doi.org/10.3109/10425170109042051","url":null,"abstract":"A full length cDNA for the β subunit of chick (Gallus gallus) eukaryotic translation initiation factor-2 is described. This cDNA was isolated by screening a chick cDNA library with a probe derived via differential display of developing chick heart tissue. Up-regulated expression of eIF-2β mRNA was confirmed by reverse Northern dot blot analysis. eIF-2β, together with eIF-2α and eIF-2γ, comprise subunits of a complex that promotes the binding of methionyl-tRNA to ribosomes during the initiation of protein translation. The nucleotide sequence of the chick eIF-2β cDNA predicts a protein of 334 amino acids that has 95%, 93%, 56% and 37% sequence identity with rabbit, human, drosophila and yeast eIF-2β, respectively. The deduced eIF-2p protein contains a number of functional motifs and domains consistent with the putative function of this protein; these include a potential C2-C2 zinc-finger binding domain, three polylysine regions, and three acidic regions.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"261 1","pages":"59 - 65"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91326275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Human BAC Contig Covering the Deleted Region in Pancreatic Cancer at 12q21 人类BAC序列覆盖胰腺癌12q21缺失区域
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109041339
E. Youssef, K. Kaneko, T. Yatsuoka, Y. Hayashi, M. Hoshi, A. Horii, T. Furukawa
{"title":"Human BAC Contig Covering the Deleted Region in Pancreatic Cancer at 12q21","authors":"E. Youssef, K. Kaneko, T. Yatsuoka, Y. Hayashi, M. Hoshi, A. Horii, T. Furukawa","doi":"10.3109/10425170109041339","DOIUrl":"https://doi.org/10.3109/10425170109041339","url":null,"abstract":"In sporadic human primary pancreatic cancer tissues, loss of heterozygosity is frequently observed in the 1-cM region between D12S81 and D12S1719 at 12q21. Loss of this chromosome arm is known to be associate with a poor prognosis in pancreatic cancer patients. Herein we report a complete contig of human bacterial artificial chromosome (BAC) clones covering the deleted region. The region was covered by 21 BAC clones in a minimum tiling path. The clones were confirmed to exist at 12q21 by fluorescence In situ hybridization. We identified novel 40 sequence tagged sites and mapped 10 expressed sequence tags in this region. The BAC contig reported here provides an avenue for determining the complete nucleotide sequence and mining putative tumor suppressor genes in the deleted region of pancreatic cancer at 12q21.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"28 1","pages":"541 - 546"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84239169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Tissue-specific Expression and Splicing of the Rat Polycystic Kidney Disease 1 Gene 大鼠多囊肾病1基因的组织特异性表达和剪接
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109084460
Hui Xu, Jianjun Shen, C. Walker, E. Kleymenova
{"title":"Tissue-specific Expression and Splicing of the Rat Polycystic Kidney Disease 1 Gene","authors":"Hui Xu, Jianjun Shen, C. Walker, E. Kleymenova","doi":"10.3109/10425170109084460","DOIUrl":"https://doi.org/10.3109/10425170109084460","url":null,"abstract":"Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic potentially lethal human disorder and the polycystic kidney disease 1 (Pkdl) gene is accounted for 85-90% of these cases. We have obtained rat Pkdl cDNA sequence and characterized splicing of Pkdl RNA transcripts in normal rat tissues. Our sequence data revealed a high conservation of the Pkdl gene between rat and other species and mapped rat Pkdl to chromosome 10 in “tail-to-tail” orientation to the tuberous sclerosis 2 (Tsc2) gene. Pkdl was found ubiquitously expressed in the normal rat tissues and the brain had a complex pattern of exon 12 splicing. A novel splicing variant lacking entire exon 31, which occurs in rat and mouse but not in humans, was also identified. As the rat appears to be a valuable model for investigating polycystic kidney disease, the characterization of the rat Pkdl gene will help facilitate future studies to elucidate the molecular mechanisms of cystogenesis in this animal model.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"18 1","pages":"361 - 366"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72674174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
ADP-Ribosylating Binary Toxin Genes of Clostridium difficile Strain CCUG 20309 艰难梭菌CCUG 20309菌株adp -核糖基化二毒素基因
DNA Sequence Pub Date : 2001-01-01 DOI: 10.3109/10425170109047564
Siao-Yun Chang, K. Song
{"title":"ADP-Ribosylating Binary Toxin Genes of Clostridium difficile Strain CCUG 20309","authors":"Siao-Yun Chang, K. Song","doi":"10.3109/10425170109047564","DOIUrl":"https://doi.org/10.3109/10425170109047564","url":null,"abstract":"The cdt genes that encode a binary ADP-ribosylating toxin in Clostridium difficile were first characterized from a toxigenic C. difficile strain CD196 in 1997. We report here C. difficile strain CCUG 20309 (ATCC 8864), a strain that produces toxin B but not toxin A, also carry a complete set of cdtA and cdtB genes. These genes were sequenced by cycle sequencing method. The 2 ORFs and the intergenic sequences of these 2 strains have a homology of 99.6 %. Interestingly, 9 extra bases were found within the cdtA gene of strain CCUG 20309 which do not affect the downstream region of the OW. Using the same homologous primers, the highly toxigenic reference strain VPI 10463 was found to carry only parts of the 2 ORFs while a nontoxigenic strain ATCC 8884 does not carry any of the cdt genes. Though it remains to be determined whether these genes are expressed, it is significant that strain CCUG 20309 contains the complete set of cdt genes. We speculate that the putative expressed proteins may contribute to pathogenesis, for example, enterotoxicity, of this unique strain of bacteria.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"2 1","pages":"115 - 120"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78516135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
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