小木虫 --- 500万硕博科研人员喜爱的学术科研平台
&&查看话题
请问如何判定是否为启动子序列呢？用什么软件分析？
欲克隆启动子，目前已克隆获得一段序列，请问如何判定是否为启动子序列呢？用什么软件分析？
plantcare？place？谢谢大神们的帮助！急急急急急。。。。。。
研究生必备与500万研究生在线互动！
扫描下载送金币
浏览器进程
打开微信扫一扫
随时随地聊科研君，已阅读到文档的结尾了呢~~
扫扫二维码，随身浏览文档
手机或平板扫扫即可继续访问
杂色鲍肌动蛋白启动子的克隆与序列分析
举报该文档为侵权文档。
举报该文档含有违规或不良信息。
反馈该文档无法正常浏览。
举报该文档为重复文档。
推荐理由：
将文档分享至：
分享完整地址
文档地址：
粘贴到BBS或博客
flash地址：
支持嵌入FLASH地址的网站使用
html代码：
&embed src='/DocinViewer-4.swf' width='100%' height='600' type=application/x-shockwave-flash ALLOWFULLSCREEN='true' ALLOWSCRIPTACCESS='always'&&/embed&
450px*300px480px*400px650px*490px
支持嵌入HTML代码的网站使用
您的内容已经提交成功
您所提交的内容需要审核后才能发布，请您等待！
3秒自动关闭窗口怎么分析一段序列的启动子和调控区有软件吗(序列,调控区,启动子,基因) - DNA技术 - 生物秀
标题: 怎么分析一段序列的启动子和调控区有软件吗(序列,调控区,启动子,基因)
摘要: [怎么分析一段序列的启动子和调控区有软件吗(序列,调控区,启动子,基因)] 各位大侠，您好!我最近分析一个序列，我需要这个序列的启动子序列，最好能分析出调控区（如果有的话），他的序列如下： 1 actccgaact cctccgaatc accgccggcc tcgccgtcga catggactga agcacttcag 61 ccagcccggt ccgaaaccac tcagacgtgc gtccacctat agttggacgc accatgtgca 121 ct 关键词:[序列 调控区 启动子 基因 析出 启动子序列]……
各位大侠，您好!我最近分析一个序列，我需要这个序列的启动子序列，最好能分析出调控区（如果有的话），他的序列如下： 1 actccgaact cctccgaatc accgccggcc tcgccgtcga catggactga agcacttcag 61 ccagcccggt ccgaaaccac tcagacgtgc gtccacctat agttggacgc accatgtgca 121 ctgcaaccag gaccccggcc ggcaaccact ggcgtcgacg gcacgtagat ctgtgccgca 181 ccgacgcatg tctgtgtatg ccgagcgcag tcacctcgac cacaccgcac acctcgagtt 241 ccagccggag agttcccgtt gtctgacaag ccgaatgccg tttccagcca caccaccccc 301 gacgtccccg aagtagcggc gacgcccgag ttgtccaccg gcatctgcgc cggtgactac 361 cgcgctgcgc ttcgccgcca ccccgccggt gtcaccgtcg tgaccctcga ttcgggtacc 421 ggcccggtgg gtttcaccgc cacctcgttc tcgtccgtct ccctcgagcc gccgctcgtc 481 tcgttcaaca tcgcggagac gtcgtcgagc atcaatgcac tcaaggcagc cgagtccttg 541 gtgatccacc ttctcggcga acatcagcag catctggccc agcgctttgc gcgtagtgcc 601 gatcagcgtt ttgcagacga gtcactgtgg gcagtgctcg acaccgggga accggtgctg 661 cacggcaccc ccagctggat gcgcgtcaag gtcgaccagc tgatccctgt cggcgaccac 721 acgctggtca tcggactcgt cacgcgggtt cacgccgaag aagacgacga atccgctgcc 781 gcgccgctgc tctaccacga gggcaagtac taccgcccga ctccgttagg tcaatagaca 841 actgtgcgcc tttattaacc gcccgcggtt aataaaggcg cacagcaagt tagagcgcta 901 cgtacttggt atcgagatac tcgtcgatac cctcggttcc gccttcacgg ccgaa基因的CDS是259--837，前面是否存在启动子？不知道怎么分析请高手指教！谢谢！！或者那位有比较好的分析软件不知道能否提供！
回复这个序列前面有250多个BP的序列，是不是启动子肯定存在这个区域？我如果直接克隆了这一段区域，是不是可以直接启动表达后面的酶？回复顶呀！我也需要相关的解答，请各位大侠帮帮我们俩，谢谢啦。回复就是阿，现在还没有人回答啊，是不是下午的时候一般很少有人来bbs啊回复这儿有一个关于启动子的分析方法的例子：Promoter search. The PRV genome sequence was submitted to the Berkeley Drosophila Genome Project’s Neural Network Promoter Prediction program, a eukaryotic (human) core promoter search engine (http://www.fruitfly.org/seq_tools/promoter.html) (59). The initial search was performed at very high stringency (cutoff score of 0.99 out of 1.00). The program returned high-scoring core promoters (50-bp-long fragments) along with a predicted transcription start site (TSS). The core promoters found in this search and all later searches were examined for the presence of a TATA box consensus using the TRANSFACFind search engine (http://motif.genome.ad.jp/) (34). The stringency for the TATA box searches was relatively low, with a cutoff score of 65 (out of 100). Of 98 high-scoring core promoters, 52 predicted transcripts able to encode 46 of the 72 known PRV ORFs and 1 predicted the large latency transcript (LLT). To find promoters for the remaining 26 ORFs, a medium-stringency promoter search (cutoff, 0.80 out of 1.00) was performed on the 350-bp DNA fragments upstream of the ORFs, followed again by a search for a TATA box consensus. This medium-stringency search yielded promoter predictions for 21 more ORFs, but four of these promoters contained no TATA box and were discarded. Of the remaining nine ORFs without assigned promoters (ORF1.2, UL33, UL36, UL23, UL11, UL8.5, UL6, and the major and minor forms of US3), UL6 and the two US3 isoforms had well-mapped TSS (51, 74). Successful low-stringency searches (cutoff, 0.40 out of 1.00) for promoters matching these TSS left six ORFs without assigned promoters. For each promoter, the predicted TSS location was noted and compared to experimentally determined TSS from published reports, if available. In the case of S1 nuclease mapping, the TSS was calculated from the reported DNA size, and the error on this measurement was assigned an arbitrary value of 5%. The minimal mRNA size, excluding the poly(A) tail, was calculated from the predicted TSS and poly(A) site of each gene. The level of DNA identity between the Kozak consensus sequence (GCCGCCRCCATGG [44]) and the 13 nucleotides around the initiator ATG of each was measured. The predicted TSS for each gene was used to calculate the expected length of the 5" UTR. 全文见： http://jvi.asm.org/cgi/content/full/78/1/424?view=full&pmid=回复要看你的序列是什么物种，不同物种promoter的特点不同， 我用预测植物的软件帮你查了一下，好像没有TATA回复sometime promoter can be as long as 2kb, so I don"t think 250bp is a good promoter回复1 网上的软件有很多，大多数dxy里都有描述，你自己找找。2 真核的启动子变化的范围非常大，250bp内是否存在启动子，能否表达出你的酶，要做实验才知道，3 建议你克隆长一点的序列，如2-3kb，在做截断体，你就知道启动子在什么地方了。回复BCR_TCR, your suggestion
is a project for a PhD student回复dylanboyu, this gene has been used in transgenic microorganism, you just need to copy its promoter from the published construct, it should be able to drive the expression of Rhodococcus erythropolis NADH-dependent FMN oxydoreductase (dszD) gene, from which your sequence originally comes回复BCR_TCR, your suggestion is a project for a PhD studenthahaIT is my project.回复wgp222,非常感谢你得建议，我现在文献中没有查到提及启动子的问题，我需要这个启动子启动表达其他的酶。你的意思是我直接克隆这个前面的片断就可以？谢谢回复please blast your sequence in DDBJ database and you will get two hits indicating a transgenic microorganism with this gene. Analysis the resulting sequence carefully to identify the promoter region. If it was not included in the submitted sequence , then refer to the original paper or ask for the plasmid directly from the authors回复谢谢wgp222， 我已经看到了这两个序列了，我看了一下都是位于dszD基因CDS的后面，肯定不是我要的启动子序列吧。看来只有向作者询问了。多谢！回复这儿有一个关于启动子的分析方法的例子：Promoter search. The PRV genome sequence was submitted to the Berkeley Drosophila Genome Project’s Neural Network Promoter Prediction program, a eukaryotic (human) core promoter search engine (http://www.fruitfly.org/seq_tools/promoter.html) (59). The initial search was performed at very high stringency (cutoff score of 0.99 out of 1.00). The program returned high-scoring core promoters (50-bp-long fragments) along with a predicted transcription start site (TSS). The core promoters found in this search and all later searches were examined for the presence of a TATA box consensus using the TRANSFACFind search engine (http://motif.genome.ad.jp/) (34). The stringency for the TATA box searches was relatively low, with a cutoff score of 65 (out of 100). Of 98 high-scoring core promoters, 52 predicted transcripts able to encode 46 of the 72 known PRV ORFs and 1 predicted the large latency transcript (LLT). To find promoters for the remaining 26 ORFs, a medium-stringency promoter search (cutoff, 0.80 out of 1.00) was performed on the 350-bp DNA fragments upstream of the ORFs, followed again by a search for a TATA box consensus. This medium-stringency search yielded promoter predictions for 21 more ORFs, but four of these promoters contained no TATA box and were discarded. Of the remaining nine ORFs without assigned promoters (ORF1.2, UL33, UL36, UL23, UL11, UL8.5, UL6, and the major and minor forms of US3), UL6 and the two US3 isoforms had well-mapped TSS (51, 74). Successful low-stringency searches (cutoff, 0.40 out of 1.00) for promoters matching these TSS left six ORFs without assigned promoters. For each promoter, the predicted TSS location was noted and compared to experimentally determined TSS from published reports, if available. In the case of S1 nuclease mapping, the TSS was calculated from the reported DNA size, and the error on this measurement was assigned an arbitrary value of 5%. The minimal mRNA size, excluding the poly(A) tail, was calculated from the predicted TSS and poly(A) site of each gene. The level of DNA identity between the Kozak consensus sequence (GCCGCCRCCATGG [44]) and the 13 nucleotides around the initiator ATG of each was measured. The predicted TSS for each gene was used to calculate the expected length of the 5" UTR. 全文见： http://jvi.asm.org/cgi/content/full/78/1/424?view=full&pmid=欢迎光临动物医学/动物科学专业yinhp01正在申请动物医学/动物科学专业斑竹,请支持，谢谢回复启动子序列的预测一定，也只能根据物种进行。有的启动子很长有几个k，而有的只有几个碱基（好像是贾第虫还是阴道毛滴虫由一个基因的启动子）。回复据我所知,启动子预测的软件虽有不少,如Genescan等等。但是预测启动子都不是100%准确, 而且往往会告诉你一大堆可能的启动子。因此预测的结果是没有用的,至多只能指导,但更可能是误导实验因而不能完全相信和依赖软件,还是要通过头脑加实验。对于已经有同源序列的序列, 可以通过BLAST来找启动子的位置,对于未知序列, 预测的结果正确与否还必须用实验证实, 也就是上面BCR_TCR所提出的方法—截断或缺失突变体, 但这是一个非常费时费力的过程。
相关热词：
生物秀是目前国内最具影响力的生物医药门户网站之一，致力于IT技术和BT的跨界融合以及生物医药领域前沿技术和成功商业模式的传播。为生物医药领域研究人员和企业提供最具价值的行业资讯、专业技术、学术交流平台、会议会展、电子商务和求职招聘等一站式服务。
官方微信号：shengwuxiu
电话：021-