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5’UTR与基因表达的关系
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【求助】外显子、3‘-UTR及polyA_site 的区别
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这个帖子发布于3年零9天前，其中的信息可能已发生改变或有所发展。
请问这个基因“”哪部分属于3’-UTR？polyA_site之后的那段外显子能否通过cDNA扩增出来？
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The CDS of mouse SOX9 mRNA is located at 376-1899 and its poly A signal is located at
. The mouse SOX9 mRNA 3 ' UTR should be in
(the third exon from ). The 3' UTR after mouse SOX9 mRNA poly A site is in .
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mpark The CDS of mouse SOX9 mRNA is located at 376-1899 and its poly A signal is located at
. The mouse SOX9 mRNA 3 ' UTR should be in
(the third exon from ). The 3' UTR after mouse SOX9 mRNA poly A site is in . 请问“poly A site’是什么意思呢？另外，为什么离最后的终止位点那么远呢？此外，3‘UTR是否都包括呢？
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From It is said: &Polyadenylation is a process that takes place after transcription termination. It involves cleavage of the
new transcript (mRNA), followed by template-independent addition of adenines at its newly synthesized 3’ end. The
cleavage site is called polyadenylation site or, in short, poly(A) site. Polyadenylation is considered to be part of the larger
process of producing mature mRNA for translation.&You have raised very interesting questions. The answer is dependent on the research you are going to perform. You need to run luciferase assay together with regulations by cytoplasmic polyadenosine polymerase and Cytoplasmic polyadenylation element binding protein (CPEB) and some specific miRNA to characterize SOX9 mRNA 3'UTR functions.Try to download the attachment for more details.
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mpark From It is said: &Polyadenylation is a process that takes place after transcription termination. It involves cleavage of the
new transcript (mRNA), followed by template-independent addition of adenines at its newly synthesized 3’ end. The
cleavage site is called polyadenylation site or, in short, poly(A) site. Polyadenylation is considered to be part of the larger
process of producing mature mRNA for translation.&You have raised very interesting questions. The answer is dependent on the research you are going to perform. You need to run luciferase assay together with regulations by cytoplasmic polyadenosine polymerase and Cytoplasmic polyadenylation element binding protein (CPEB) and some specific miRNA to characterize SOX9 mRNA 3'UTR functions.Try to download the attachment for more details.按照您提供的文献，我找了找文献中提到的 calcitonin和CGRP基因（见链接“http://www.ncbi.nlm.nih.gov/nuccore/X02330.1”）以及我要找的基因（见链接“http://www.ncbi.nlm.nih.gov/nuccore/NM_”）是否可以得出这样的结论呢：1、在nucleotide数据库中，寻找到的基因，就单基因而言，CDS区之后的就是3‘UTR；多基因会有显示。2、及可以包含在3'UTR，也可以不包含；如果是包含在3’UTR至内的话，不一定非的在末尾，也可以靠前一点，有远有近。3、在构建某个基因3'UTR全长载体时，可以用Olig（dT）反转录的cDNA直接进行扩增。
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The three conclusions are nothing to do with your project.You need to prepare high quality of RNA from cell lines that you have detectedthe gene expression. Try to run reverse transcription and PCR amplification ofthe first-stranded cDNA with different primers covering the whole mRNA 3’UTR.You may need to clone them and sequence them for preparing functional assay forthese gene mRNA 3’UTR.
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mpark The three conclusions are nothing to do with your project.You need to prepare high quality of RNA from cell lines that you have detectedthe gene expression. Try to run reverse transcription and PCR amplification ofthe first-stranded cDNA with different primers covering the whole mRNA 3’UTR.You may need to clone them and sequence them for preparing functional assay forthese gene mRNA 3’UTR. 其实，我想寻找这个基因是否是某个miRNA的作用靶点，按理说只构建它的3‘UTR至报告基因载体上就行。但是在nucleotide寻找到该基因的mRNA里看到了这些信息，由此也产生了这些疑问。楼上能否明确回答我的这些疑问，不胜感激！
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In gene bank data base, a gene with nucleotide sequences is shown, displaying the DNA unit or mRNA unit. It is usually not shown multiple gene sequences though some mRNA can be produced in alternative splicing. It is right that the mRNA 3' UTR is emerged following the mRNA's CDS.Poly A site and poly A signal are quite complicated in mammalian genes. Poly A signal and the poly A sites should be within a gene mRNA 3' UTR. At present time, Support Vector Machine (SVM) models have been developed for predicting poly(A) signals in a DNA sequence using 100 nucleotides, each upstream and downstream of this signal. Dr. Firoz Ahmed of Institute of Microbial Technology, India, in a 2009 paper said: &In human, ~93% of all mRNAs have AAUAAA or single nucleotide variants of this motif as poly(A) signals. The most abundant among this group are AAUAAA and AUUAAA, which constitute ~53% and ~17%, respectively. In human, poly(A) signals are located 15-30 nucleotides (nt) upstream and GU/U-rich elements are located 20-40 nt downstream of the cleavage sites. The cleavage site is characterized by the presence of different cis-regulatory elements in its proximity.&The whole 3' UTR of some gene transcripts, such as lncRNA or ceRNA, different from mRNA, may be beyond poly A tracks, therefore, poly dT oligonucleotides used as primer for first stranded cDNA reverse transcription may not be appropriate for cloning the entire transcirpt 3' UTR.
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mpark 确实是高手啊。对基因结构的分析真的很透彻！
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