【在 B*******e 的大作中提到】 : i5-2400 + Intel H67 Micro ATX motherboard + 8GB GSkill Ripjaws DDR3 1333, : 用集成的显卡, windows 7 ultimate 64 bit : 大的网页上下翻动的时候声音有时候会有迟顿, 还有几次看netflix 的时候蓝屏死机 : 。 我感觉至少是显卡driver 还有bug。 : 主板上5 个SATA 接口( 3 SATA II, 2 SATA III), 不够用, 而且没有IDE 接口。 用 : SATA 光驱还要占SATA 口。 : 现在用了一块pci-e 的sata/ide 接口卡, 正在排查其他的蓝屏是否跟这块卡有关。 : 现在1155 的主板一般就5-6 sata 接口, 有ide 接口的也很少。
w*n
9 楼
1. a) It is not surprising that a gene has multiple transcription start sites. b) You can use the Kozak sequence to PREDICT which ATG is likely to be used as translational start site. 2). This looks odd.Are you sure the direction of the gene you look at is correct? Because in the kit, there use random oligo to synthesize cDNA, followed by gene-specific primer for PCR. Good luck!
For 5'RACE, choose the longest one. Short ones may be degenerated mRNA, although the longest one is most likely degenerated too. ATGATGATG is a way to start an effective translation.
谢谢wenqian and chamgrape。 1.如果gene有很多不同的转录起始点,那这些都是capped的吗?如果miss掉了ATG那岂 不是造成能量的浪费了吗? 2.direction 可以确定是对的,不太明白怎么可以方向不对,因为kit里面是forward primer, you have your gene specific primer as reverse primer. pubmed里那么多的gene都是primer extension得到的全序列吗?
a*e
18 楼
一堆250G小硬盘,机箱够大
【在 f*****t 的大作中提到】 : 5个sata都不够用?你都接啥了?
m*o
19 楼
谢谢Ka84.the first 2 ATG do is together like ATGATG, the third ATG is 3 AA downstream. so I check the sequence, maybe the second is most strong one.
Just my personal opinions for your reference. Maybe I am wrong. 1. If it is up to me, I will subclone the longest fragment and fuse it to the upstream of a reporter gene, then mutate the three respective ATG to see if there is any difference. Ususlly, the first ATG is dominant in transcription. 2. Is it possible that your GSP acutally recognize a sequence in the reverse orientation and there is a transcript generated in the reverse orientation? There maybe duplicated sequence in genome.
Thanks, whitesand. 1. We are thinking of doing that way. But most plasmid has a strong promoter , I am guessing whenever they meet ATG they all will transcribe. The other possible is we clone this gene's own promoter and mutate each of the 3 ATG to see. There will be a lot of work and now I do not have any idea how long the promoter will be. 2. If my GSP recoginze a sequence in the reverse orientation, why it transcript the complete exon not part of it? I am thinking of what wenqian said because the kit use random primer,it is possible the second structure of the mRNA is speicial and make the cDNA from the exon 5 very near exon2 and by some unknown reason they connect together . I am planning to design primer at exon5, 6, and 2 to do RTPCR and see what I got. To Juzbox,My 1st ATG do not have -3A and +4G, the 2nd one because is ATGATG together so it has -3A but no +4G. the 3rd ATG which is 2 amino acid away has -3A but no +4G. looks I should considering the 2nd ATG.
转录的起始位点: 如果有TATA BOX, 很可能是single transcription start site, 但是大多数真核gene都没有TATA BOX,所以都是有好几个TSS clusters,每个TSS cluster里面的TSS们大概在200bp这么大的范围之内 如果有几个相聚较远的TSS cluster,那么这个gene有可能有不同的mRNA species,但 是还是要做实验去验证 是不是应该针对每一个mRNA species,再单独考虑start codon 的问题? however... 貌似很多gene都有不同的mRNA species,但是不一定这些mRNA species都 有功能,更不一定都会translate成蛋白 你说你的目的是得到一个蛋白的short form, 你expect short form和wild type的区别是什么? after all, if there is nothing new about this short form, you cannot publish , right? 是不是可以把可能的short form的ORF都表达出来,然后和wild type做对比?
Philipli,十分感谢你的建议。 做short form 的目的是:wild type 和short form是在不同的组织中表达。以前认为 这个gene only expressed in one specific tissue A, but after the lab got the knock out mice, it has different phenotype. We trying to figure out the mechanism if these related with the specific tissue A or the gene also expressed in other tissue but at short form. 我现在是打算把这个short form最长的ORF表达出来看看,但是老板感兴趣的那个组织 我没有检测到,所以还会继续race. 还有问题没有彻底明白: 1 现在这个short form的TSS,我测到的是大概90bp的差别,是不是可以说是一个TSS cluster? 2 你说每个cluster里面有大概200bp的差别,记得看过一篇文章说短的5UTR,可能就意 味着很强的表达,那如果有200bp的差别,那细胞岂不是有很多mRNA就miss掉了ATG,那 岂不是一种浪费? 3 mRNA species 是不是就指不同的tss 而且会导致产生不同长度的蛋白,和 alternative splicing 是两个概念吗? 谢谢!
c*r
37 楼
有证据证明这个short form存在吗?
the
【在 m***o 的大作中提到】 : Philipli,十分感谢你的建议。 : 做short form 的目的是:wild type 和short form是在不同的组织中表达。以前认为 : 这个gene only expressed in one specific tissue A, but after the lab got the : knock out mice, it has different phenotype. We trying to figure out the : mechanism if these related with the specific tissue A or the gene also : expressed in other tissue but at short form. : 我现在是打算把这个short form最长的ORF表达出来看看,但是老板感兴趣的那个组织 : 我没有检测到,所以还会继续race. : 还有问题没有彻底明白: : 1 现在这个short form的TSS,我测到的是大概90bp的差别,是不是可以说是一个TSS