t********9
发帖数: 536 | 1 各位大侠，我对基因方面懂得不多，现在有一个基因方面的问题向大家请教。我想找一
个基因tag-24 的promoter sequence，这个基因是c.elegans中的。下面是有关的信息
（包括了tag-24 的一个上游基因和一个下游基因）。请大侠帮忙算一下这个promoter
sequence 是多长呢？请讲讲是怎么算的。（因为tag-24 给的是complement, 我不知道
怎么办）（就按tag-24 得第一个isoform 为例吧。）多谢了！！！
gene 5604536..5609082
/locus_tag="F14D12.1"
/db_xref="GeneID:180829"
/db_xref="WormBase:WBGene00017463"
mRNA join(5604536..5604550,5604616..5604684,5604731..5604985,
| a***e
发帖数: 1010 | 2 go to wormbase.org
search tag-24
go to "location", click the picture, "Showing 2.515 kbp from X, positions 5,
608,905 to 5,611,419"
in "landmark or region", change "X:5608905..5611419" to "X:5608905..5613419"
In "reports & analysis", change to "download sequence files", click "go"
it will give you the 2k promoter plus the whole gene sequence. | a***e
发帖数: 1010 | 3 and for "tag-24", the upstream gene is 20kb away. | t********9
发帖数: 536 | 4 Thanks a lot Arche!!!
Could you let me know why I need to change "X:5608905..5611419" to "X:
5608905..5613419"in "landmark or region"?
5,
5613419"
【在 a***e 的大作中提到】
: go to wormbase.org
: search tag-24
: go to "location", click the picture, "Showing 2.515 kbp from X, positions 5,
: 608,905 to 5,611,419"
: in "landmark or region", change "X:5608905..5611419" to "X:5608905..5613419"
: In "reports & analysis", change to "download sequence files", click "go"
: it will give you the 2k promoter plus the whole gene sequence.
| t********9
发帖数: 536 | 5 Arche. I think I know why I need to change the number.This way it will give
me 2 kb promoter sequence. Thanks!!!
However, do you or anyone know how to figure out the promoter sequence based
on the information from pubmed.com as I pasted in the first message?
【在 t********9 的大作中提到】
: Thanks a lot Arche!!!
: Could you let me know why I need to change "X:5608905..5611419" to "X:
: 5608905..5613419"in "landmark or region"?
:
: 5,
: 5613419"
| t********9
发帖数: 536 | 6 ahche, why I can not find the tag-24 gene sequence from the "2k promoter
plus the whole gene sequence"? tag-24 gene starts with atgtggaaccttaactg.....
5,
5613419"
【在 a***e 的大作中提到】
: go to wormbase.org
: search tag-24
: go to "location", click the picture, "Showing 2.515 kbp from X, positions 5,
: 608,905 to 5,611,419"
: in "landmark or region", change "X:5608905..5611419" to "X:5608905..5613419"
: In "reports & analysis", change to "download sequence files", click "go"
: it will give you the 2k promoter plus the whole gene sequence.
| a***e
发帖数: 1010 | 7 you can download the cosmid sequence to your computer, and then according
to the position of tag-24 on that cosmid, you can select out the sequence
you need.
however, I never did that way. I prefer wormbase.
give
based
【在 t********9 的大作中提到】
: Arche. I think I know why I need to change the number.This way it will give
: me 2 kb promoter sequence. Thanks!!!
: However, do you or anyone know how to figure out the promoter sequence based
: on the information from pubmed.com as I pasted in the first message?
| a***e
发帖数: 1010 | 8 change that to "reverse complementation" first.
atgtggaaccttaactg.....
【在 t********9 的大作中提到】
: ahche, why I can not find the tag-24 gene sequence from the "2k promoter
: plus the whole gene sequence"? tag-24 gene starts with atgtggaaccttaactg.....
:
: 5,
: 5613419"
| t********9
发帖数: 536 | 9 arche, thank you very much! I found it.
I really appreciate your help!!!
【在 a***e 的大作中提到】
: change that to "reverse complementation" first.
:
: atgtggaaccttaactg.....
|
|
