Retrieve upstream non-coding sequenses of genes from Ensembl or phytozome

Question

[zizigolu]

I don't know how I can download 2 kb from 5"UTR of my genes

Can you help me?

[Ashutosh Pandey]

Have you tried searching for similar posts that have already been answered ? Type "upstream sequence" in the search box and then go through some of the posts.

[zizigolu]

thanks i will try

[Ashutosh Pandey]

I just came across your older question and have answered it there (retrieval of upstream non-coding sequences).

Answer 1

[Emily]

Have you looked at BioMart in Ensembl Plants?

[zizigolu]

Yes I'm trying there since last night

Thank you

[zizigolu]

Hello

May you please tell me how I can get the Ensembl gene ID of my gene (TGL1)

[Ashutosh Pandey]

https://www.google.com/search?q=TGL1+ENSEMBL+GENE+ID

Go to first page and check for ENSEMBL version.

[zizigolu]

Sorry I was shy to ask you again then I asked Emily

In the page you proposed I just found SGD;Acc:S000001623

but for example accidentally for IDS-001 in human, there was Gene IDS: ENSG00000010404

then I got confused why there is not Ensembl gene ID for my gene

Anyway excuse me

[Ashutosh Pandey]

Hey Sarah, Please dont feel shy while asking questions :-) There are different Gene IDs used by NCBI, Ensembl and Saccharomyces Gene Database for yeast genes. So your genes of interest will have at least three different IDs depending on your source. This is the page I was referring to http://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?g=YKL140W;r=XI:180779-182425;t=YKL140W

TGL1 is the SGD id

YKL140W.1 is the Ensembl ID.

[zizigolu]

really thanks