Isoforms of a gene!! - how to find all isoforms of a gene using bioinfo tools?! (Feb/10/2010 )
I m searching for isoforms of SAMDC gene in Lycopersicon(Tomato).....
I searched genes in NCBI but I m not getting all the isoforms of this gene...
I m designing primers for this gene n want to consider all isoforms present in Tomato....as i will be disrupting this gene function in this plant....... to maximize the disruption phenotype all isoforms should be disrupted..... so I need to design such a primer that can ampilfy a region of this gene ..which can be used to disrupt the gene function by silencing it....
plz suugest what tool can be userd to locate all the isoforms n then getting most conserved region out of those all obtained...
-amazig2bSJ-
amazig2bSJ on Feb 10 2010, 09:14 PM said:
I m searching for isoforms of SAMDC gene in Lycopersicon(Tomato).....
I searched genes in NCBI but I m not getting all the isoforms of this gene...
I m designing primers for this gene n want to consider all isoforms present in Tomato....as i will be disrupting this gene function in this plant....... to maximize the disruption phenotype all isoforms should be disrupted..... so I need to design such a primer that can ampilfy a region of this gene ..which can be used to disrupt the gene function by silencing it....
plz suugest what tool can be userd to locate all the isoforms n then getting most conserved region out of those all obtained...
I searched genes in NCBI but I m not getting all the isoforms of this gene...
I m designing primers for this gene n want to consider all isoforms present in Tomato....as i will be disrupting this gene function in this plant....... to maximize the disruption phenotype all isoforms should be disrupted..... so I need to design such a primer that can ampilfy a region of this gene ..which can be used to disrupt the gene function by silencing it....
plz suugest what tool can be userd to locate all the isoforms n then getting most conserved region out of those all obtained...
... I'm not sure if it's got plant genetics in there (I'm a study human genes - I just had a quick look and I'm still none-the-wiser!) ... but try Ensembl (www. ensembl.org) - it will give you all the different transcripts of the gene and how verified they are using different programs/tools etc... It certainly works well for me... I hope it has some plants in there!
Good luck
-DrAnt1-
maybe www.tigr.org has some tomato databases?
-toejam-