[Genome] Annotation-confused

[Ewan Birney]

On 4 Dec 2007, at 16:23, Chandrashekara Mallappa wrote:

> Hi I am trying to clone CHD2 gene from mouse. As for as my  
> knowledge goes
> full length cDNA of this gene is never cloned. This gene is  
> annotated to
> have 6 exons and a transcript length of 739bp in Ensemble and the  
> same gene
> is annotated to have more than 25 exons with a transcript length of  
> 5794bp
> in NCBI and UCSC genome browser. It is very important for me to  
> clone this
> gene for my research. So please guide me about what transcript  
> should I
> consider...Thanks a lot for your time and help.
>

Looking into this, the NCBI/UCSC model looks far better. The Ensembl  
model has
broken the gene into two portions due to two partial cDNAs which have  
not
been linked together. This is a split/merge decision therefore that we
(Ensembl) called incorrectly.


I'm also going to forward this to the Ensembl gene builders to look  
into this
case to work out if we could have called it better from the evidence.

>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome