[Genome] question about UCSC 'Human ESTs Including Unspliced' track

[Kayla Smith]

Hello Xu Jerry,

Thank you for your close reading of the EST description page.

There are many genes with introns longer than 200kb.  In fact it's 
possible to use the Table Browser to make a Custom Track of just the 
introns of the UCSC Genes track, if you're interested in looking at 
introns.

Unspliced ESTs in the browser are not "pre-mRNAs".  They are ESTs where 
we don't find any canonical splice sites when we align the EST.  These 
could be single exon ESTs that will never be spliced, DNA contamination, 
or possibly even "pre-mRNAs" that got caught before splicing that are 
included the genbank data set.

Meanwhile, if you do find any data on our website that seems 
questionable to you, feel free to send us specific examples and we can 
look into them.  More often than not it's a case of us simply displaying 
what is available from genbank (we don't curate here!), but sometimes it 
is a bad alignment or filter.

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

xu_jianzhen wrote:
> Dear Genome Help,
>   I've a question about UCSC 'Human ESTs Including Unspliced' track.The methods of this track said,"To generate this track, human ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align".However,to my knowledge of biology,i do not think there are too much such long pre-mRNA that is more than 750kb, so my question is when I find a unspliced EST more than 200kb,does it mean this is a false positive?
>  
>  
> Thank you all!
>  
>  
>  
> Xu Jerry
> GIBH,CAS 
> 
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