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very large intron in c. elegans

Ken Howe howe at DARWIN.UCSC.EDU
Wed Dec 20 18:57:00 EST 1995

although kilobase introns in metazoans are common, trypanosomes splice 
using trans-splicing, so introns are not necessarily contiguous.  In 
other words, your gene of interest may indeed span several tens of 
kilobases, separated by non-coding sequence, but this intervening 
region is probably not a continuous intron and your exons with 
associated intron sequences are probably transcribed separately.  The 
exons are then joined in an intermolecular splicing reaction in vivo.

Hope this helps.

Ken Howe
"the onions expressed here are my own"

On 20 
Dec 1995, Mr V. Schoenfeld wrote:

> Date: 20 Dec 1995 10:00:49 GMT
> From: Mr V. Schoenfeld <vs10005 at crc.ac.uk>
> To: methods at net.bio.net
> Subject: Re: very large intron in c. elegans
> In article <marcvdc.148.001E43DB at lmb1.rug.ac.be>, marcvdc at lmb1.rug.ac.be writes:
> > Dear Netters,
> > 
> > 
> > First of all, I am not at all familiar with the c. elegans genome.
> > 
> > However, I found protein homology between a mammalian cDNA and a c. elegans 
> > cosmid by doing a blast search. Now I am wondering wether this is significant. 
> > There are already several open reading frames known in this c. elegans cosmid 
> > but they are quiet small. My cDNA has homology over 40.000 bp of the cosmid, 
> > implicating that I have putative introns of 5000 kb and 20.000 kb. Moreover, 
> > this putative c. elegans cDNA would overspan several characterised c. elegans 
> > cDNA's.  
> > 
> > Does anyone know wether this would be possible in c.elegans?
> > 
> > 
> > Please also reply to my personal e-mail address.
> > 
> > 
> > 
> > Marc
> > 
> > Marcvdc at lmb1.rug.ac.be
> It sounds very strange to me! Are you 100% sure your cDNA is homologous to most of the cosmid?
> Do you know this by hybridisation only? The worm genome is full of gene clusters, which makes it
> a very useful tool to identify gene familes (see the recent stories about smell/taste receptors).
> Is your cDNA part of a gene family? How much do you know about it?
> Maybe you could shotgun clone the whole cosmid and sequence about 30 cDNA positives, to see
> if you get different homolgues of your gene. I would be very careful with hybridisation results
> from mammalian/C.elegans species jumps. The worm genome is so AT rich that an AT rich probe picks up
> loads of crap. You said there are several ORF characterised in this cosmid, are they mapped?
> Does the map leave any room for your gene? I don't think there's been any ORFs found in introns
> in the worm, but please could somebody from that filed confirm this!
> Good luck 
> Vince
> -----------------------------------------------------------------
> Vincent Schoenfeld
> Graduate Student
> University Department of Medicine
> Addenbrooke's Hospital
> Cambridge CB2 2QQ, UK
> vs10005 at med.cam.ac.uk          | Phone: (0223)402436/336853
>                                | Fax:   (0223)21136
> 'If we knew what we were doing, it would not be called research'
> -----------------------------------------------------------------

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