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very large intron in c. elegans

Mr V. Schoenfeld DOM vs10005 at crc.ac.uk
Wed Dec 20 05:00:49 EST 1995

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 


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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