[Genome] Segment duplication on zebrafish chr 16?

[Brooke Rhead]

Hello Vince,

I see the two adjacent sets of the genes you mention on the danRer5 
assembly, but I can't really tell you if the duplication is "real" or not.

The RefSeq Genes and Human Proteins (mapped by chained tBLASTn) tracks 
were both made here by aligning sequence to the zebrafish assembly. 
However, the assembly of the genomic sequence was done at Sanger:
http://www.sanger.ac.uk/Projects/D_rerio/Zv7_assembly_information.shtml

I see this note on their site:

"This is still a *preliminary* assembly and there are a number of points 
to remember. The regions of the assembly covered by WGS contigs are of 
lower quality. In general regions which are highly variable do not form 
clusters since they are quite likely from different haplotypes. This 
also affects the generation of the physical map resulting in assembly 
dropouts and false duplications. In this assembly special attention has 
been paid to these issues and over 200 Mb of duplicated sequence has 
been removed compared to Zv6."

Another thing to note is that our mapping of the genes you mention 
(BC092825, for instance) is only duplicated in the most recent zebrafish 
assembly (Zv7/danRer5).  In our four previous assemblies, they only 
mapped to one location.

I suggest contacting Sanger to see if they can provide better insight to 
what is occurring in this region.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Vince Tropepe wrote:
> Hi,
> 
> We are in the process of mapping a mutation in zebrafish. We though  
> we had mapped the mutation to chr 16 matching contig BX255877.14.  
> However, upon closer inspection it seems that some of the genes on  
> this contig (e.g. BC092825, BC076364, BC096802) are predicted to also  
> be present on contig CU104697.5, based on sequence comparisons with  
> the chained tBLASTn  and zebrafish refseq genes.
> 
> This is the interval I am focusing on: chr16:5,740,301-6,199,660  
> (zebrafish danRer5 July 2007 assembly).
> 
> My question is whether there is a real segment duplication in this  
> region.
> 
> Thanks for your help!
> vince
> 
> 
> ------
> Vince Tropepe
> Department of Cell & Systems Biology
> University of Toronto
> 25 Harbord Street
> Toronto, ON, M5S 3G5
> Canada
> 
> T: 416-946-0338
> F: 416-978-8532
> v.tropepe at utoronto.ca
> 
> 
> 
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