[Genome] zebrafish genes

[Rachel Harte]

Hello Shahar,

I have taken a look at this gene on the Zebrafish Mar.2006 (danRer4)
assembly on our browser and I see that this gene maps only to position
chr3:76,396,454-76,402,049.

But when I did a BLAT on this gene sequence,  I got a 98.3% alignment on
the position,  chr3:76,722,749-76,728,279, whereas it has 99.1%
alignment on chr3:76,396,454-76,401,999. According to our methods:
"RefSeq mRNAs were aligned against the zebrafish genome using blat;
those with an alignment of less than 15% were discarded. When a single
mRNA aligned in multiple places, the alignment having the highest base
identity was identified. Only alignments having a base identity level
within 0.1% of the best and at least 96% base identity with the genomic
sequence were kept".

NM_131411.1     1088     1  1114  1131  99.1%     3   -   76396454
76402049   5596
NM_131411.1     1069     1  1114  1131  98.3%     3   -   76722749
76728329   5581

However, the zebrafish assembly is still in progress. There have been
some problems due to multiple haplotypes being rpesent in the WGS assembly.
Highly variable regions have caused false duplications in the assembly may
be what you are seeing here although the sequence is slightly different in
the two regions resulting in the two different identities for the
alignments. This could just be a result of differences in sequencing
error and/or variation for just a few bases. Although the assembly has
improved a lot with each release and the sequencing centre (Wellcome Trust
Sanger Institute) have used zebrafish markers to help place contigs in the
correct position, there are still some cases of false duplications - see this
page for more details:

http://www.sanger.ac.uk/Projects/D_rerio/Zv6_assembly_information.shtml

If you have more questions about the assembly then please contact the
Wellcome Trust Sanger Institute zebrafish sequencing group. The e-mail
address for questions about the zebrafish assembly is:
zfish-help at sanger.ac.uk.

I hope that this helps you. If you have any further questions about our
mRNA alignments then please let us know.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Sun, 18 Mar 2007, shahar alon wrote:

> While using ucsc browser I found out that the gene aanat2 seems to appear
> twice in the zebrafish genome: chr3:76,722,749-76,728,279
>
> chr3:76,396,454-76,401,999
>
> How can I know if this gene really appear twice in the genome or maybe this
> is a sequencing error?
>
> Thank you
>
> Shahar Alon
>
> Tel Aviv university, Israel
>
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