There is another cow genome assembly available in
ftp://ftp.cbcb.umd.edu/pub/data/assembly/Bos_taurus/Bos_taurus_UMD_3.1/.
Please put it on your browser if possible.  I found some bovine genes
are in older assenbly but not in the new assembly.  This new assembly
may have all.  Thanks.
 
 
James
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