Identification of putative homology between horse microsatellite flanking sequences and cross-species ESTs, mRNAs and genomic sequences.
In this study the flanking sequences of 1534 horse microsatellites were used in a BLAST search to identify putative human-horse homologies. BLAST searches revealed 129 flanking sequences with significant blastn matches [alignment scores (S) > or = 60 and sum probability values (E) < or = 3.0E-6], also, 25 of these produced significant blastx matches. To provide a reference point in the human genome the flanking sequences with matches were subjected to a BLAT search of the University of California Santa Cruz (UCSC) human genome assembly (July 2003 freeze). Eighty-three of the flanking sequences showed high similarity to sequence of known or putative human genes and the remaining 46 demonstrated high similarity to human intragenic regions. Interestingly, 87 of the microsatellites showed conservation of the tandem repeat in addition to flanking regions. Overall, 41 of the microsatellites had been mapped in the horse and of these 37 localized to the expected syntenic location. The other four did not and represent new putative regions of human-horse synteny. The results of this study contribute 79 new putative human-horse homologies, increasing the density of markers on the human-horse comparative map.
Farber
C R
CR
Department of Animal Science, University of California, Davis, One Shields Ave, Davis, CA 95616-8521, USA.
Medrano
J F
JF
D000818:Animals; D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D006736:Horses / Q000235:genetics*; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D017385:Sequence Homology; D020079:Terminal Repeat Sequences / Q000235:genetics