Human Protein
  Human position: chr17:10336460-10360684
Human mRNA: NM_005963
Protein length: 1939

The alignment you clicked on is first in the table below.

ALIGNMENT PEPTIDE COVERAGE IDENTITY  START END EXTENT  STRAND   LINK TO BROWSER 
--------------------------------------------------------------------------------
alignment peptide  92.9%     86.3%     1  1939 100.0%    -   chr11:52,974,075-53,118,116 
alignment peptide 91.0% 96.3% 1 1939 100.0% - chr11:52,916,852-52,997,347
alignment peptide 92.1% 94.1% 1 1938 99.9% - chr11:52,864,808-53,025,982
alignment peptide 98.2% 81.4% 4 1935 99.6% - chr1:161,476,773-161,526,751
alignment peptide 83.4% 89.5% 1 1931 99.6% - chr11:52,795,471-52,937,010
alignment peptide 84.4% 71.4% 70 1930 96.0% + chr22:25,803,560-25,825,183
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Data last updated at UCSC: 2008-08-19

Description

This track contains tBLASTn alignments of the peptides from the predicted and known genes identified in the hg18 UCSC Genes track.

Methods

First, the predicted proteins from the human UCSC Genes track were aligned with the human genome using the Blat program to discover exon boundaries. Next, the amino acid sequences that make up each exon were aligned with the horse sequence using the tBLASTn program. Finally, the putative horse exons were chained together using an organism-specific maximum gap size but no gap penalty. The single best exon chains extending over more than 60% of the query protein were included. Exon chains that extended over 60% of the query and matched at least 60% of the protein's amino acids were also included.

Credits

tBLASTn is part of the NCBI BLAST tool set. For more information on BLAST, see Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-410.

Blat was written by Jim Kent. The remaining utilities used to produce this track were written by Jim Kent or Brian Raney.