Kinase duplications

     

    In plant genomes, tandem arrays of protein kinase genes are common.  Some regions of interest below

    Arabidopsis

    • chromosome 1: 22,635,000 to 22,755,000 - S-locus receptor kinase
    • chromosome 4: 12,120,000 to 12,195,000

     

    22,635,000 to 22,755,000 - S-locus receptor kinase

    approximately 13 repeated genes, all lie in the same direction.  Extract region above and use DNA sequence of At1g61360 as blastn query to identify gene regions.  the following DNA regions were found (approximate coordinates with some buffer around the gene).  These genes are more closely related to each other than to any other kinase genes, except a similar cluster including At1g11330, At1g11350, At1g11370.

    At1g61360  S like receptor protein kinase (PPC:1.7.2), [Arabidop..    1605 1e-184
    At1g61370  S like receptor protein kinase (PPC:1.7.2), [Arabidop..    1029 1e-184
    At1g61380  S like receptor protein kinase (PPC:1.7.2), [Arabidop..    1091 1e-184
    At1g61390  S like receptor protein kinase (PPC:1.7.2), [Arabidop..    1077 1e-184
    At1g61400  S like receptor protein kinase (PPC:1.7.2), [Arabidop..     974 1e-184
    At1g61420  S like receptor protein kinase (PPC:1.7.2), [Arabidop..     985 1e-184
    At1g61430  S like receptor protein kinase (PPC:1.7.2), [Arabidop..     965 1e-184
    At1g61440  S like receptor protein kinase (PPC:1.7.2), [Arabidop..     987 1e-184
    At1g61460  S like receptor protein kinase (PPC:1.7.2), [Arabidop..     716 1e-184
    At1g61480  S like receptor protein kinase (PPC:1.7.2), [Arabidop..    1019 1e-184
    At1g61490  S like receptor protein kinase (PPC:1.7.2), [Arabidop..    1005 1e-184
    At1g61500  ser/thr kinase (PPC:1.7.2), [Arabidopsis thaliana] pp..     992 1e-184
    At1g61550  ser/thr kinase (PPC:1.7.2), [Arabidopsis thaliana] pp..    1004 1e-184
    
    Region PP AGI begin end length
    Gene Regions
    1 21415 At1g61360 7000 1750 5250
    2 21058

    At1g61370

    10650 6800 3850
    3 21414

    At1g61380

    14800 10650 4150
    4 21413

    At1g61390

    19025 14800 4225
    5 21057

    At1g61400

    24050 19025 5025
    6 21063

    At1g61420

    29050 24050 5000
    7 21062

    At1g61430

    33425 29050 4375
    8 21061

    At1g61440

    38150 33425 4725
    9 21060

    At1g61460

    44250 38150 6100
    10 21059

    At1g61480

    49775 44250 5525
    11 21412

    At1g61490

    53925 49775 4150
    12 21053

    At1g61500

    63425 53925 9500
    13 21052

    At1g61550

    73500 63425 10075
    Tag page (Edit tags)
    • No tags

    Files 6

    FileSizeDateAttached by 
     aa.gff
    gff format example
    133.88 kB14:28, 12 Jan 2011gribskovActions
     ch1.gff.txt
    gff format for Apollo
    142.21 kB00:15, 4 Mar 2011bjiangActions
     ch1_22635000_22755000.fa
    ch1_22635000_22755000.fa
    119.6 kB14:16, 12 Jan 2011gribskovActions
     ch4.gff.txt
    gff format for Apollo
    102.68 kB00:15, 4 Mar 2011bjiangActions
     ch4_12120000_12195000.fa
    ch4_12120000_12195000.fa
    75.42 kB00:20, 4 Mar 2011bjiangActions
     Hits_Levels_blastNX_1_4.pdf
    Illustration of Hits along Chromosome 1_4 from BLAST_n_x
    104.01 kB21:06, 21 Feb 2011bjiangActions
    You must login to post a comment.