Distribution of restriction sites in the human genome

Enzyme:  SdeAI               Longest uncut segments
Specificity:  CAGRAG               Repeats in uncut segments
Number of sites:  6500243               Genes in uncut segments
Mean distance between sites:  440 base pairs
Standard deviation:  521 base pairs
Site density2271.7 per megabase               Help


Distribution of closely spaced sites

Distribution of sites within 7 STD distance


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Longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeat content Gene content
1   487764  chr15  NT_037852.6  1398682-1886446    0.01 % in   1 repeats    0.00 % in 0 genes
2   401857  chr6  NT_167244.1  2359772-2761629    0.05 % in   1 repeats    0.00 % in 0 genes
3   208453  chr6  NT_167244.1  4389446-4597899    0.28 % in   5 repeats    0.00 % in 0 genes
4   181373  chr6  NT_167244.1  3789640-3971013    0.35 % in   4 repeats    0.00 % in 0 genes
5   175467  chr6  NT_167244.1  3179925-3355392    0.11 % in   4 repeats    0.17 % in 1 genes
6   172466  chr6  NT_167247.1  4421963-4594429    0.10 % in   2 repeats    100.00 % in 1 genes
7   164997  chr6  NT_167249.1  2138420-2303417    0.09 % in   2 repeats    0.00 % in 0 genes
8   159603  chr6  NT_167248.1  521630-681233    0.18 % in   2 repeats    0.00 % in 0 genes
9   151022  chr9  NT_008470.19  21692717-21843739    0.40 % in   3 repeats    0.00 % in 0 genes
10   142863  chr6  NT_167244.1  2894638-3037501    0.03 % in   2 repeats    0.00 % in 0 genes
11   118082  chr6  NT_167245.1  2605895-2723977    0.47 % in   3 repeats    0.00 % in 0 genes
12   115373  chr6  NT_167247.1  1177206-1292579    0.40 % in   1 repeats    0.00 % in 0 genes
13   108380  chr6  NT_167245.1  137750-246130    0.44 % in   2 repeats    0.00 % in 0 genes
14   105292  chr6  NT_167244.1  1451557-1556849    0.67 % in   2 repeats    0.00 % in 0 genes
15   104931  chr6  NT_167244.1  588277-693208    0.32 % in   2 repeats    0.00 % in 0 genes
16   104065  chr6  NT_167244.1  1833688-1937753    0.07 % in   1 repeats    0.00 % in 0 genes


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Repeats in longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeats
Total  Distinct    Most  Second  Third 
487764  chr15  NT_037852.6  1398682-1886446    1       AT_rich (1) 
401857  chr6  NT_167244.1  2359772-2761629    1       AluSp (1) 
208453  chr6  NT_167244.1  4389446-4597899    5       (TTCC)n (1)  MER57-int (1)  AluY (1) 
181373  chr6  NT_167244.1  3789640-3971013    4       MLT1H-int (1)  MER52D (1)  AluSc (1) 
175467  chr6  NT_167244.1  3179925-3355392    3       GC_rich (2)  (CCG)n (1)  AluSp (1) 
172466  chr6  NT_167247.1  4421963-4594429    2       MER11A (1)  AluSc (1) 
164997  chr6  NT_167249.1  2138420-2303417    2       L1MB8 (1)  AluSx (1) 
159603  chr6  NT_167248.1  521630-681233    2       L1PREC2 (1)  HERVH-int (1) 
151022  chr9  NT_008470.19  21692717-21843739    3       MIR3 (1)  LTR67B (1)  L1M5 (1) 
10  142863  chr6  NT_167244.1  2894638-3037501    2       AluY (1)  AluSg1 (1) 
11  118082  chr6  NT_167245.1  2605895-2723977    3       MLT1E2 (1)  L2a (1)  L2 (1) 
12  115373  chr6  NT_167247.1  1177206-1292579    1       ERV3-16A3_I-int (1) 
13  108380  chr6  NT_167245.1  137750-246130    2       MLT1E2 (1)  LTR12C (1) 
14  105292  chr6  NT_167244.1  1451557-1556849    2       ERV3-16A3_I-int (1)  AluSg1 (1) 
15  104931  chr6  NT_167244.1  588277-693208    2       L1ME3D (1)  L1MA9 (1) 
16  104065  chr6  NT_167244.1  1833688-1937753    1       AluSx (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   175467       chr6  NT_167244.1  3179925-3355392    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
6   172466       chr6  NT_167247.1  4421963-4594429    LOC100507722  hypothetical_protein_LOC100507722



Posfai@neb.com
May 11, 2011