Distribution of restriction sites in the human genome

Enzyme:  HpyAIV               Longest uncut segments
Specificity:  GANTC               Repeats in uncut segments
Number of sites:  8581651               Genes in uncut segments
Mean distance between sites:  333 base pairs
Standard deviation:  343 base pairs
Site density2999.2 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   487579  chr15  NT_037852.6  1398493-1886072    0.01 % in   1 repeats    0.00 % in 0 genes
2   401739  chr6  NT_167244.1  2359768-2761507    0.05 % in   1 repeats    0.00 % in 0 genes
3   208209  chr6  NT_167244.1  4389943-4598152    0.16 % in   2 repeats    0.00 % in 0 genes
4   181133  chr6  NT_167244.1  3789563-3970696    0.20 % in   3 repeats    0.00 % in 0 genes
5   176457  chr6  NT_167244.1  3179298-3355755    0.26 % in   6 repeats    0.53 % in 1 genes
6   173951  chr6  NT_167247.1  4421596-4595547    0.74 % in   3 repeats    100.00 % in 1 genes
7   165327  chr6  NT_167247.1  1562941-1728268    0.41 % in   4 repeats    0.01 % in 1 genes
8   165270  chr6  NT_167249.1  2137979-2303249    0.04 % in   2 repeats    0.00 % in 0 genes
9   159876  chr6  NT_167248.1  521804-681680    0.35 % in   2 repeats    0.00 % in 0 genes
10   150377  chr9  NT_008470.19  21693188-21843565    0.05 % in   1 repeats    0.00 % in 0 genes
11   143368  chr6  NT_167244.1  2894626-3037994    0.38 % in   5 repeats    0.00 % in 0 genes
12   117992  chr6  NT_167245.1  2605641-2723633    0.51 % in   1 repeats    0.00 % in 0 genes
13   115141  chr6  NT_167247.1  1177494-1292635    0.15 % in   1 repeats    0.00 % in 0 genes
14   108472  chr6  NT_167245.1  137582-246054    0.52 % in   2 repeats    0.00 % in 0 genes
15   104903  chr6  NT_167244.1  1451453-1556356    0.29 % in   3 repeats    0.00 % in 0 genes
16   104791  chr6  NT_167244.1  588366-693157    0.27 % in   2 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 
487579  chr15  NT_037852.6  1398493-1886072    1       AT_rich (1) 
401739  chr6  NT_167244.1  2359768-2761507    1       AluSp (1) 
208209  chr6  NT_167244.1  4389943-4598152    2       AluSg/x (1)  AluJo (1) 
181133  chr6  NT_167244.1  3789563-3970696    3       MLT1H-int (1)  MER52D (1)  AluJb (1) 
176457  chr6  NT_167244.1  3179298-3355755    4       GC_rich (3)  Charlie4a (1)  (CCG)n (1) 
173951  chr6  NT_167247.1  4421596-4595547    3       MER11A (1)  AluSg/x (1)  AluSc (1) 
165327  chr6  NT_167247.1  1562941-1728268    3       MIR (2)  (GGAA)n (1)  AluSq (1) 
165270  chr6  NT_167249.1  2137979-2303249    2       L1MC4a (1)  AT_rich (1) 
159876  chr6  NT_167248.1  521804-681680    2       L1PREC2 (1)  HERVH-int (1) 
10  150377  chr9  NT_008470.19  21693188-21843565    1       L1M5 (1) 
11  143368  chr6  NT_167244.1  2894626-3037994    5       L1MC5 (1)  AluY (1)  AluSp (1) 
12  117992  chr6  NT_167245.1  2605641-2723633    1       L2a (1) 
13  115141  chr6  NT_167247.1  1177494-1292635    1       ERV3-16A3_I-int (1) 
14  108472  chr6  NT_167245.1  137582-246054    2       MLT1E2 (1)  LTR12C (1) 
15  104903  chr6  NT_167244.1  1451453-1556356    3       ERV3-16A3_I-int (1)  AluY (1)  AluSg1 (1) 
16  104791  chr6  NT_167244.1  588366-693157    2       L1ME3D (1)  L1MA9 (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   176457       chr6  NT_167244.1  3179298-3355755    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
6   173951       chr6  NT_167247.1  4421596-4595547    LOC100507722  hypothetical_protein_LOC100507722
7   165327       chr6  NT_167247.1  1562941-1728268    LOC100421582  tripartite_motif-containing_protein_26



Posfai@neb.com
May 11, 2011