Distribution of restriction sites in the human genome

Enzyme:  PspGI               Longest uncut segments
Specificity:  CCWGG               Repeats in uncut segments
Number of sites:  9802056               Genes in uncut segments
Mean distance between sites:  291 base pairs
Standard deviation:  431 base pairs
Site density3425.7 per megabase               Help

Distribution of closely spaced sites
Distribution of sites within 7 STD distance

 Help
Longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeat content Gene content
1   488658  chr15  NT_037852.6  1397394-1886052    0.10 % in   5 repeats    0.00 % in 0 genes
2   401644  chr6  NT_167244.1  2359967-2761611    0.00 % in   1 repeats    0.00 % in 0 genes
3   208194  chr6  NT_167244.1  4389983-4598177    0.14 % in   3 repeats    0.00 % in 0 genes
4   180703  chr6  NT_167244.1  3790076-3970779    0.20 % in   3 repeats    0.00 % in 0 genes
5   175413  chr6  NT_167244.1  3180046-3355459    0.15 % in   4 repeats    0.10 % in 1 genes
6   172386  chr6  NT_167247.1  4422042-4594428    0.10 % in   2 repeats    100.00 % in 1 genes
7   164437  chr6  NT_167247.1  1562810-1727247    0.02 % in   1 repeats    0.09 % in 1 genes
8   159433  chr6  NT_167248.1  521893-681326    0.08 % in   2 repeats    0.00 % in 0 genes
9   150667  chr9  NT_008470.19  21692801-21843468    0.31 % in   2 repeats    0.00 % in 0 genes
10   142914  chr6  NT_167244.1  2894571-3037485    0.06 % in   2 repeats    0.00 % in 0 genes
11   117595  chr6  NT_167245.1  2606075-2723670    0.14 % in   1 repeats    0.00 % in 0 genes
12   113667  chr6  NT_167246.1  3261233-3374900    0.16 % in   2 repeats    0.00 % in 0 genes
13   110439  chr6  NT_167245.1  135845-246284    2.08 % in   5 repeats    0.00 % in 0 genes
14   106747  chr6  NT_167244.1  587738-694485    1.63 % in   9 repeats    0.00 % in 0 genes
15   104684  chr6  NT_167244.1  1451574-1556258    0.09 % in   2 repeats    0.00 % in 0 genes
16   103963  chr6  NT_167244.1  1833721-1937684    0.00 % in   1 repeats    0.00 % in 0 genes

Help
Repeats in longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeats
Total  Distinct    Most  Second  Third 
1  488658  chr15  NT_037852.6  1397394-1886052    5  5       MIRc (1)  MIRb (1)  L1M3 (1) 
2  401644  chr6  NT_167244.1  2359967-2761611    1  1       AluSp (1) 
3  208194  chr6  NT_167244.1  4389983-4598177    3  3       AluSx (1)  AluSg/x (1)  AluJo (1) 
4  180703  chr6  NT_167244.1  3790076-3970779    3  3       MLT1H-int (1)  MER52D (1)  AluJb (1) 
5  175413  chr6  NT_167244.1  3180046-3355459    4  3       GC_rich (2)  (CCG)n (1)  AluSp (1) 
6  172386  chr6  NT_167247.1  4422042-4594428    2  2       MER11A (1)  AluSc (1) 
7  164437  chr6  NT_167247.1  1562810-1727247    1  1       MIR (1) 
8  159433  chr6  NT_167248.1  521893-681326    2  2       L1PREC2 (1)  HERVH-int (1) 
9  150667  chr9  NT_008470.19  21692801-21843468    2  2       LTR67B (1)  L1M5 (1) 
10  142914  chr6  NT_167244.1  2894571-3037485    2  2       AluY (1)  AluSg1 (1) 
11  117595  chr6  NT_167245.1  2606075-2723670    1  1       L2a (1) 
12  113667  chr6  NT_167246.1  3261233-3374900    2  2       MIRb (1)  AluSx (1) 
13  110439  chr6  NT_167245.1  135845-246284    5  5       MLT1F (1)  MLT1E2 (1)  MER6 (1) 
14  106747  chr6  NT_167244.1  587738-694485    9  7       L1MA9 (3)  MER77 (1)  L1PB1 (1) 
15  104684  chr6  NT_167244.1  1451574-1556258    2  2       ERV3-16A3_I-int (1)  AluSg1 (1) 
16  103963  chr6  NT_167244.1  1833721-1937684    1  1       AluSx (1) 

Help
Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   175413       chr6  NT_167244.1  3180046-3355459    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
6   172386       chr6  NT_167247.1  4422042-4594428    LOC100507722  hypothetical_protein_LOC100507722
7   164437       chr6  NT_167247.1  1562810-1727247    LOC100421582  tripartite_motif-containing_protein_26


Posfai@neb.com
May 11, 2011