Distribution of restriction sites in the human genome

Enzyme:  LlaGI               Longest uncut segments
Specificity:  CTNGAYG               Repeats in uncut segments
Number of sites:  1240806               Genes in uncut segments
Mean distance between sites:  2306 base pairs
Standard deviation:  2395 base pairs
Site density 433.6 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   490509  chr15  NT_037852.6  1395056-1885565    0.27 % in   8 repeats    0.00 % in 0 genes
2   408488  chr6  NT_167244.1  2358235-2766723    0.82 % in   14 repeats    0.00 % in 0 genes
3   211415  chr6  NT_167244.1  4388572-4599987    1.32 % in   12 repeats    0.00 % in 0 genes
4   183858  chr6  NT_167244.1  3788047-3971905    1.13 % in   11 repeats    0.00 % in 0 genes
5   182399  chr6  NT_167247.1  4414858-4597257    2.17 % in   14 repeats    98.76 % in 1 genes
6   179563  chr6  NT_167244.1  3175897-3355460    1.51 % in   23 repeats    2.41 % in 1 genes
7   167647  chr6  NT_167249.1  2137005-2304652    1.18 % in   9 repeats    0.00 % in 0 genes
8   166464  chr6  NT_167247.1  1562631-1729095    0.56 % in   6 repeats    0.19 % in 1 genes
9   165050  chr6  NT_167248.1  518388-683438    3.48 % in   2 repeats    0.00 % in 0 genes
10   152692  chr9  NT_008470.19  21692379-21845071    0.68 % in   5 repeats    0.00 % in 0 genes
11   149757  chr7  NT_023603.5  42892-192649    100.00 % in   1 repeats    0.00 % in 0 genes
12   145152  chr6  NT_167244.1  2893340-3038492    0.93 % in   9 repeats    0.00 % in 0 genes
13   120659  chr6  NT_167246.1  3258603-3379262    2.20 % in   16 repeats    0.00 % in 0 genes
14   119571  chr6  NT_167245.1  2605554-2725125    1.70 % in   4 repeats    0.00 % in 0 genes
15   116207  chr6  NT_167247.1  1176735-1292942    0.80 % in   1 repeats    0.00 % in 0 genes
16   112323  chr6  NT_167245.1  134838-247161    2.75 % in   7 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 
490509  chr15  NT_037852.6  1395056-1885565    8       MIRc (1)  MIRb (1)  L1MDa (1) 
408488  chr6  NT_167244.1  2358235-2766723    14  10       AluY (3)  LTR84b (2)  AluJb (2) 
211415  chr6  NT_167244.1  4388572-4599987    12  10       MER57-int (2)  AluSx (2)  (TTCC)n (1) 
183858  chr6  NT_167244.1  3788047-3971905    11  9       MLT1H-int (2)  AT_rich (2)  MIR (1) 
182399  chr6  NT_167247.1  4414858-4597257    14  13       MLT1J (2)  (TTAAA)n (1)  MIRc (1) 
179563  chr6  NT_167244.1  3175897-3355460    23  14       AluSx (4)  L1MB3 (3)  GC_rich (3) 
167647  chr6  NT_167249.1  2137005-2304652    5       L1MB8 (3)  AluSx (3)  L1MC4a (1) 
166464  chr6  NT_167247.1  1562631-1729095    4       MIR (2)  L1MEe (2)  (GGAA)n (1) 
165050  chr6  NT_167248.1  518388-683438    2       L1PREC2 (1)  HERVH-int (1) 
10  152692  chr9  NT_008470.19  21692379-21845071    4       L2 (2)  MIR3 (1)  LTR67B (1) 
11  149757  chr7  NT_023603.5  42892-192649    1       ALR/Alpha (1) 
12  145152  chr6  NT_167244.1  2893340-3038492    7       L1MC5 (2)  AluJo (2)  (TCC)n (1) 
13  120659  chr6  NT_167246.1  3258603-3379262    16  11       L1MC5 (3)  AluSx (3)  MIRb (2) 
14  119571  chr6  NT_167245.1  2605554-2725125    3       L2 (2)  MLT1E2 (1)  L2a (1) 
15  116207  chr6  NT_167247.1  1176735-1292942    1       ERV3-16A3_I-int (1) 
16  112323  chr6  NT_167245.1  134838-247161    7       tRNA-Ala-GCY_ (1)  MLT1F (1)  MLT1E2 (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   182399       chr6  NT_167247.1  4414858-4597257    LOC100507722  hypothetical_protein_LOC100507722
6   179563       chr6  NT_167244.1  3175897-3355460    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
8   166464       chr6  NT_167247.1  1562631-1729095    LOC100421582  tripartite_motif-containing_protein_26



Posfai@neb.com
May 11, 2011