Distribution of restriction sites in the human genome

Enzyme:  SphI               Longest uncut segments
Specificity:  GCATGC               Repeats in uncut segments
Number of sites:  545628               Genes in uncut segments
Mean distance between sites:  5244 base pairs
Standard deviation:  5663 base pairs
Site density 190.7 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   496822  chr15  NT_037852.6  1391081-1887903    1.12 % in   18 repeats    0.00 % in 0 genes
2   411219  chr6  NT_167244.1  2359809-2771028    1.04 % in   18 repeats    0.00 % in 0 genes
3   277983  chrY  NT_011875.12  8474054-8752037    79.95 % in   82 repeats    0.29 % in 1 genes
4   211047  chr6  NT_167244.1  4387748-4598795    1.48 % in   9 repeats    0.00 % in 0 genes
5   187729  chr6  NT_167244.1  3785044-3972773    1.89 % in   19 repeats    1.30 % in 1 genes
6   180350  chr6  NT_167248.1  508672-689022    9.64 % in   13 repeats    0.44 % in 1 genes
7   180293  chr6  NT_167244.1  3180139-3360432    1.47 % in   13 repeats    2.40 % in 2 genes
8   178926  chr6  NT_167247.1  4420969-4599895    2.12 % in   18 repeats    100.00 % in 1 genes
9   177801  chr6  NT_167247.1  1562298-1740099    5.13 % in   30 repeats    0.00 % in 0 genes
10   172514  chr6  NT_167249.1  2132085-2304599    3.14 % in   25 repeats    0.00 % in 0 genes
11   162834  chr9  NT_008470.19  21683543-21846377    4.61 % in   25 repeats    0.00 % in 0 genes
12   160238  chr7  NT_023603.5  40708-200946    100.00 % in   4 repeats    0.00 % in 0 genes
13   156556  chr6  NT_167244.1  2008636-2165192    0.32 % in   3 repeats    0.00 % in 0 genes
14   149903  chr6  NT_167244.1  2890439-3040342    3.83 % in   29 repeats    0.00 % in 0 genes
15   132614  chr6  NT_167246.1  3255895-3388509    4.64 % in   30 repeats    0.00 % in 0 genes
16   130509  chr14  NT_026437.12  191795-322304    97.03 % in   17 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 
496822  chr15  NT_037852.6  1391081-1887903    18  14       L1MDa (5)  MLT1L (1)  MIRc (1) 
411219  chr6  NT_167244.1  2359809-2771028    18  13       AluY (3)  LTR84b (2)  L2b (2) 
277983  chrY  NT_011875.12  8474054-8752037    82  35       LTR12B (13)  A-rich (9)  L1PA16 (8) 
211047  chr6  NT_167244.1  4387748-4598795    7       MER57-int (2)  AluSx (2)  (TTCC)n (1) 
187729  chr6  NT_167244.1  3785044-3972773    19  15       MLT1H-int (2)  L2a (2)  AT_rich (2) 
180350  chr6  NT_167248.1  508672-689022    13  12       AT_rich (2)  (TA)n (1)  LTR7 (1) 
180293  chr6  NT_167244.1  3180139-3360432    13  8       AluSx (3)  MIRb (2)  L2c (2) 
178926  chr6  NT_167247.1  4420969-4599895    18  14       AluSx (3)  MLT1J (2)  L1MC5 (2) 
177801  chr6  NT_167247.1  1562298-1740099    30  19       L1PB2 (4)  L1MEf (3)  MSTB (2) 
10  172514  chr6  NT_167249.1  2132085-2304599    25  13       AluSx (5)  L1MB8 (3)  AluJo (3) 
11  162834  chr9  NT_008470.19  21683543-21846377    25  16       L1M5 (3)  AluSq (3)  MER5B (2) 
12  160238  chr7  NT_023603.5  40708-200946    2       L1PA2 (2)  ALR/Alpha (2) 
13  156556  chr6  NT_167244.1  2008636-2165192    3       MIRb (1)  MIR (1)  AluSx (1) 
14  149903  chr6  NT_167244.1  2890439-3040342    29  15       L1MC5 (6)  AluY (5)  AluSc (3) 
15  132614  chr6  NT_167246.1  3255895-3388509    30  18       AluSx (6)  MIRb (4)  L1MC5 (3) 
16  130509  chr14  NT_026437.12  191795-322304    17  12       CER (4)  AluY (2)  AluSp (2) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
3   277983       chrY  NT_011875.12  8474054-8752037    ZNF884P 
5   187729       chr6  NT_167244.1  3785044-3972773    HLA-DRB3  major_histocompatibility_complex,_class_II,_DR_beta_3_precursor
6   180350       chr6  NT_167248.1  508672-689022    OR12D1P 
7   180293       chr6  NT_167244.1  3180139-3360432    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor
8   178926       chr6  NT_167247.1  4420969-4599895    LOC100507722  hypothetical_protein_LOC100507722



Posfai@neb.com
May 11, 2011