Distribution of restriction sites in the human genome

Enzyme:  Bpu10IB               Longest uncut segments
Specificity:  CCTNAGC               Repeats in uncut segments
Number of sites:  2388170               Genes in uncut segments
Mean distance between sites:  1198 base pairs
Standard deviation:  1496 base pairs
Site density 834.6 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   494168  chr15  NT_037852.6  1397320-1891488    0.76 % in   18 repeats    0.00 % in 0 genes
2   402549  chr6  NT_167244.1  2359953-2762502    0.01 % in   1 repeats    0.00 % in 0 genes
3   209599  chr6  NT_167244.1  4389169-4598768    0.80 % in   9 repeats    0.00 % in 0 genes
4   180721  chr6  NT_167244.1  3790237-3970958    0.22 % in   3 repeats    0.00 % in 0 genes
5   176534  chr4  NT_006316.16  378663-555197    7.15 % in   72 repeats    20.39 % in 23 genes
6   175990  chr6  NT_167244.1  3179395-3355385    0.12 % in   5 repeats    0.47 % in 1 genes
7   173755  chr7  NT_023603.5  20521-194276    99.32 % in   12 repeats    0.00 % in 0 genes
8   173141  chr6  NT_167247.1  4421327-4594468    0.19 % in   3 repeats    100.00 % in 1 genes
9   165995  chr6  NT_167249.1  2137772-2303767    0.46 % in   6 repeats    0.00 % in 0 genes
10   164734  chr6  NT_167247.1  1562792-1727526    0.19 % in   2 repeats    0.00 % in 0 genes
11   160436  chr6  NT_167248.1  521795-682231    0.70 % in   2 repeats    0.00 % in 0 genes
12   152661  chr9  NT_008470.19  21691701-21844362    0.81 % in   5 repeats    0.00 % in 0 genes
13   144003  chrY  NT_011875.12  8542596-8686599    65.17 % in   10 repeats    0.00 % in 0 genes
14   143652  chr6  NT_167244.1  2894137-3037789    0.35 % in   5 repeats    0.00 % in 0 genes
15   134834  chr9  NT_078070.3  951707-1086541    59.42 % in   32 repeats    0.00 % in 0 genes
16   120958  chr10  NT_008705.16  38708003-38828961    26.78 % in   221 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 
1  494168  chr15  NT_037852.6  1397320-1891488    18  15       L2a (3)  L1M5 (2)  U2 (1) 
2  402549  chr6  NT_167244.1  2359953-2762502    1  1       AluSp (1) 
3  209599  chr6  NT_167244.1  4389169-4598768    9  7       MER57-int (2)  AluSx (2)  (TTCC)n (1) 
4  180721  chr6  NT_167244.1  3790237-3970958    3  3       MLT1H-int (1)  MER52D (1)  AluSc (1) 
5  176534  chr4  NT_006316.16  378663-555197    72  18       (CA)n (48)  L1M4 (7)  L1PA10 (2) 
6  175990  chr6  NT_167244.1  3179395-3355385    5  3       GC_rich (3)  (CCG)n (1)  AluSp (1) 
7  173755  chr7  NT_023603.5  20521-194276    12  7       L1PA2 (3)  L1MB7 (2)  AT_rich (2) 
8  173141  chr6  NT_167247.1  4421327-4594468    3  3       MIR (1)  MER11A (1)  AluSc (1) 
9  165995  chr6  NT_167249.1  2137772-2303767    6  4       L1MB8 (2)  AluSx (2)  L1MC4a (1) 
10  164734  chr6  NT_167247.1  1562792-1727526    2  2       MIR (1)  AluSq (1) 
11  160436  chr6  NT_167248.1  521795-682231    2  2       L1PREC2 (1)  HERVH-int (1) 
12  152661  chr9  NT_008470.19  21691701-21844362    5  4       LTR67B (2)  MSTA (1)  MIR3 (1) 
13  144003  chrY  NT_011875.12  8542596-8686599    10  1       LTR12B (10) 
14  143652  chr6  NT_167244.1  2894137-3037789    5  5       L1MC5 (1)  AluY (1)  AluSg1 (1) 
15  134834  chr9  NT_078070.3  951707-1086541    32  14       ERVL-E-int (5)  (TAA)n (3)  L1PA3 (3) 
16  120958  chr10  NT_008705.16  38708003-38828961    221  33       GA-rich (24)  (GAATG)n (22)  (AAATG)n (22) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   176534       chr4  NT_006316.16  378663-555197    LOC100287144  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287178  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287205  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287238  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287270 
LOC100288520  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287302 
LOC100287327  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287364  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287404  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287441  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287478  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287513  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728369  ubiquitin_carboxyl-terminal_hydrolase_17
LOC728373  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728379  ubiquitin_carboxyl-terminal_hydrolase_17-like
USP17L5  ubiquitin_specific_peptidase_17-like_5
LOC728393  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728400  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728405  ubiquitin_carboxyl-terminal_hydrolase_17-like
USP17  ubiquitin_carboxyl-terminal_hydrolase_17
LOC728419  ubiquitin_carboxyl-terminal_hydrolase_17-like
USP17L6P  ubiquitin_specific_peptidase_17-like_6_(pseudogene)
6   175990       chr6  NT_167244.1  3179395-3355385    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
8   173141       chr6  NT_167247.1  4421327-4594468    LOC100507722  hypothetical_protein_LOC100507722


Posfai@neb.com
May 11, 2011