Distribution of restriction sites in the human genome

Enzyme:  BglII               Longest uncut segments
Specificity:  AGATCT               Repeats in uncut segments
Number of sites:  770515               Genes in uncut segments
Mean distance between sites:  3713 base pairs
Standard deviation:  3890 base pairs
Site density 269.3 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   487985  chr15  NT_037852.6  1398193-1886178    0.01 % in   1 repeats    0.00 % in 0 genes
2   406106  chr6  NT_167244.1  2359396-2765502    0.42 % in   8 repeats    0.00 % in 0 genes
3   258491  chr6  NT_167244.1  2002417-2260908    3.36 % in   41 repeats    3.86 % in 3 genes
4   220769  chr6  NT_167244.1  4380077-4600846    2.95 % in   23 repeats    1.62 % in 1 genes
5   189473  chr6  NT_167244.1  3785329-3974802    2.65 % in   23 repeats    1.14 % in 1 genes
6   182281  chr6  NT_167244.1  3175265-3357546    2.14 % in   29 repeats    3.47 % in 2 genes
7   177487  chr6  NT_167247.1  4420604-4598091    1.81 % in   14 repeats    100.00 % in 1 genes
8   171147  chr6  NT_167249.1  2133645-2304792    2.52 % in   20 repeats    0.00 % in 0 genes
9   166995  chr6  NT_167247.1  1560862-1727857    1.01 % in   7 repeats    0.00 % in 0 genes
10   161665  chr9  NT_008470.19  21684869-21846534    4.31 % in   22 repeats    0.00 % in 0 genes
11   161094  chr6  NT_167248.1  521677-682771    1.11 % in   2 repeats    0.00 % in 0 genes
12   150546  chr6  NT_167244.1  2890024-3040570    4.12 % in   32 repeats    0.00 % in 0 genes
13   126414  chr6  NT_167245.1  2602459-2728873    4.80 % in   18 repeats    0.00 % in 0 genes
14   126389  chr10  NT_008705.16  38710898-38837287    27.64 % in   226 repeats    0.00 % in 0 genes
15   119520  chr6  NT_167245.1  133371-252891    6.20 % in   20 repeats    0.00 % in 0 genes
16   119359  chr6  NT_167246.1  3260732-3380091    2.26 % in   16 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 
487985  chr15  NT_037852.6  1398193-1886178    1       AT_rich (1) 
406106  chr6  NT_167244.1  2359396-2765502    6       LTR84b (2)  AluY (2)  MLT1B (1) 
258491  chr6  NT_167244.1  2002417-2260908    41  25       AluSx (5)  MIRb (3)  FRAM (3) 
220769  chr6  NT_167244.1  4380077-4600846    23  17       MER57-int (3)  AluSx (3)  AluY (2) 
189473  chr6  NT_167244.1  3785329-3974802    23  18       L2a (3)  MLT1H-int (2)  AT_rich (2) 
182281  chr6  NT_167244.1  3175265-3357546    29  16       AluSx (5)  L1MB3 (4)  GC_rich (3) 
177487  chr6  NT_167247.1  4420604-4598091    14  12       MLT1J (2)  AluSx (2)  (TTAAA)n (1) 
171147  chr6  NT_167249.1  2133645-2304792    20  11       AluSx (4)  L1MB8 (3)  MLT1H1 (2) 
166995  chr6  NT_167247.1  1560862-1727857    6       MIR (2)  MIRc (1)  L1MC3 (1) 
10  161665  chr9  NT_008470.19  21684869-21846534    22  14       L1M5 (3)  AluSq (3)  MER5B (2) 
11  161094  chr6  NT_167248.1  521677-682771    2       L1PREC2 (1)  HERVH-int (1) 
12  150546  chr6  NT_167244.1  2890024-3040570    32  16       L1MC5 (6)  AluY (5)  AluSc (3) 
13  126414  chr6  NT_167245.1  2602459-2728873    18  15       Tigger1 (2)  MLT1N2 (2)  L2 (2) 
14  126389  chr10  NT_008705.16  38710898-38837287    226  37       GA-rich (24)  (GAATG)n (22)  (AAATG)n (22) 
15  119520  chr6  NT_167245.1  133371-252891    20  18       L2c (2)  AluSx (2)  (TTTC)n (1) 
16  119359  chr6  NT_167246.1  3260732-3380091    16  11       L1MC5 (3)  AluSx (3)  MIRb (2) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
3   258491       chr6  NT_167244.1  2002417-2260908    LOC100294090  hypothetical_LOC100294090,_transcript_variant_1
FLOT1  flotillin-1
DDR1  epithelial_discoidin_domain-containing_receptor_1_isoform_DDR1c
4   220769       chr6  NT_167244.1  4380077-4600846    HLA-DPB2  major_histocompatibility_complex,_class_II,_DP_beta_2_(pseudogene)
5   189473       chr6  NT_167244.1  3785329-3974802    HLA-DRB3  major_histocompatibility_complex,_class_II,_DR_beta_3_precursor
6   182281       chr6  NT_167244.1  3175265-3357546    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor
7   177487       chr6  NT_167247.1  4420604-4598091    LOC100507722  hypothetical_protein_LOC100507722



Posfai@neb.com
May 11, 2011