Distribution of restriction sites in the human genome

Enzyme:  PciI               Longest uncut segments
Specificity:  ACATGT               Repeats in uncut segments
Number of sites:  1058509               Genes in uncut segments
Mean distance between sites:  2703 base pairs
Standard deviation:  3084 base pairs
Site density 369.9 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   493323  chr15  NT_037852.6  1393242-1886565    0.60 % in   11 repeats    0.00 % in 0 genes
2   406181  chr6  NT_167244.1  2357452-2763633    0.57 % in   10 repeats    0.00 % in 0 genes
3   257568  chr6  NT_167244.1  2004996-2262564    3.61 % in   42 repeats    2.88 % in 3 genes
4   214366  chr6  NT_167244.1  4384859-4599225    2.31 % in   16 repeats    0.00 % in 0 genes
5   186002  chr6  NT_167244.1  3787092-3973094    1.48 % in   16 repeats    0.21 % in 1 genes
6   178849  chr6  NT_167244.1  3177388-3356237    0.80 % in   14 repeats    1.62 % in 2 genes
7   176866  chr6  NT_167249.1  2131070-2307936    4.96 % in   37 repeats    0.00 % in 0 genes
8   174870  chr6  NT_167247.1  4420229-4595099    0.79 % in   6 repeats    100.00 % in 1 genes
9   166895  chr6  NT_167247.1  1562248-1729143    0.61 % in   7 repeats    0.00 % in 0 genes
10   165795  chr6  NT_167248.1  520519-686314    3.46 % in   2 repeats    0.00 % in 0 genes
11   165422  chr9  NT_008470.19  21693281-21858703    3.08 % in   20 repeats    0.00 % in 0 genes
12   148760  chr6  NT_167244.1  2891576-3040336    3.20 % in   24 repeats    0.00 % in 0 genes
13   127375  chr1  NT_077389.3  264218-391593    99.34 % in   57 repeats    0.00 % in 0 genes
14   125542  chr6  NT_167245.1  2603414-2728956    4.43 % in   18 repeats    0.00 % in 0 genes
15   125327  chr1  NT_004350.19  2058146-2183473    4.59 % in   13 repeats    0.00 % in 0 genes
16   124486  chr10  NT_008705.16  38710070-38834556    27.54 % in   225 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 
493323  chr15  NT_037852.6  1393242-1886565    11  9       L1MDa (3)  MIRc (1)  MIRb (1) 
406181  chr6  NT_167244.1  2357452-2763633    10  8       L4 (2)  AluJb (2)  MER8 (1) 
257568  chr6  NT_167244.1  2004996-2262564    42  25       AluSx (5)  MIRb (3)  L1MEe (3) 
214366  chr6  NT_167244.1  4384859-4599225    16  11       MER57-int (3)  AluSx (3)  AluY (2) 
186002  chr6  NT_167244.1  3787092-3973094    16  13       MLT1H-int (2)  L2a (2)  AT_rich (2) 
178849  chr6  NT_167244.1  3177388-3356237    14  11       GC_rich (3)  LTR23 (2)  MER66C (1) 
176866  chr6  NT_167249.1  2131070-2307936    37  19       Charlie2b (6)  AluSx (6)  L1MB8 (3) 
174870  chr6  NT_167247.1  4420229-4595099    6       MIR (1)  MER11A (1)  L2b (1) 
166895  chr6  NT_167247.1  1562248-1729143    5       MIR (2)  L1MEe (2)  (GGAA)n (1) 
10  165795  chr6  NT_167248.1  520519-686314    2       L1PREC2 (1)  HERVH-int (1) 
11  165422  chr9  NT_008470.19  21693281-21858703    20  16       MIRb (2)  L2 (2)  HAL1 (2) 
12  148760  chr6  NT_167244.1  2891576-3040336    24  13       L1MC5 (6)  AluY (3)  AluSc (3) 
13  127375  chr1  NT_077389.3  264218-391593    57  5       ALR/Alpha (52)  MLT1J (2)  L2 (1) 
14  125542  chr6  NT_167245.1  2603414-2728956    18  15       Tigger1 (2)  MLT1N2 (2)  L2 (2) 
15  125327  chr1  NT_004350.19  2058146-2183473    13  9       L1MB3 (4)  AluSg (2)  MIR (1) 
16  124486  chr10  NT_008705.16  38710070-38834556    225  36       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 
3   257568       chr6  NT_167244.1  2004996-2262564    LOC100294090  hypothetical_LOC100294090,_transcript_variant_1
FLOT1  flotillin-1
DDR1  epithelial_discoidin_domain-containing_receptor_1_isoform_DDR1c
5   186002       chr6  NT_167244.1  3787092-3973094    HLA-DRB3  major_histocompatibility_complex,_class_II,_DR_beta_3_precursor
6   178849       chr6  NT_167244.1  3177388-3356237    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor
8   174870       chr6  NT_167247.1  4420229-4595099    LOC100507722  hypothetical_protein_LOC100507722



Posfai@neb.com
May 11, 2011