Distribution of restriction sites in the human genome

Enzyme:  Van91II               Longest uncut segments
Specificity:  GAATTC               Repeats in uncut segments
Number of sites:  778599               Genes in uncut segments
Mean distance between sites:  3674 base pairs
Standard deviation:  3884 base pairs
Site density 272.1 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   406628  chr6  NT_167244.1  2356218-2762846    0.73 % in   13 repeats    0.00 % in 0 genes
2   212218  chr6  NT_167244.1  4389562-4601780    1.53 % in   13 repeats    0.00 % in 0 genes
3   196983  chr6  NT_167244.1  3169821-3366804    5.13 % in   56 repeats    10.67 % in 2 genes
4   189903  chr6  NT_167249.1  2117833-2307736    7.18 % in   65 repeats    0.00 % in 0 genes
5   183695  chr6  NT_167244.1  3786957-3970652    0.49 % in   7 repeats    0.29 % in 1 genes
6   174648  chr6  NT_167247.1  4421551-4596199    0.96 % in   6 repeats    100.00 % in 1 genes
7   174281  chr6  NT_167244.1  2869024-3043305    11.20 % in   99 repeats    5.38 % in 4 genes
8   172026  chr6  NT_167247.1  1555804-1727830    2.71 % in   24 repeats    4.16 % in 1 genes
9   168130  chr6  NT_167246.1  3060724-3228854    10.53 % in   72 repeats    0.00 % in 0 genes
10   167253  chr9  NT_008470.19  21676075-21843328    5.02 % in   30 repeats    0.00 % in 0 genes
11   165397  chr6  NT_167248.1  516583-681980    3.68 % in   4 repeats    0.00 % in 0 genes
12   159314  chr6  NT_167244.1  2006446-2165760    1.07 % in   7 repeats    0.00 % in 0 genes
13   126119  chrY  NT_011875.12  8494982-8621101    60.30 % in   5 repeats    0.00 % in 0 genes
14   123632  chr6  NT_167247.1  1174113-1297745    3.93 % in   10 repeats    0.00 % in 0 genes
15   119918  chrX  NT_011786.16  4273267-4393185    10.07 % in   64 repeats    0.00 % in 0 genes
16   119629  chr6  NT_167245.1  2604399-2724028    1.40 % in   6 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 
406628  chr6  NT_167244.1  2356218-2762846    13  10       AluJb (3)  L4 (2)  MLT2D (1) 
212218  chr6  NT_167244.1  4389562-4601780    13  10       HERVH-int (2)  AluSx (2)  AluSg/x (2) 
196983  chr6  NT_167244.1  3169821-3366804    56  26       AluSx (9)  MIR (4)  L2b (4) 
189903  chr6  NT_167249.1  2117833-2307736    65  34       AluSx (9)  Charlie2b (6)  AluJb (5) 
183695  chr6  NT_167244.1  3786957-3970652    6       AT_rich (2)  MLT1H-int (1)  MIR (1) 
174648  chr6  NT_167247.1  4421551-4596199    6       (TTAAA)n (1)  MLT1J (1)  MER11A (1) 
174281  chr6  NT_167244.1  2869024-3043305    99  33       AluSx (14)  AluJo (11)  AluY (8) 
172026  chr6  NT_167247.1  1555804-1727830    24  19       L2c (3)  Tigger7 (2)  MSTD (2) 
168130  chr6  NT_167246.1  3060724-3228854    72  33       AluSx (10)  AluY (8)  AluJb (7) 
10  167253  chr9  NT_008470.19  21676075-21843328    30  22       L1M5 (3)  MLT1G1 (2)  MER5B (2) 
11  165397  chr6  NT_167248.1  516583-681980    4       LTR7 (1)  L1PREC2 (1)  L1P4 (1) 
12  159314  chr6  NT_167244.1  2006446-2165760    5       AluSx (3)  MIRb (1)  MIR (1) 
13  126119  chrY  NT_011875.12  8494982-8621101    2       LTR12B (4)  LTR12D (1) 
14  123632  chr6  NT_167247.1  1174113-1297745    10  7       ERV3-16A3_I-int (3)  L2 (2)  MLT1E2 (1) 
15  119918  chrX  NT_011786.16  4273267-4393185    64  16       MER33 (14)  AluSx (13)  AluSc (13) 
16  119629  chr6  NT_167245.1  2604399-2724028    6       MLT1N2 (1)  MLT1E2 (1)  MER5B (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
3   196983       chr6  NT_167244.1  3169821-3366804    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor
5   183695       chr6  NT_167244.1  3786957-3970652    HLA-DRB3  major_histocompatibility_complex,_class_II,_DR_beta_3_precursor
6   174648       chr6  NT_167247.1  4421551-4596199    LOC100507722  hypothetical_protein_LOC100507722
7   174281       chr6  NT_167244.1  2869024-3043305    LST1  leukocyte-specific_transcript_1_protein_isoform_5
NCR3  natural_cytotoxicity_triggering_receptor_3_isoform_c
UQCRHP1 
MSH5  mutS_protein_homolog_5_isoform_c
8   172026       chr6  NT_167247.1  1555804-1727830    LOC100421582  tripartite_motif-containing_protein_26



Posfai@neb.com
May 11, 2011