Distribution of restriction sites in the human genome

Enzyme:  MamI               Longest uncut segments
Specificity:  GATNNNNATC               Repeats in uncut segments
Number of sites:  444546               Genes in uncut segments
Mean distance between sites:  6436 base pairs
Standard deviation:  6799 base pairs
Site density 155.4 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   495398  chr15  NT_037852.6  1396433-1891831    0.92 % in   20 repeats    0.00 % in 0 genes
2   405883  chr6  NT_167244.1  2358709-2764592    0.37 % in   7 repeats    0.00 % in 0 genes
3   263390  chr6  NT_167244.1  1994421-2257811    3.56 % in   44 repeats    5.81 % in 4 genes
4   228501  chr6  NT_167244.1  4378880-4607381    5.99 % in   31 repeats    2.09 % in 1 genes
5   218086  chr6  NT_167244.1  3147911-3365997    8.62 % in   100 repeats    18.99 % in 3 genes
6   187692  chr6  NT_167247.1  4406977-4594669    2.80 % in   20 repeats    96.33 % in 2 genes
7   183649  chr6  NT_167247.1  1546000-1729649    5.30 % in   51 repeats    9.23 % in 1 genes
8   181811  chr6  NT_167244.1  3790216-3972027    0.79 % in   7 repeats    0.00 % in 0 genes
9   175897  chr6  NT_167249.1  2128987-2304884    4.06 % in   32 repeats    0.00 % in 0 genes
10   175798  chr6  NT_167248.1  505966-681764    9.02 % in   17 repeats    0.00 % in 0 genes
11   172568  chr7  NT_023603.5  19717-192285    99.17 % in   12 repeats    0.00 % in 0 genes
12   167719  chr9  NT_008470.19  21684299-21852018    5.63 % in   32 repeats    0.00 % in 0 genes
13   154128  chr14  NT_026437.12  86629871-86783999    32.18 % in   239 repeats    0.00 % in 0 genes
14   148404  chr12  NT_009714.17  27173692-27322096    81.86 % in   156 repeats    0.00 % in 0 genes
15   145058  chr6  NT_167244.1  2892763-3037821    0.86 % in   8 repeats    0.00 % in 0 genes
16   137781  chr6  NT_167245.1  2597437-2735218    8.70 % in   37 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 
495398  chr15  NT_037852.6  1396433-1891831    20  17       L2a (3)  L1M5 (2)  U2 (1) 
405883  chr6  NT_167244.1  2358709-2764592    6       AluJb (2)  LTR84b (1)  L4 (1) 
263390  chr6  NT_167244.1  1994421-2257811    44  27       AluSx (7)  MIR (3)  L2c (3) 
228501  chr6  NT_167244.1  4378880-4607381    31  21       HERVH-int (4)  AluSx (4)  MER57-int (3) 
218086  chr6  NT_167244.1  3147911-3365997    100  39       AluSx (11)  L1MC5 (8)  MIR (7) 
187692  chr6  NT_167247.1  4406977-4594669    20  14       L2b (3)  L1PB1 (3)  (TGGA)n (2) 
183649  chr6  NT_167247.1  1546000-1729649    51  31       MIRc (4)  MIR3 (4)  L2c (4) 
181811  chr6  NT_167244.1  3790216-3972027    6       MLT1H-int (2)  MLT1H (1)  MER52D (1) 
175897  chr6  NT_167249.1  2128987-2304884    32  17       AluSx (5)  MamGypLTR1b (3)  L1MB8 (3) 
10  175798  chr6  NT_167248.1  505966-681764    17  14       MER4D (2)  L1PA14 (2)  L1M5 (2) 
11  172568  chr7  NT_023603.5  19717-192285    12  8       L1PA2 (2)  L1MB7 (2)  AT_rich (2) 
12  167719  chr9  NT_008470.19  21684299-21852018    32  22       L1M5 (3)  AluSq (3)  MIRb (2) 
13  154128  chr14  NT_026437.12  86629871-86783999    239  72       AluSx (23)  AluJb (20)  AluJo (17) 
14  148404  chr12  NT_009714.17  27173692-27322096    156  25       GSATII (116)  GSATX (4)  AluSg (4) 
15  145058  chr6  NT_167244.1  2892763-3037821    7       AluY (2)  (TCC)n (1)  MER21C (1) 
16  137781  chr6  NT_167245.1  2597437-2735218    37  31       MER21-int (3)  Tigger1 (2)  MLT1N2 (2) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
3   263390       chr6  NT_167244.1  1994421-2257811    MDC1  mediator_of_DNA_damage_checkpoint_protein_1
LOC100294090  hypothetical_LOC100294090,_transcript_variant_1
FLOT1  flotillin-1
DDR1  epithelial_discoidin_domain-containing_receptor_1_isoform_DDR1c
4   228501       chr6  NT_167244.1  4378880-4607381    HLA-DPB2  major_histocompatibility_complex,_class_II,_DP_beta_2_(pseudogene)
5   218086       chr6  NT_167244.1  3147911-3365997    SLC44A4  choline_transporter-like_protein_4_isoform_3
EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor
6   187692       chr6  NT_167247.1  4406977-4594669    COL11A2P 
LOC100507722  hypothetical_protein_LOC100507722
7   183649       chr6  NT_167247.1  1546000-1729649    LOC100421582  tripartite_motif-containing_protein_26



Posfai@neb.com
May 11, 2011