Distribution of restriction sites in the human genome

Enzyme:  AflIII               Longest uncut segments
Specificity:  ACRYGT               Repeats in uncut segments
Number of sites:  1466993               Genes in uncut segments
Mean distance between sites:  1950 base pairs
Standard deviation:  2206 base pairs
Site density 512.7 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   489116  chr15  NT_037852.6  1397449-1886565    0.09 % in   4 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   255472  chr6  NT_167244.1  2005460-2260932    3.26 % in   38 repeats    2.72 % 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   176866  chr6  NT_167249.1  2131070-2307936    4.96 % in   37 repeats    0.00 % in 0 genes
7   176319  chr6  NT_167244.1  3179918-3356237    0.24 % in   5 repeats    0.20 % in 2 genes
8   174870  chr6  NT_167247.1  4420229-4595099    0.79 % in   6 repeats    100.00 % in 1 genes
9   165888  chr6  NT_167247.1  1562248-1728136    0.43 % in   5 repeats    0.00 % in 0 genes
10   165071  chr6  NT_167248.1  521243-686314    3.04 % in   2 repeats    0.00 % in 0 genes
11   156366  chr9  NT_008470.19  21693281-21849647    1.10 % in   10 repeats    0.00 % in 0 genes
12   146628  chr6  NT_167244.1  2893708-3040336    2.11 % in   19 repeats    0.00 % in 0 genes
13   124486  chr10  NT_008705.16  38710070-38834556    27.54 % in   225 repeats    0.00 % in 0 genes
14   124444  chr6  NT_167245.1  2603889-2728333    3.84 % in   15 repeats    0.00 % in 0 genes
15   123939  chr6  NT_167246.1  3260375-3384314    3.09 % in   21 repeats    0.00 % in 0 genes
16   117789  chr6  NT_167247.1  1175951-1293740    1.45 % in   2 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 
489116  chr15  NT_037852.6  1397449-1886565    4       MIRc (1)  MIRb (1)  L1M3 (1) 
406181  chr6  NT_167244.1  2357452-2763633    10  8       L4 (2)  AluJb (2)  MER8 (1) 
255472  chr6  NT_167244.1  2005460-2260932    38  23       AluSx (5)  MIRb (3)  AluSg (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) 
176866  chr6  NT_167249.1  2131070-2307936    37  19       Charlie2b (6)  AluSx (6)  L1MB8 (3) 
176319  chr6  NT_167244.1  3179918-3356237    4       GC_rich (2)  Charlie4a (1)  (CCG)n (1) 
174870  chr6  NT_167247.1  4420229-4595099    6       MIR (1)  MER11A (1)  L2b (1) 
165888  chr6  NT_167247.1  1562248-1728136    4       MIR (2)  (GGAA)n (1)  A-rich (1) 
10  165071  chr6  NT_167248.1  521243-686314    2       L1PREC2 (1)  HERVH-int (1) 
11  156366  chr9  NT_008470.19  21693281-21849647    10  7       MIRb (2)  L2 (2)  (CA)n (2) 
12  146628  chr6  NT_167244.1  2893708-3040336    19  10       L1MC5 (6)  AluSc (3)  AluY (2) 
13  124486  chr10  NT_008705.16  38710070-38834556    225  36       GA-rich (24)  (GAATG)n (22)  (AAATG)n (22) 
14  124444  chr6  NT_167245.1  2603889-2728333    15  13       Tigger1 (2)  L2 (2)  (TG)n (1) 
15  123939  chr6  NT_167246.1  3260375-3384314    21  15       L1MC5 (3)  AluSx (3)  MIRb (2) 
16  117789  chr6  NT_167247.1  1175951-1293740    1       ERV3-16A3_I-int (2) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
3   255472       chr6  NT_167244.1  2005460-2260932    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
7   176319       chr6  NT_167244.1  3179918-3356237    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