Distribution of restriction sites in the human genome

Enzyme:  EcoRV               Longest uncut segments
Specificity:  GATATC               Repeats in uncut segments
Number of sites:  430614               Genes in uncut segments
Mean distance between sites:  6644 base pairs
Standard deviation:  7674 base pairs
Site density 150.5 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   490064  chr15  NT_037852.6  1397638-1887702    0.17 % in   6 repeats    0.00 % in 0 genes
2   430842  chr6  NT_167244.1  2334074-2764916    3.51 % in   66 repeats    1.32 % in 1 genes
3   271609  chr6  NT_167244.1  2003105-2274714    5.49 % in   63 repeats    5.70 % in 4 genes
4   248408  chr6  NT_167244.1  3171976-3420384    5.12 % in   65 repeats    8.34 % in 2 genes
5   246077  chr20  NT_011362.10  31159829-31405906    17.01 % in   242 repeats    31.97 % in 7 genes
6   245230  chr6  NT_167244.1  4369903-4615133    10.62 % in   64 repeats    5.61 % in 1 genes
7   200833  chr6  NT_167244.1  3777419-3978252    4.25 % in   39 repeats    5.02 % in 1 genes
8   200018  chrY  NT_011875.12  8474134-8674152    74.93 % in   11 repeats    0.00 % in 0 genes
9   191704  chr7  NT_007933.15  39730499-39922203    47.65 % in   409 repeats    0.00 % in 0 genes
10   181136  chr6  NT_167249.1  2137965-2319101    6.37 % in   45 repeats    0.00 % in 0 genes
11   180366  chr6  NT_167246.1  3056075-3236441    13.70 % in   102 repeats    0.00 % in 0 genes
12   175522  chr7  NT_023603.5  33558-209080    100.00 % in   6 repeats    0.00 % in 0 genes
13   175451  chr16  NT_010542.15  242703-418154    23.75 % in   224 repeats    0.00 % in 0 genes
14   174969  chr6  NT_167247.1  4419957-4594926    0.69 % in   6 repeats    0.00 % in 0 genes
15   171347  chr6  NT_167247.1  1561158-1732505    2.07 % in   16 repeats    0.00 % in 0 genes
16   167148  chr9  NT_008470.19  21685556-21852704    5.48 % in   28 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 
490064  chr15  NT_037852.6  1397638-1887702    6       MLT1L (1)  MIRc (1)  MIRb (1) 
430842  chr6  NT_167244.1  2334074-2764916    66  38       AluSx (6)  AluJb (6)  L1ME4a (3) 
271609  chr6  NT_167244.1  2003105-2274714    63  36       AluSx (9)  MIR (5)  MIRb (3) 
248408  chr6  NT_167244.1  3171976-3420384    65  28       AluSx (10)  MIR (4)  L1MC5 (4) 
246077  chr20  NT_011362.10  31159829-31405906    242  87       MIRb (19)  MIR (16)  (TG)n (10) 
245230  chr6  NT_167244.1  4369903-4615133    64  34       HUERS-P3-int (7)  AluSx (7)  Harlequin-int (5) 
200833  chr6  NT_167244.1  3777419-3978252    39  27       L2a (6)  AT_rich (3)  MLT1H-int (2) 
200018  chrY  NT_011875.12  8474134-8674152    11  2       LTR12B (10)  LTR12D (1) 
191704  chr7  NT_007933.15  39730499-39922203    409  93       AluSx (97)  AluJo (44)  AluJb (21) 
10  181136  chr6  NT_167249.1  2137965-2319101    45  24       Charlie2b (6)  AluSx (5)  HAL1 (4) 
11  180366  chr6  NT_167246.1  3056075-3236441    102  42       AluSx (15)  AluY (12)  AluJb (7) 
12  175522  chr7  NT_023603.5  33558-209080    3       ALR/Alpha (3)  L1PA2 (2)  L1PA3 (1) 
13  175451  chr16  NT_010542.15  242703-418154    224  68       AluSx (30)  AluJo (16)  AluY (14) 
14  174969  chr6  NT_167247.1  4419957-4594926    6       MIR (1)  MER11A (1)  L2b (1) 
15  171347  chr6  NT_167247.1  1561158-1732505    16  13       MSTB (2)  MIR (2)  L1MEe (2) 
16  167148  chr9  NT_008470.19  21685556-21852704    28  19       L1M5 (3)  MIRb (2)  MER5B (2) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
2   430842       chr6  NT_167244.1  2334074-2764916    HCG22  HLA_complex_group_22
3   271609       chr6  NT_167244.1  2003105-2274714    LOC100294090  hypothetical_LOC100294090,_transcript_variant_1
FLOT1  flotillin-1
DDR1  epithelial_discoidin_domain-containing_receptor_1_isoform_DDR1c
MUC21  mucin-21_precursor
4   248408       chr6  NT_167244.1  3171976-3420384    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor
5   246077       chr20  NT_011362.10  31159829-31405906    CABLES2  CDK5_and_ABL1_enzyme_substrate_2
C20orf151  hypothetical_protein_LOC140893
GATA5  transcription_factor_GATA-5
C20orf200  chromosome_20_open_reading_frame_200
MIR133A2  microRNA:hsa-mir-133a-2
RPL7P3 
LOC100131174  hypothetical_LOC100131174
6   245230       chr6  NT_167244.1  4369903-4615133    HLA-DPB2  major_histocompatibility_complex,_class_II,_DP_beta_2_(pseudogene)
7   200833       chr6  NT_167244.1  3777419-3978252    HLA-DRB3  major_histocompatibility_complex,_class_II,_DR_beta_3_precursor



Posfai@neb.com
May 11, 2011