Distribution of restriction sites in the human genome

Enzyme:  SdaI               Longest uncut segments
Specificity:  CCTGCAGG               Repeats in uncut segments
Number of sites:  76937               Genes in uncut segments
Mean distance between sites:  37190 base pairs
Standard deviation:  53243 base pairs
Site density 26.9 per megabase               Help

Distribution of closely spaced sites
Distribution of sites within 7 STD distance

 Help
Longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeat content Gene content
1   1056072  chr3  NT_005612.16  70706663-71762735    49.73 % in   1758 repeats    10.37 % in 2 genes
2   865730  chr13  NT_024524.14  64294729-65160459    52.13 % in   1375 repeats    0.20 % in 1 genes
3   810071  chr9  NT_008413.18  20746649-21556720    48.65 % in   1169 repeats    48.67 % in 27 genes
4   746365  chr6  NT_007299.13  5766099-6512464    56.49 % in   1191 repeats    0.12 % in 1 genes
5   744422  chr4  NT_016354.19  87405585-88150007    49.63 % in   1260 repeats    30.64 % in 2 genes
6   732510  chr13  NT_024524.14  52879572-53612082    34.23 % in   1078 repeats    58.66 % in 2 genes
7   706626  chr3  NT_005612.16  50812302-51518928    52.53 % in   1163 repeats    0.00 % in 0 genes
8   668417  chr21  NT_011512.11  9034969-9703386    56.38 % in   1158 repeats    0.69 % in 2 genes
9   661694  chr13  NT_009952.14  2470353-3132047    52.91 % in   1083 repeats    0.00 % in 0 genes
10   660942  chr2  NT_022135.16  31821990-32482932    35.19 % in   967 repeats    0.00 % in 0 genes
11   656771  chr5  NT_006576.16  22235429-22892200    41.96 % in   1044 repeats    0.00 % in 0 genes
12   637271  chr1  NT_004487.19  25603637-26240908    59.84 % in   1101 repeats    0.00 % in 0 genes
13   636974  chr5  NT_006576.16  29023040-29660014    55.88 % in   1030 repeats    0.00 % in 0 genes
14   632482  chr8  NT_008046.16  7025068-7657550    44.96 % in   989 repeats    0.00 % in 0 genes
15   629881  chr18  NT_025028.14  14229292-14859173    41.67 % in   1021 repeats    0.00 % in 0 genes
16   622614  chr12  NT_029419.12  52723324-53345938    52.68 % in   1070 repeats    0.00 % in 0 genes

Help
Repeats in longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeats
Total  Distinct    Most  Second  Third 
1  1056072  chr3  NT_005612.16  70706663-71762735    1758  339       AT_rich (233)  L2a (57)  MIRb (51) 
2  865730  chr13  NT_024524.14  64294729-65160459    1375  322       AT_rich (176)  (TA)n (40)  AluSx (35) 
3  810071  chr9  NT_008413.18  20746649-21556720    1169  260       AT_rich (111)  MIRb (57)  AluSx (45) 
4  746365  chr6  NT_007299.13  5766099-6512464    1191  278       AT_rich (169)  L2a (44)  (TA)n (43) 
5  744422  chr4  NT_016354.19  87405585-88150007    1260  307       AT_rich (133)  L2a (49)  AluY (45) 
6  732510  chr13  NT_024524.14  52879572-53612082    1078  235       AT_rich (154)  MIR (53)  MIRb (47) 
7  706626  chr3  NT_005612.16  50812302-51518928    1163  288       AT_rich (143)  L2a (39)  MIRb (33) 
8  668417  chr21  NT_011512.11  9034969-9703386    1158  295       AT_rich (136)  (TA)n (35)  AluY (32) 
9  661694  chr13  NT_009952.14  2470353-3132047    1083  268       AT_rich (143)  AluSx (37)  L2a (28) 
10  660942  chr2  NT_022135.16  31821990-32482932    967  232       AT_rich (127)  MIRb (47)  L2c (38) 
11  656771  chr5  NT_006576.16  22235429-22892200    1044  243       AT_rich (130)  L2a (48)  AluY (37) 
12  637271  chr1  NT_004487.19  25603637-26240908    1101  239       AT_rich (81)  AluSx (64)  MIR (38) 
13  636974  chr5  NT_006576.16  29023040-29660014    1030  264       AT_rich (117)  L1M5 (31)  AluSx (30) 
14  632482  chr8  NT_008046.16  7025068-7657550    989  256       AT_rich (92)  MIRb (51)  L2c (49) 
15  629881  chr18  NT_025028.14  14229292-14859173    1021  249       AT_rich (136)  MIRb (31)  L2a (31) 
16  622614  chr12  NT_029419.12  52723324-53345938    1070  267       AT_rich (94)  L2a (45)  L2c (34) 

Help
Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   1056072       chr3  NT_005612.16  70706663-71762735    SI  sucrase-isomaltase,_intestinal
SLITRK3  SLIT_and_NTRK-like_protein_3_precursor
2   865730       chr13  NT_024524.14  64294729-65160459    LOC647317 
3   810071       chr9  NT_008413.18  20746649-21556720    MIR491  microRNA:hsa-mir-491
PTPLAD2  3-hydroxyacyl-CoA_dehydratase_4
IFNNP1 
IFNB1  interferon_beta_precursor
IFNW1  interferon_omega-1_precursor
IFNA21  interferon_alpha-21_precursor
IFNWP15 
IFNA4  interferon_alpha-4_precursor
IFNWP9 
IFNA7  interferon_alpha-7_precursor
IFNA10  interferon_alpha-10_precursor
IFNWP18 
IFNA16  interferon_alpha-16_precursor
IFNA17  interferon_alpha-17_precursor
IFNWP5 
IFNA14  interferon_alpha-14_precursor
IFNA22P 
IFNA5  interferon_alpha-5_precursor
KLHL9  kelch-like_protein_9
IFNA6  interferon_alpha-6_precursor
IFNA13  interferon_alpha-1/13_precursor
IFNA2  interferon_alpha-2_precursor
IFNWP12 
IFNA8  interferon_alpha-8_precursor
IFNWP2 
IFNA1  interferon_alpha-1/13_precursor
MIR31  microRNA:hsa-mir-31
4   746365       chr6  NT_007299.13  5766099-6512464    LOC100420211 
5   744422       chr4  NT_016354.19  87405585-88150007    FSTL5  follistatin-related_protein_5_isoform_c
LOC100131135 
6   732510       chr13  NT_024524.14  52879572-53612082    RPL35AP31  dachshund_homolog_1_isoform_c
RPS10P21 
8   668417       chr21  NT_011512.11  9034969-9703386    LOC100420035 
MAPK6PS2 


Posfai@neb.com
May 11, 2011