Distribution of restriction sites in the human genome

Enzyme:  AclI               Longest uncut segments
Specificity:  AACGTT               Repeats in uncut segments
Number of sites:  162140               Genes in uncut segments
Mean distance between sites:  17647 base pairs
Standard deviation:  18473 base pairs
Site density 56.7 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   517786  chr15  NT_037852.6  1376835-1894621    3.92 % in   68 repeats    0.30 % in 1 genes
2   440642  chr6  NT_167246.1  3050489-3491131    14.84 % in   302 repeats    22.35 % in 11 genes
3   432033  chr6  NT_167244.1  2353750-2785783    3.62 % in   63 repeats    1.21 % in 1 genes
4   314469  chr6  NT_167244.1  3148579-3463048    12.07 % in   193 repeats    23.65 % in 9 genes
5   272590  chr6  NT_167247.1  4383440-4656030    9.12 % in   101 repeats    89.60 % in 10 genes
6   266078  chr6  NT_167244.1  1994698-2260776    4.29 % in   55 repeats    5.65 % in 4 genes
7   262379  chr5  NT_034772.6  16032453-16294832    65.29 % in   465 repeats    0.20 % in 1 genes
8   262206  chr6  NT_167247.1  1065601-1327807    33.19 % in   260 repeats    21.39 % in 23 genes
9   253407  chr6  NT_167247.1  1477096-1730503    16.61 % in   176 repeats    0.00 % in 0 genes
10   246332  chr1  NT_004487.19  6366873-6613205    38.26 % in   495 repeats    0.00 % in 0 genes
11   241657  chr6  NT_167244.1  2803351-3045008    12.75 % in   156 repeats    0.00 % in 0 genes
12   232123  chr11  NT_167190.1  17556468-17788591    34.05 % in   424 repeats    0.00 % in 0 genes
13   221751  chr10  NT_030059.13  55047421-55269172    45.37 % in   466 repeats    0.00 % in 0 genes
14   219965  chr6  NT_167244.1  4387352-4607317    4.95 % in   21 repeats    0.00 % in 0 genes
15   209068  chr11  NT_009237.18  15086907-15295975    40.85 % in   393 repeats    0.00 % in 0 genes
16   208598  chr17  NT_010783.15  38851377-39059975    37.28 % in   401 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 
517786  chr15  NT_037852.6  1376835-1894621    68  39       Tigger2 (6)  L1MDa (6)  AluSx (4) 
440642  chr6  NT_167246.1  3050489-3491131    302  84       AluSx (48)  AluY (19)  AluSq (15) 
432033  chr6  NT_167244.1  2353750-2785783    63  36       AluY (6)  L4 (3)  L1ME4a (3) 
314469  chr6  NT_167244.1  3148579-3463048    193  55       AluSx (25)  MIR (11)  AluSq (11) 
272590  chr6  NT_167247.1  4383440-4656030    101  56       MIRb (5)  MIR (5)  L1PB1 (5) 
266078  chr6  NT_167244.1  1994698-2260776    55  30       AluSx (7)  MIRb (3)  MIR (3) 
262379  chr5  NT_034772.6  16032453-16294832    465  181       AT_rich (22)  AluJo (15)  L2a (13) 
262206  chr6  NT_167247.1  1065601-1327807    260  106       ERV3-16A3_I-int (12)  Charlie9 (12)  MLT1F1 (9) 
253407  chr6  NT_167247.1  1477096-1730503    176  77       L2a (12)  MIR3 (10)  L2c (9) 
10  246332  chr1  NT_004487.19  6366873-6613205    495  102       AluSx (68)  L2c (29)  AluJo (29) 
11  241657  chr6  NT_167244.1  2803351-3045008    156  48       AluSx (22)  AluJo (15)  AluJb (10) 
12  232123  chr11  NT_167190.1  17556468-17788591    424  91       MIRb (44)  L2b (39)  MIR (35) 
13  221751  chr10  NT_030059.13  55047421-55269172    466  102       AluSx (68)  AluJb (33)  AluY (30) 
14  219965  chr6  NT_167244.1  4387352-4607317    21  14       HERVH-int (4)  AluSx (3)  MER57-int (2) 
15  209068  chr11  NT_009237.18  15086907-15295975    393  115       MIRb (60)  MIR (36)  L2c (26) 
16  208598  chr17  NT_010783.15  38851377-39059975    401  83       AluSx (61)  AluY (28)  AluJo (27) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   517786       chr15  NT_037852.6  1376835-1894621    LOC100418897 
2   440642       chr6  NT_167246.1  3050489-3491131    MSH5  mutS_protein_homolog_5_isoform_c
NEU1  sialidase-1_precursor
C2  complement_C2_isoform_3
CFB  complement_factor_B_preproprotein_preproprotein
TNXB  tenascin-X_isoform_1_precursor
PRRT1  proline-rich_transmembrane_protein_1
LOC100294186  hypothetical_LOC100294186,_transcript_variant_2
PPT2  lysosomal_thioesterase_PPT2_isoform_a_precursor
EGFL8  epidermal_growth_factor-like_protein_8_precursor
AGPAT1  1-acyl-sn-glycerol-3-phosphate_acyltransferase_alpha
RNF5  E3_ubiquitin-protein_ligase_RNF5
3   432033       chr6  NT_167244.1  2353750-2785783    MICB  MHC_class_I_polypeptide-related_sequence_B_precursor
4   314469       chr6  NT_167244.1  3148579-3463048    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
PRRT1  proline-rich_transmembrane_protein_1
LOC100294105  hypothetical_LOC100294105,_transcript_variant_2
PPT2  lysosomal_thioesterase_PPT2_isoform_a_precursor
EGFL8  epidermal_growth_factor-like_protein_8_precursor
AGPAT1  1-acyl-sn-glycerol-3-phosphate_acyltransferase_alpha
RNF5  E3_ubiquitin-protein_ligase_RNF5
5   272590       chr6  NT_167247.1  4383440-4656030    RPL32P1  HLA_class_II_histocompatibility_antigen,_DP_beta_1_chain_precursor
HLA-DPA2 
COL11A2P 
LOC100507722  hypothetical_protein_LOC100507722
COL11A2  collagen_alpha-2(XI)_chain_isoform_4_precursor
RNY4P10  retinoic_acid_receptor_RXR-beta
SLC39A7  zinc_transporter_SLC39A7
HSD17B8  estradiol_17-beta-dehydrogenase_8
MIR219-1  microRNA:hsa-mir-219-1
RING1  E3_ubiquitin-protein_ligase_RING1
6   266078       chr6  NT_167244.1  1994698-2260776    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
7   262379       chr5  NT_034772.6  16032453-16294832    RPS20P3 
8   262206       chr6  NT_167247.1  1065601-1327807    HCG4P9 
HLA-P 
RPL7AP7 
HCG2P8 
MICG 
HCP5P12 
HCG4P8 
HLA-G  HLA_class_I_histocompatibility_antigen,_alpha_chain_G_precursor
LOC100133214  hypothetical_protein_LOC100133214
HCGVIII-2 
MICF 
3.8-1.4 
HCG4P7 
P5-09  major_histocompatibility_complex,_class_I,_H_(pseudogene)
P5-07 
HLA-T 
HCG2P7  HLA_complex_group_2_pseudogene_7
3.8-1.3 
LOC100507680  HLA_class_I_histocompatibility_antigen,_A-69_alpha_chain-like_isoform_13
HLA-W 
HCG2P6 
MICD 
HCG9  HLA_complex_group_9



Posfai@neb.com
May 11, 2011