Distribution of restriction sites in the human genome

Enzyme:  BsiWI               Longest uncut segments
Specificity:  CGTACG               Repeats in uncut segments
Number of sites:  11327               Genes in uncut segments
Mean distance between sites:  252613 base pairs
Standard deviation:  300468 base pairs
Site density 4.0 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   3704546  chr6  NT_007299.13  13754805-17459351    55.50 % in   5671 repeats    21.76 % in 12 genes
2   3160673  chr1  NT_032977.9  48483273-51643946    50.04 % in   5015 repeats    15.60 % in 16 genes
3   3084035  chr6  NT_025741.15  16774519-19858554    48.60 % in   5042 repeats    7.00 % in 19 genes
4   2911707  chr11  NT_033899.8  7870462-10782169    50.17 % in   4762 repeats    31.21 % in 18 genes
5   2875121  chr4  NT_016354.19  80635202-83510323    46.90 % in   4601 repeats    24.55 % in 20 genes
6   2747548  chr3  NT_005612.16  20672664-23420212    40.47 % in   4137 repeats    52.83 % in 8 genes
7   2733096  chr1  NT_167186.1  14101513-16834609    49.29 % in   4641 repeats    20.99 % in 25 genes
8   2680511  chr3  NT_005612.16  2774969-5455480    51.75 % in   3822 repeats    52.21 % in 41 genes
9   2597662  chr9  NT_008413.18  29926623-32524285    54.82 % in   4020 repeats    0.00 % in 0 genes
10   2537054  chrX  NT_011651.17  32349930-34886984    53.66 % in   4429 repeats    0.00 % in 0 genes
11   2473475  chr2  NT_005403.17  37564887-40038362    50.72 % in   3926 repeats    0.00 % in 0 genes
12   2466753  chr11  NT_009237.18  36487162-38953915    53.70 % in   4095 repeats    0.00 % in 0 genes
13   2420078  chrY  NT_011875.12  3564332-5984410    60.74 % in   4048 repeats    0.00 % in 0 genes
14   2408220  chr18  NT_010966.14  22561337-24969557    45.07 % in   3780 repeats    0.00 % in 0 genes
15   2373226  chr11  NT_167190.1  32440702-34813928    52.26 % in   4041 repeats    0.00 % in 0 genes
16   2370369  chr4  NT_016354.19  25887889-28258258    51.02 % in   3762 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 
1  3704546  chr6  NT_007299.13  13754805-17459351    5671  559       AT_rich (476)  AluSx (246)  L2a (215) 
2  3160673  chr1  NT_032977.9  48483273-51643946    5015  563       AT_rich (493)  L2a (208)  MIRb (205) 
3  3084035  chr6  NT_025741.15  16774519-19858554    5042  528       AT_rich (443)  MIRb (204)  AluSx (199) 
4  2911707  chr11  NT_033899.8  7870462-10782169    4762  539       AT_rich (415)  MIRb (227)  L2c (190) 
5  2875121  chr4  NT_016354.19  80635202-83510323    4601  558       AT_rich (466)  L2a (178)  MIR (161) 
6  2747548  chr3  NT_005612.16  20672664-23420212    4137  462       AT_rich (332)  MIRb (228)  L2c (193) 
7  2733096  chr1  NT_167186.1  14101513-16834609    4641  528       MIRb (223)  AluSx (221)  AT_rich (211) 
8  2680511  chr3  NT_005612.16  2774969-5455480    3822  505       AT_rich (371)  AluSx (146)  MIR (134) 
9  2597662  chr9  NT_008413.18  29926623-32524285    4020  513       AT_rich (406)  MIRb (115)  L2a (104) 
10  2537054  chrX  NT_011651.17  32349930-34886984    4429  471       MIR (282)  MIRb (263)  L2c (211) 
11  2473475  chr2  NT_005403.17  37564887-40038362    3926  495       AT_rich (427)  AluSx (129)  MIR (122) 
12  2466753  chr11  NT_009237.18  36487162-38953915    4095  509       AT_rich (371)  MIRb (181)  MIR (163) 
13  2420078  chrY  NT_011875.12  3564332-5984410    4048  499       AT_rich (290)  AluSx (190)  AluJo (159) 
14  2408220  chr18  NT_010966.14  22561337-24969557    3780  462       AT_rich (204)  MIRb (195)  MIR (192) 
15  2373226  chr11  NT_167190.1  32440702-34813928    4041  479       MIRb (344)  AT_rich (260)  MIR (195) 
16  2370369  chr4  NT_016354.19  25887889-28258258    3762  458       AT_rich (305)  MIRb (181)  MIR (165) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   3704546       chr6  NT_007299.13  13754805-17459351    COL12A1  collagen_alpha-1(XII)_chain_short_isoform_precursor
COX7A2  cytochrome_c_oxidase_subunit_7A2,_mitochondrial_precursor
TMEM30A  cell_cycle_control_protein_50A_isoform_2
LOC100506804  hypothetical_LOC100506804,_transcript_variant_2
LOC100288170  filamin-A-interacting_protein_1
RPL26P20 
LOC100421091  sentrin-specific_protease_6_isoform_2
MYO6  myosin-VI
IMPG1  interphotoreceptor_matrix_proteoglycan_1_precursor
LOC100131680 
HTR1B  5-hydroxytryptamine_receptor_1B
RPS6P7 
2   3160673       chr1  NT_032977.9  48483273-51643946    LOC100422537  PDZ_domain-containing_protein_GIPC2
LOC100132264 
MGC27382  hypothetical_MGC27382
PTGFR  prostaglandin_F2-alpha_receptor_isoform_b_precursor
IFI44L  interferon-induced_protein_44-like
IFI44  interferon-induced_protein_44
RPL23P3 
LOC652549 
ELTD1  EGF,_latrophilin_and_seven_transmembrane_domain-containing_protein_1_precursor
LOC729779 
ADH5P2 
LOC553139 
HMGB1P18 
LOC100129325 
LOC100129325 
RPL7P10 
3   3084035       chr6  NT_025741.15  16774519-19858554    LAMA4  laminin_subunit_alpha-4_isoform_3_precursor
LOC100128588 
RFPL4B  ret_finger_protein-like_4B
RPSAP45 
LOC442249 
LOC643859 
PA2G4P5 
LOC100287612  hypothetical_LOC100287612
LOC643884 
RPS27AP11 
RPL30P8 
MARCKS  myristoylated_alanine-rich_C-kinase_substrate
FLJ34503  hypothetical_FLJ34503
HDAC2  histone_deacetylase_2
LOC100422450 
HS3ST5  heparan_sulfate_glucosamine_3-O-sulfotransferase_5
RPSAP43 
LOC441167  hCG1820801
LOC728614 
4   2911707       chr11  NT_033899.8  7870462-10782169    LOC100506742  inactive_caspase-12-like_isoform_2
LOC643733  caspase_4,_apoptosis-related_cysteine_peptidase_pseudogene,_transcript_variant_2
CASP4  caspase-4_isoform_gamma_precursor
CASP5  caspase-5_isoform_f_precursor
CASP1  caspase-1_isoform_gamma_precursor
CARD16  caspase_recruitment_domain-containing_protein_16_isoform_2
LOC440067 
CARD17  caspase_recruitment_domain-containing_protein_17
CARD18  caspase_recruitment_domain-containing_protein_18
OR2AL1P 
HSPD1P13  glutamate_receptor_4_isoform_3_precursor
KIAA1826  hypothetical_protein_LOC84437
KBTBD3  kelch_repeat_and_BTB_domain-containing_protein_3
AASDHPPT  L-aminoadipate-semialdehyde_dehydrogenase-phosphopantetheinyl_transferase
LOC643855 
LOC100422300  guanylate_cyclase_soluble_subunit_alpha-2
ASS1P13 
LOC100271884  CWF19-like_protein_2
5   2875121       chr4  NT_016354.19  80635202-83510323    NPY2R  neuropeptide_Y_receptor_type_2
MAP9  microtubule-associated_protein_9
LOC100420289 
LOC100287939 
TRNAQ54P 
LOC100287591 
-  tRNA-Leu
GUCY1A3  guanylate_cyclase_soluble_subunit_alpha-3_isoform_B
GUCY1B3  guanylate_cyclase_soluble_subunit_beta-1
ACCN5  amiloride-sensitive_cation_channel_5
TDO2  tryptophan_2,3-dioxygenase
CTSO  cathepsin_O_preproprotein_preproprotein
FTH1P21 
LOC100505784  hypothetical_LOC100505784
PDGFC  platelet-derived_growth_factor_C_precursor
GLRB  glycine_receptor_subunit_beta_isoform_B_precursor
LOC391707 
GRIA2  glutamate_receptor_2_isoform_3
LOC340017  hypothetical_LOC340017
RPL6P11 
6   2747548       chr3  NT_005612.16  20672664-23420212    LOC100506673  hypothetical_LOC100506673
LOC645207 
GAP43  neuromodulin_isoform_1
LOC100506708  hypothetical_LOC100506708
BZW1P2 
LOC285194  hypothetical_LOC285194
LOC100506724  hypothetical_LOC100506724
LOC728873 
7   2733096       chr1  NT_167186.1  14101513-16834609    LOC100129664 
LOC100421052 
LOC100419489  serine/threonine-protein_kinase_MARK1
C1orf115  hypothetical_protein_LOC79762
MOSC2  MOSC_domain-containing_protein_2,_mitochondrial_precursor
MOSC1  MOSC_domain-containing_protein_1,_mitochondrial_precursor
HLX  H2.0-like_homeobox_protein
LOC100132626 
LOC400804  hypothetical_LOC400804
LOC100132179 
DUSP10  dual_specificity_protein_phosphatase_10_isoform_b
LOC100422330 
-  tRNA-Thr
CICP13 
LOC653056 
LOC653056  hypothetical_LOC728417
HHIPL2  HHIP-like_protein_2_precursor
TAF1A  TATA_box-binding_protein-associated_factor_RNA_polymerase_I_subunit_A_isoform_2
LOC100506161  hypothetical_LOC100506161
LOC100291899  melanoma_inhibitory_activity_protein_3_precursor
AIDA  axin_interactor,_dorsalization-associated_protein
C1orf58  BRO1_domain-containing_protein_BROX
FAM177B  hypothetical_protein_LOC400823
NDUFB1P2  protein_dispatched_homolog_1
TLR5  toll-like_receptor_5_precursor
8   2680511       chr3  NT_005612.16  2774969-5455480    LOC391556 
MTRNR2L12 
RPL18AP8 
LOC100131442 
LOC100129736 
EPHA6  ephrin_type-A_receptor_6_isoform_b
ARL6  ADP-ribosylation_factor-like_protein_6
LOC100506362  hypothetical_LOC100506362
CRYBG3  hypothetical_protein_LOC131544
MINA  MYC-induced_nuclear_antigen_isoform_b
GABRR3  gamma-aminobutyric_acid_receptor_subunit_rho-3_precursor
OR5BM1P 
OR5AC1 
OR5AC2  olfactory_receptor_5AC2
OR5AC4P 
POU5F1P7 
OR5H1  olfactory_receptor_5H1
OR5H14  olfactory_receptor_5H14
OR5H15  olfactory_receptor_5H15
OR5H5P 
OR5H3P 
OR5H4P 
OR5H7P 
OR5H6  olfactory_receptor_5H6
OR5H2  olfactory_receptor_5H2
OR5H8P 
OR5K4  olfactory_receptor_5K4
OR5K3  olfactory_receptor_5K3
LOC100130484 
OR5K1  olfactory_receptor_5K1
OR5K2  olfactory_receptor_5K2
CLDND1  claudin_domain-containing_protein_1_isoform_a
LOC100130963 
GPR15  G-protein_coupled_receptor_15
CPOX  coproporphyrinogen-III_oxidase,_mitochondrial_precursor
RPL19P7 
LOC339843 
LOC100419185  type_2_lactosamine_alpha-2,3-sialyltransferase
DCBLD2  discoidin,_CUB_and_LCCL_domain-containing_protein_2_precursor
LOC100506377  hypothetical_LOC100506377
LOC100418920 


Posfai@neb.com
May 11, 2011