Distribution of restriction sites in the human genome

Enzyme:  NotI               Longest uncut segments
Specificity:  GCGGCCGC               Repeats in uncut segments
Number of sites:  9471               Genes in uncut segments
Mean distance between sites:  302116 base pairs
Standard deviation:  600864 base pairs
Site density 3.3 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   10851418  chr1  NT_004487.19  37807300-48658718    51.98 % in   17531 repeats    16.23 % in 43 genes
2   9446724  chr10  NT_030059.13  2827061-12273785    48.71 % in   15157 repeats    37.84 % in 38 genes
3   8171432  chr3  NT_022459.15  12834673-21006105    47.19 % in   12536 repeats    29.32 % in 11 genes
4   7112846  chr18  NT_010966.14  16635366-23748212    45.03 % in   11099 repeats    15.50 % in 13 genes
5   6874001  chr11  NT_009237.18  20559852-27433853    52.10 % in   11664 repeats    35.83 % in 21 genes
6   6678389  chr1  NT_032977.9  70977511-77655900    55.75 % in   10616 repeats    14.14 % in 33 genes
7   6402637  chr14  NT_026437.12  62980042-69382679    47.55 % in   10605 repeats    2.05 % in 11 genes
8   6068735  chrX  NT_011651.17  7485555-13554290    70.21 % in   9065 repeats    21.20 % in 26 genes
9   5922557  chr8  NT_008046.16  22369115-28291672    50.19 % in   9651 repeats    0.00 % in 0 genes
10   5711848  chr5  NT_034772.6  6423965-12135813    52.13 % in   8910 repeats    0.00 % in 0 genes
11   5626170  chr3  NT_022517.18  58163419-63789589    46.39 % in   10257 repeats    0.00 % in 0 genes
12   5577278  chr4  NT_022778.16  2278923-7856201    51.27 % in   8487 repeats    0.00 % in 0 genes
13   5536645  chr4  NT_016354.19  99991371-105528016    51.42 % in   8987 repeats    0.00 % in 0 genes
14   5395584  chr4  NT_016354.19  54281504-59677088    53.79 % in   8266 repeats    0.00 % in 0 genes
15   5294689  chr11  NT_009237.18  36471561-41766250    52.38 % in   8912 repeats    0.00 % in 0 genes
16   5279650  chr4  NT_016354.19  84573115-89852765    50.97 % in   8381 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  10851418  chr1  NT_004487.19  37807300-48658718    17531  798       AT_rich (2062)  L2a (641)  AluSx (530) 
2  9446724  chr10  NT_030059.13  2827061-12273785    15157  784       AT_rich (1423)  MIRb (685)  MIR (624) 
3  8171432  chr3  NT_022459.15  12834673-21006105    12536  741       AT_rich (1567)  L2a (391)  MIR (360) 
4  7112846  chr18  NT_010966.14  16635366-23748212    11099  707       AT_rich (886)  MIRb (472)  MIR (430) 
5  6874001  chr11  NT_009237.18  20559852-27433853    11664  704       AT_rich (959)  MIRb (711)  MIR (572) 
6  6678389  chr1  NT_032977.9  70977511-77655900    10616  701       AT_rich (1154)  L2a (417)  MIR (344) 
7  6402637  chr14  NT_026437.12  62980042-69382679    10605  730       AT_rich (869)  MIRb (502)  MIR (427) 
8  6068735  chrX  NT_011651.17  7485555-13554290    9065  674       AT_rich (719)  AluSx (227)  (TA)n (192) 
9  5922557  chr8  NT_008046.16  22369115-28291672    9651  710       AT_rich (1054)  L2a (385)  MIRb (357) 
10  5711848  chr5  NT_034772.6  6423965-12135813    8910  681       AT_rich (942)  AluSx (292)  L2a (280) 
11  5626170  chr3  NT_022517.18  58163419-63789589    10257  629       MIRb (781)  MIR (615)  L2a (508) 
12  5577278  chr4  NT_022778.16  2278923-7856201    8487  688       AT_rich (1112)  L2a (297)  MIR (250) 
13  5536645  chr4  NT_016354.19  99991371-105528016    8987  679       AT_rich (906)  AluSx (377)  L2a (284) 
14  5395584  chr4  NT_016354.19  54281504-59677088    8266  705       AT_rich (1047)  L2a (281)  AluSx (227) 
15  5294689  chr11  NT_009237.18  36471561-41766250    8912  666       AT_rich (730)  MIRb (473)  MIR (372) 
16  5279650  chr4  NT_016354.19  84573115-89852765    8381  679       AT_rich (865)  AluSx (292)  L2a (284) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   10851418       chr1  NT_004487.19  37807300-48658718    TPR  nucleoprotein_TPR
OCLM  oculomedin
PDC  phosducin_isoform_b
LOC100131939 
PTGS2  prostaglandin_G/H_synthase_2_precursor
PLA2G4A  cytosolic_phospholipase_A2
FDPSP1 
LOC100422527 
LOC100129274 
LOC100421343 
RPS3AP9 
LOC647132 
FAM5C  family_with_sequence_similarity_5,_member_C_precursor
LOC440704  hypothetical_LOC440704
LOC100421399 
LOC100506420  hypothetical_LOC100506420
RGS18  regulator_of_G-protein_signaling_18
LOC647150 
RGS21  regulator_of_G-protein_signaling_21
RGS1  regulator_of_G-protein_signaling_1
RGS13  regulator_of_G-protein_signaling_13
RPS27AP5 
LOC100130137 
RGS2  regulator_of_G-protein_signaling_2
LOC730190 
LOC100506438  hypothetical_LOC100506438
UCHL5  ubiquitin_carboxyl-terminal_hydrolase_isozyme_L5
TROVE2  60_kDa_SS-A/Ro_ribonucleoprotein_isoform_2
GLRX2  glutaredoxin-2,_mitochondrial_isoform_2
B3GALT2  beta-1,3-galactosyltransferase_2
RPL23AP22 
EEF1A1P14 
KCNT2  potassium_channel_subfamily_T_member_2
CFH  complement_factor_H_isoform_b_precursor
CFHR3  complement_factor_H-related_protein_3_isoform_2_precursor
CFHR1  complement_factor_H-related_protein_1_precursor
LOC100289145 
CFHR4  complement_factor_H-related_protein_4_precursor
CFHR2  complement_factor_H-related_protein_2_precursor
CFHR5  complement_factor_H-related_protein_5_precursor
F13B  coagulation_factor_XIII_B_chain_precursor
ASPM  abnormal_spindle-like_microcephaly-associated_protein
ZBTB41  zinc_finger_and_BTB_domain-containing_protein_41
2   9446724       chr10  NT_030059.13  2827061-12273785    LOC728532 
SGMS1  phosphatidylcholine:ceramide_cholinephosphotransferase_1
LOC644451 
LOC644459 
LOC729023 
LOC100421009 
LOC100420827 
CTSLL4 
LOC653895 
ASAH2B  putative_inactive_neutral_ceramidase_B
LOC100506921  hypothetical_LOC100506921
A1CF  APOBEC1_complementation_factor_isoform_3
LOC100287708 
CSTF2T  cleavage_stimulation_factor_subunit_2_tau_variant
LOC100506939  hypothetical_LOC100506939,_transcript_variant_1
DKK1  dickkopf-related_protein_1_precursor
LOC100506967  hypothetical_LOC100506967
RPL31P44 
LOC399774 
MBL2  mannose-binding_protein_C_precursor
MIR548F1  microRNA_548f-1
MTRNR2L5  MTRNR2-like_5
GAPDHP21 
LOC100419872 
ZWINT  ZW10_interactor_isoform_b
MRPS35P3 
LOC100506981  inositol_polyphosphate_multikinase
CISD1  CDGSH_iron-sulfur_domain-containing_protein_1
UBE2D1  ubiquitin-conjugating_enzyme_E2_D1
TFAM  transcription_factor_A,_mitochondrial_precursor
LOC100421635  family_with_sequence_similarity_133,_member_B_pseudogene
LOC100507008  hypothetical_LOC100507008
RPLP1P10 
LOC644871 
PHYHIPL  phytanoyl-CoA_hydroxylase-interacting_protein-like_isoform_2
FAM13C  hypothetical_protein_LOC220965_isoform_4
MRPL50P4 
SLC16A9  monocarboxylate_transporter_9
3   8171432       chr3  NT_022459.15  12834673-21006105    RPS12P6  roundabout_homolog_1_isoform_d
LOC100130821 
LOC100129557 
LOC100419178  1,4-alpha-glucan-branching_enzyme
RPL7AP23 
CYP51P1 
SRRM1P2 
LOC100130326  similar_to_MUF1_protein
LOC100422711  cell_adhesion_molecule_2_isoform_3
VGLL3  transcription_cofactor_vestigial-like_protein_3
LOC100289640 
4   7112846       chr18  NT_010966.14  16635366-23748212    LOC100506837  hypothetical_LOC100506837
MIR4318  microRNA_4318
RPL12P40 
LOC100506854  hypothetical_LOC100506854
RPL17P45 
KC6  keratoconus_gene_6
NPM1P1 
LOC100301521 
PIK3C3  phosphatidylinositol_3-kinase_catalytic_subunit_type_3
RIT2  GTP-binding_protein_Rit2
SYT4  synaptotagmin-4
IBTKP1 
KRT8P5 
5   6874001       chr11  NT_009237.18  20559852-27433853    SLC6A5  sodium-_and_chloride-dependent_glycine_transporter_2
NELL1  protein_kinase_C-binding_protein_NELL1_isoform_2_precursor
ANO5  anoctamin-5_isoform_b
SLC17A6  vesicular_glutamate_transporter_2
FANCF  Fanconi_anemia_group_F_protein
GAS2  growth_arrest-specific_protein_2
SVIP  small_VCP/p97-interacting_protein
LOC100131557 
LOC645598 
LOC100129382 
RPS2P38 
LOC100288844 
LUZP2  leucine_zipper_protein_2_precursor
LOC100130747 
RPL36AP40 
MUC15  mucin-15_isoform_b
SLC5A12  sodium-coupled_monocarboxylate_transporter_2
FIBIN  fin_bud_initiation_factor_homolog_precursor
BBOX1  gamma-butyrobetaine_dioxygenase
CCDC34  coiled-coil_domain-containing_protein_34_isoform_2
LGR4  leucine-rich_repeat-containing_G-protein_coupled_receptor_4_precursor
6   6678389       chr1  NT_032977.9  70977511-77655900    GPR88  probable_G-protein_coupled_receptor_88
RPL7AP17 
RPL36AP12 
VCAM1  vascular_cell_adhesion_protein_1_isoform_b_precursor
EXTL2  exostosin-like_2
LOC100421397  zinc_transporter_7
DPH5  diphthine_synthase_isoform_b
LOC100506051  hypothetical_LOC100506051
LOC100506029  hypothetical_LOC100506029
S1PR1  sphingosine_1-phosphate_receptor_1
RPS20P6 
PPIAP7 
RPSAP19 
LOC100421469  DnaJ_(Hsp40)_homolog,_subfamily_A,_member_1_pseudogene
LOC100421046  collagen_alpha-1(XI)_chain_isoform_E_preproprotein
RNPC3  RNA-binding_protein_40
AMY2B  alpha-amylase_2B_precursor
AMY2A  pancreatic_alpha-amylase_precursor
AMY1A  alpha-amylase_1_precursor
AMY1B  alpha-amylase_1_precursor
AMYP1 
AMY1C  alpha-amylase_1_precursor
LOC100131348 
LOC100129138  THAP_domain_containing,_apoptosis_associated_protein_3_pseudogene
FTLP17 
CDK4PS 
LOC100499497 
LOC401957 
LOC126987 
LOC100289022 
LOC100422372 
PRMT6  protein_arginine_N-methyltransferase_6
NTNG1  netrin-G1_isoform_3
7   6402637       chr14  NT_026437.12  62980042-69382679    SEL1L  protein_sel-1_homolog_1_precursor
EEF1A1P2 
RPL9P6 
EIF3LP1 
ENSAP2 
RNU7-51P 
LOC100421611 
RNU3P3 
LOC100506731  hypothetical_LOC100506731
FLRT2  leucine-rich_repeat_transmembrane_protein_FLRT2_precursor
LOC100421119 
8   6068735       chrX  NT_011651.17  7485555-13554290    UBE2DNL  ubiquitin-conjugating_enzyme_E2D_N-terminal_like_(pseudogene)
APOOL  apolipoprotein_O-like_precursor
SATL1  spermidine/spermine_N(1)-acetyltransferase-like_protein_1
LOC100421745 
ZNF711  zinc_finger_protein_711
POF1B  protein_POF1B
MIR1321  microRNA_1321
LOC730792 
CHM  rab_proteins_geranylgeranyltransferase_component_A_1_isoform_b
LOC441505 
LOC100129298 
BA345E19.2  dachshund_homolog_2_isoform_c
KLHL4  kelch-like_protein_4_isoform_1
RPSAP15 
MRPS22P1 
LOC100129133 
CAPZA1P 
CPXCR1  CPX_chromosomal_region_candidate_gene_1_protein
LOC100421038 
SRIP2 
TGIF2LX  homeobox_protein_TGIF2LX
LOC100130134 
USP12PX 
RNF19BPX 
LOC100419789 
LOC100131981 


Posfai@neb.com
May 11, 2011