Distribution of restriction sites in the human genome

Enzyme:  PmeI               Longest uncut segments
Specificity:  GTTTAAAC               Repeats in uncut segments
Number of sites:  41009               Genes in uncut segments
Mean distance between sites:  69773 base pairs
Standard deviation:  75434 base pairs
Site density 14.3 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   1423308  chr6  NT_167244.1  1649356-3072664    17.06 % in   934 repeats    12.74 % in 27 genes
2   1303948  chr19  NT_011295.11  7932291-9236239    57.21 % in   3691 repeats    78.95 % in 39 genes
3   998261  chr19  NT_077812.2  144401-1142662    56.28 % in   2746 repeats    57.45 % in 44 genes
4   933183  chr16  NT_010393.16  28190657-29123840    59.59 % in   2677 repeats    48.45 % in 33 genes
5   852096  chr2  NT_005334.16  2653575-3505671    39.62 % in   1409 repeats    44.09 % in 3 genes
6   836312  chr12  NT_009775.17  1794467-2630779    56.28 % in   2316 repeats    71.03 % in 9 genes
7   832968  chr8  NT_008046.16  56322810-57155778    31.79 % in   1139 repeats    44.94 % in 15 genes
8   801864  chr12  NT_029419.12  14964194-15766058    40.06 % in   1494 repeats    43.67 % in 39 genes
9   798196  chr19  NT_011295.11  2316294-3114490    60.98 % in   2324 repeats    0.00 % in 0 genes
10   775408  chr17  NT_010783.15  37434760-38210168    43.05 % in   1559 repeats    0.00 % in 0 genes
11   755165  chr11  NT_009237.18  3202478-3957643    55.06 % in   1605 repeats    0.00 % in 0 genes
12   753780  chr9  NT_008470.19  19197081-19950861    48.28 % in   1374 repeats    0.00 % in 0 genes
13   747346  chr15  NT_037852.6  1175977-1923323    18.73 % in   525 repeats    0.00 % in 0 genes
14   745964  chr17  NT_010783.15  1450757-2196721    48.77 % in   1787 repeats    0.00 % in 0 genes
15   718737  chr15  NT_010194.17  1275230-1993967    52.42 % in   1318 repeats    0.00 % in 0 genes
16   710925  chr1  NT_021937.19  2619609-3330534    47.22 % in   1433 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  1423308  chr6  NT_167244.1  1649356-3072664    934  209       AluSx (99)  AluJo (44)  AluJb (44) 
2  1303948  chr19  NT_011295.11  7932291-9236239    3691  299       AluSx (663)  AluJo (310)  AluJb (212) 
3  998261  chr19  NT_077812.2  144401-1142662    2746  265       AluSx (453)  AluJo (261)  AluY (144) 
4  933183  chr16  NT_010393.16  28190657-29123840    2677  257       AluSx (401)  AluJo (200)  AluSq (137) 
5  852096  chr2  NT_005334.16  2653575-3505671    1409  303       MIRb (102)  MIR (71)  AT_rich (67) 
6  836312  chr12  NT_009775.17  1794467-2630779    2316  273       AluSx (304)  MIR (155)  MIRb (152) 
7  832968  chr8  NT_008046.16  56322810-57155778    1139  268       MIRb (87)  MIR (46)  (CA)n (37) 
8  801864  chr12  NT_029419.12  14964194-15766058    1494  230       AluSx (138)  MIRb (78)  MIR (68) 
9  798196  chr19  NT_011295.11  2316294-3114490    2324  232       AluSx (364)  AluJo (183)  AluY (155) 
10  775408  chr17  NT_010783.15  37434760-38210168    1559  246       AluSx (209)  AluJb (68)  AluJo (67) 
11  755165  chr11  NT_009237.18  3202478-3957643    1605  250       AluSx (175)  MIRb (78)  AluJo (76) 
12  753780  chr9  NT_008470.19  19197081-19950861    1374  298       AluSx (114)  AluY (51)  MIRb (44) 
13  747346  chr15  NT_037852.6  1175977-1923323    525  174       AluSx (25)  AT_rich (22)  AluJb (17) 
14  745964  chr17  NT_010783.15  1450757-2196721    1787  220       AluSx (231)  AluJb (101)  AluJo (88) 
15  718737  chr15  NT_010194.17  1275230-1993967    1318  258       AluY (99)  AluSx (81)  AT_rich (60) 
16  710925  chr1  NT_021937.19  2619609-3330534    1433  244       AluSx (140)  L2a (77)  AluJo (68) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   1423308       chr6  NT_167244.1  1649356-3072664    LOC100507701 
GNL1  guanine_nucleotide-binding_protein-like_1
DHX16  putative_pre-mRNA-splicing_factor_ATP-dependent_RNA_helicase_DHX16_isoform_1
KIAA1949  phostensin
NRM  nurim
RPL7P4 
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
MUC21  mucin-21_precursor
LOC100507702  hypothetical_protein_LOC100507702
HCG22  HLA_complex_group_22
MICB  MHC_class_I_polypeptide-related_sequence_B_precursor
PPIAP9 
RPL15P4 
MCCD1  mitochondrial_coiled-coil_domain_protein_1_precursor
SNORD117  small_nucleolar_RNA,_C/D_box_117
TNF  tumor_necrosis_factor
LTB  lymphotoxin-beta_isoform_b
LST1  leukocyte-specific_transcript_1_protein_isoform_5
NCR3  natural_cytotoxicity_triggering_receptor_3_isoform_c
UQCRHP1 
MSH5  mutS_protein_homolog_5_isoform_c
C6orf26  protein_G7d
C6orf27  protein_G7c_precursor
VARS  valyl-tRNA_synthetase
2   1303948       chr19  NT_011295.11  7932291-9236239    SLC35E1  solute_carrier_family_35_member_E1
MED26  mediator_of_RNA_polymerase_II_transcription_subunit_26
LOC100507522  hypothetical_LOC100507522
C19orf42  hypothetical_protein_LOC79086_precursor
TMEM38A  trimeric_intracellular_cation_channel_type_A
NWD1  NACHT_and_WD_repeat_domain-containing_protein_1
SIN3B  paired_amphipathic_helix_protein_Sin3b
F2RL3  proteinase-activated_receptor_4_precursor
CPAMD8  C3_and_PZP-like_alpha-2-macroglobulin_domain-containing_protein_8
HAUS8  HAUS_augmin-like_complex_subunit_8_isoform_b
MYO9B  myosin-IXb_isoform_2
USE1  vesicle_transport_protein_USE1
OCEL1  occludin/ELL_domain-containing_protein_1
NR2F6  nuclear_receptor_subfamily_2_group_F_member_6
USHBP1  Usher_syndrome_type-1C_protein-binding_protein_1
C19orf62  BRCA1-A_complex_subunit_MERIT40
ANKLE1  ankyrin_repeat_and_LEM_domain-containing_protein_1
ABHD8  abhydrolase_domain-containing_protein_8
MRPL34  39S_ribosomal_protein_L34,_mitochondrial_precursor
DDA1  DET1-_and_DDB1-associated_protein_1
ANO8  anoctamin-8
GTPBP3  tRNA_modification_GTPase_GTPBP3,_mitochondrial_isoform_V
PLVAP  plasmalemma_vesicle-associated_protein
BST2  bone_marrow_stromal_antigen_2_precursor
FAM125A  multivesicular_body_subunit_12A
TMEM221  transmembrane_protein_221
NXNL1  nucleoredoxin-like_protein_1
LOC100507551  hypothetical_protein_LOC100507551
PGLS  6-phosphogluconolactonase
FAM129C  niban-like_protein_2_isoform_b
GLT25D1  procollagen_galactosyltransferase_1_precursor
RPL21P130 
UNC13A  protein_unc-13_homolog_A
MAP1S  microtubule-associated_protein_1S
FCHO1  FCH_domain_only_protein_1_isoform_c
B3GNT3  UDP-GlcNAc:betaGal_beta-1,3-N-acetylglucosaminyltransferase_3
INSL3  insulin-like_3_precursor
JAK3  tyrosine-protein_kinase_JAK3
SNORA68  small_nucleolar_RNA,_H/ACA_box_68
3   998261       chr19  NT_077812.2  144401-1142662    PEX11G  peroxisomal_membrane_protein_11C
C19orf45  hypothetical_protein_LOC374877
ZNF358  zinc_finger_protein_358
MCOLN1  mucolipin-1
PNPLA6  neuropathy_target_esterase_isoform_d
KIAA1543  calmodulin-regulated_spectrin-associated_protein_3_isoform_2
XAB2  pre-mRNA-splicing_factor_SYF1
LOC100131801  hypothetical_protein_LOC100131801
PCP2  Purkinje_cell_protein_2_homolog
STXBP2  syntaxin-binding_protein_2_isoform_b
RETN  resistin
C19orf59  mast_cell-expressed_membrane_protein_1
TRAPPC5  trafficking_protein_particle_complex_subunit_5
FCER2  low_affinity_immunoglobulin_epsilon_Fc_receptor
CLEC4G  C-type_lectin_domain_family_4_member_G
CD209  CD209_antigen_isoform_8
RPL21P129 
CLEC4M  C-type_lectin_domain_family_4_member_M_isoform_3
CLEC4GP1  C-type_lectin_domain_family_4,_member_G_pseudogene_1
EXOSC3P2 
EVI5L  EVI5-like_protein_isoform_2
FLJ22184  hypothetical_protein_LOC80164
LOC100419300  hCG2003956
LRRC8E  leucine-rich_repeat-containing_protein_8E
MAP2K7  dual_specificity_mitogen-activated_protein_kinase_kinase_7
LOC100507588  hypothetical_protein_LOC100507588
SNAPC2  small_nuclear_RNA_activating_complex,_polypeptide_2,_45kDa,_transcript_variant_2
CTXN1  cortexin-1
TIMM44  mitochondrial_import_inner_membrane_translocase_subunit_TIM44_precursor
ELAVL1  ELAV-like_protein_1
CCL25  C-C_motif_chemokine_25_precursor
FBN3  fibrillin-3_precursor
LOC100422633 
LASS4  LAG1_longevity_assurance_homolog_4
CD320  CD320_antigen_isoform_2_precursor
NDUFA7  NADH_dehydrogenase_[ubiquinone]_1_alpha_subcomplex_subunit_7
RPS28  40S_ribosomal_protein_S28
KANK3  KN_motif_and_ankyrin_repeat_domain-containing_protein_3
LOC100129682 
ANGPTL4  angiopoietin-related_protein_4_isoform_b_precursor
LOC100507567  hypothetical_LOC100507567
RAB11B  ras-related_protein_Rab-11B
MARCH2  E3_ubiquitin-protein_ligase_MARCH2_isoform_2
HNRNPM  heterogeneous_nuclear_ribonucleoprotein_M_isoform_b
4   933183       chr16  NT_010393.16  28190657-29123840    GAPDHP35 
LOC100506705  hypothetical_LOC100506705
SBK1  serine/threonine-protein_kinase_SBK1
LOC388237  nuclear_pore_complex-interacting_protein-like_1-like
EIF3CL  eukaryotic_translation_initiation_factor_3_subunit_C
CDC37P2 
NPIPL1 
CLN3  battenin
APOB48R  apolipoprotein_B-100_receptor
IL27  interleukin-27_subunit_alpha_precursor
NUPR1  nuclear_protein_1_isoform_b
CCDC101  SAGA-associated_factor_29_homolog
SULT1A2  sulfotransferase_1A2
SULT1A1  sulfotransferase_1A1_isoform_a
LOC728734  nuclear_pore_complex-interacting_protein-like_3-like_isoform_1
CDC37P1 
EIF3C  eukaryotic_translation_initiation_factor_3_subunit_C
LOC100420535 
LOC100507607  nuclear_pore_complex-interacting_protein-like_3-like
LOC100506786  nuclear_pore_complex-interacting_protein-like_3-like_isoform_2
RPS15AP33 
ATXN2L  ataxin-2-like_protein_isoform_A
TUFM  elongation_factor_Tu,_mitochondrial_precursor
SH2B1  SH2B_adapter_protein_1_isoform_3
LOC100289092  hypothetical_LOC100289092
RABEP2  rab_GTPase-binding_effector_protein_2
CD19  B-lymphocyte_antigen_CD19_isoform_2_precursor
NFATC2IP  NFATC2-interacting_protein
SPNS1  protein_spinster_homolog_1_isoform_2
LAT  linker_for_activation_of_T-cells_family_member_1_isoform_c
LOC730153 
LOC100506862  hypothetical_LOC100506862
LOC100129184 
5   852096       chr2  NT_005334.16  2653575-3505671    LOC100130731 
LOC339788  hypothetical_LOC339788
C2orf46  chromosome_2_open_reading_frame_46
6   836312       chr12  NT_009775.17  1794467-2630779    RPL29P25 
CCDC63  coiled-coil_domain-containing_protein_63
MYL2  myosin_regulatory_light_chain_2,_ventricular/cardiac_muscle_isoform
LOC100131138  hypothetical_LOC100131138
CUX2  homeobox_protein_cut-like_2
FAM109A  protein_FAM109A_isoform_2
LOC642580 
SH2B3  SH2B_adapter_protein_3
LOC100101246  ataxin-2
7   832968       chr8  NT_008046.16  56322810-57155778    LOC100131146 
NCRNA00051  non-protein_coding_RNA_51
TSNARE1  t-SNARE_domain-containing_protein_1
BAI1  brain-specific_angiogenesis_inhibitor_1_precursor
ARC  activity-regulated_cytoskeleton-associated_protein
JRK  jerky_protein_homolog_isoform_a
PSCA  prostate_stem_cell_antigen_preproprotein_preproprotein
LY6K  lymphocyte_antigen_6K_isoform_2
LOC100288181  hypothetical_LOC100288181
C8orf55  mesenchymal_stem_cell_protein_DSCD75_precursor
SLURP1  secreted_Ly-6/uPAR-related_protein_1_precursor
LYPD2  ly6/PLAUR_domain-containing_protein_2_precursor
LYNX1  ly-6/neurotoxin-like_protein_1_isoform_c
LY6D  lymphocyte_antigen_6D_precursor
LOC100288207  hypothetical_protein_LOC100288207
8   801864       chr12  NT_029419.12  14964194-15766058    KRT75  keratin,_type_II_cytoskeletal_75
KRT6B  keratin,_type_II_cytoskeletal_6B
KRT6C  keratin,_type_II_cytoskeletal_6C
KRT6A  keratin,_type_II_cytoskeletal_6A
KRT5  keratin,_type_II_cytoskeletal_5
KRT71  keratin,_type_II_cytoskeletal_71
KRT74  keratin,_type_II_cytoskeletal_74
KRT72  keratin,_type_II_cytoskeletal_72_isoform_2
KRT73  keratin,_type_II_cytoskeletal_73
KRT2  keratin,_type_II_cytoskeletal_2_epidermal
KRT1  keratin,_type_II_cytoskeletal_1
KRT77  keratin,_type_II_cytoskeletal_1b
KRT126P 
LOC400036 
LOC100418828 
LOC100128678 
LOC100418779 
LOC643898 
KRT76  keratin,_type_II_cytoskeletal_2_oral
KRT3  keratin,_type_II_cytoskeletal_3
KRT4  keratin,_type_II_cytoskeletal_4
KRT79  keratin,_type_II_cytoskeletal_79
KRT78  keratin,_type_II_cytoskeletal_78
RPL7P41 
KRT8  keratin,_type_II_cytoskeletal_8
KRT18  keratin,_type_I_cytoskeletal_18
EIF4B  eukaryotic_translation_initiation_factor_4B
LOC283335  hypothetical_LOC283335
TENC1  tensin-like_C1_domain-containing_phosphatase_isoform_3
SPRYD3  SPRY_domain-containing_protein_3
IGFBP6  insulin-like_growth_factor-binding_protein_6_precursor
SOAT2  sterol_O-acyltransferase_2
LOC100127976 
HIGD1DP 
EIF4A1P4 
CSAD  cysteine_sulfinic_acid_decarboxylase
ZNF740  zinc_finger_protein_740
ITGB7  integrin_beta-7_precursor
RARG  retinoic_acid_receptor_gamma_isoform_2


Posfai@neb.com
May 11, 2011