Distribution of restriction sites in the human genome

Enzyme:  PacI               Longest uncut segments
Specificity:  TTAATTAA               Repeats in uncut segments
Number of sites:  158626               Genes in uncut segments
Mean distance between sites:  18038 base pairs
Standard deviation:  22316 base pairs
Site density 55.4 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   521238  chrX  NT_167198.1  3485212-4006450    33.31 % in   771 repeats    48.86 % in 25 genes
2   504041  chr15  NT_037852.6  1395408-1899449    1.18 % in   31 repeats    1.26 % in 1 genes
3   482810  chr1  NT_004350.19  578201-1061011    34.29 % in   765 repeats    70.71 % in 36 genes
4   427989  chr1  NT_004350.19  1806494-2234483    18.00 % in   336 repeats    64.33 % in 12 genes
5   413058  chr5  NT_023133.13  22271415-22684473    46.49 % in   897 repeats    70.96 % in 10 genes
6   411865  chr6  NT_167244.1  2356699-2768564    1.33 % in   24 repeats    0.00 % in 0 genes
7   393159  chr12  NT_024477.14  28635-421794    27.35 % in   573 repeats    52.33 % in 6 genes
8   386286  chr9  NT_024000.16  169428-555714    31.42 % in   564 repeats    50.46 % in 21 genes
9   375450  chr12  NT_029419.12  333676-709126    88.47 % in   301 repeats    0.00 % in 0 genes
10   370052  chr6  NT_167244.1  3072827-3442879    16.71 % in   300 repeats    0.00 % in 0 genes
11   358326  chr7  NT_007933.15  258145-616471    83.15 % in   312 repeats    0.00 % in 0 genes
12   349518  chr16  NT_010498.15  41163211-41512729    42.15 % in   693 repeats    0.00 % in 0 genes
13   349290  chrY  NT_011875.12  8375859-8725149    81.04 % in   97 repeats    0.00 % in 0 genes
14   348310  chr6  NT_167246.1  3029642-3377952    12.67 % in   202 repeats    0.00 % in 0 genes
15   342375  chr20  NT_011362.10  31051504-31393879    18.04 % in   352 repeats    0.00 % in 0 genes
16   342163  chr17  NT_010783.15  37513263-37855426    46.25 % in   734 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  521238  chrX  NT_167198.1  3485212-4006450    771  204       AluSx (46)  AluJb (34)  L1M5 (25) 
2  504041  chr15  NT_037852.6  1395408-1899449    31  22       (TA)n (3)  L2a (3)  MER44C (2) 
3  482810  chr1  NT_004350.19  578201-1061011    765  143       AluSx (102)  AluY (87)  GC_rich (43) 
4  427989  chr1  NT_004350.19  1806494-2234483    336  119       AluSx (20)  MIRb (17)  MIR (16) 
5  413058  chr5  NT_023133.13  22271415-22684473    897  180       AluSx (102)  MIRb (51)  AluY (41) 
6  411865  chr6  NT_167244.1  2356699-2768564    24  16       AluY (3)  AluJb (3)  LTR84b (2) 
7  393159  chr12  NT_024477.14  28635-421794    573  178       AluSx (29)  MIR (23)  (CA)n (17) 
8  386286  chr9  NT_024000.16  169428-555714    564  147       AluSx (61)  AluY (23)  GC_rich (21) 
9  375450  chr12  NT_029419.12  333676-709126    301  100       ALR/Alpha (37)  AluSx (20)  AluSg (14) 
10  370052  chr6  NT_167244.1  3072827-3442879    300  67       AluSx (49)  AluY (18)  AluSq (17) 
11  358326  chr7  NT_007933.15  258145-616471    312  89       ALR/Alpha (32)  AluSx (31)  AluY (18) 
12  349518  chr16  NT_010498.15  41163211-41512729    693  179       AluSx (79)  MIRb (40)  AluY (37) 
13  349290  chrY  NT_011875.12  8375859-8725149    97  46       LTR12B (17)  AT_rich (7)  L1PA16 (6) 
14  348310  chr6  NT_167246.1  3029642-3377952    202  64       AluSx (35)  AluY (13)  L2c (11) 
15  342375  chr20  NT_011362.10  31051504-31393879    352  106       MIRb (21)  MIR (18)  AluSx (16) 
16  342163  chr17  NT_010783.15  37513263-37855426    734  152       AluSx (98)  AluJb (45)  AluJo (36) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   521238       chrX  NT_167198.1  3485212-4006450    LOC649201  hypothetical_protein_LOC649201
ZNF275  zinc_finger_protein_275
LOC649238  similar_to_hCG1645335
ZFP92  zinc_finger_protein_92_homolog
TREX2  three_prime_repair_exonuclease_2
HAUS7  HAUS_augmin-like_complex_subunit_7
LOC100507326  extracellular_matrix_protein_2-like
LOC100507352  extracellular_matrix_protein_2-like
BGN  biglycan_preproprotein_preproprotein
ATP2B3  plasma_membrane_calcium-transporting_ATPase_3_isoform_3a
FAM58A  cyclin-related_protein_FAM58A_isoform_2
KRT18P48 
LOC100131652 
LOC100507371  hypothetical_LOC100507371
DUSP9  dual_specificity_protein_phosphatase_9
RPL18AP16 
PNCK  calcium/calmodulin-dependent_protein_kinase_type_1B_isoform_b
SLC6A8  sodium-_and_chloride-dependent_creatine_transporter_1_isoform_3
BCAP31  B-cell_receptor-associated_protein_31_isoform_b
ABCD1  ATP-binding_cassette_sub-family_D_member_1
PLXNB3  plexin-B3_isoform_2
SRPK3  serine/threonine-protein_kinase_SRPK3_isoform_3
IDH3G  isocitrate_dehydrogenase_[NAD]_subunit_gamma,_mitochondrial_isoform_b_precursor
SSR4  translocon-associated_protein_subunit_delta_precursor
PDZD4  PDZ_domain-containing_protein_4
2   504041       chr15  NT_037852.6  1395408-1899449    LOC100418897 
3   482810       chr1  NT_004350.19  578201-1061011    MIR200B  microRNA:hsa-mir-200b
MIR200A  microRNA:hsa-mir-200a
MIR429  microRNA:hsa-mir-429
LOC100506376  hypothetical_protein_LOC100506376
TTLL10  inactive_polyglycylase_TTLL10_isoform_2
TNFRSF18  tumor_necrosis_factor_receptor_superfamily_member_18_isoform_3_precursor
TNFRSF4  tumor_necrosis_factor_receptor_superfamily_member_4_precursor
SDF4  45_kDa_calcium-binding_protein_isoform_1_precursor
B3GALT6  beta-1,3-galactosyltransferase_6
FAM132A  family_with_sequence_similarity_132,_member_A_precursor
UBE2J2  ubiquitin-conjugating_enzyme_E2_J2_isoform_3
SCNN1D  amiloride-sensitive_sodium_channel_subunit_delta_isoform_2
ACAP3  arf-GAP_with_coiled-coil,_ANK_repeat_and_PH_domain-containing_protein_3
PUSL1  tRNA_pseudouridine_synthase-like_1
CPSF3L  integrator_complex_subunit_11
GLTPD1  glycolipid_transfer_protein_domain-containing_protein_1
TAS1R3  taste_receptor_type_1_member_3_precursor
DVL1  segment_polarity_protein_dishevelled_homolog_DVL-1
MXRA8  matrix-remodeling-associated_protein_8_precursor
AURKAIP1  aurora_kinase_A-interacting_protein
CCNL2  cyclin-L2_isoform_B
LOC148413  hypothetical_LOC148413
MRPL20  39S_ribosomal_protein_L20,_mitochondrial_precursor
LOC441869  hypothetical_protein_LOC441869
TMEM88B  transmembrane_protein_88B
LOC100288271  hypothetical_LOC100288271,_transcript_variant_2
VWA1  von_Willebrand_factor_A_domain-containing_protein_1_isoform_2_precursor
ATAD3C  ATPase_family_AAA_domain-containing_protein_3C
ATAD3B  ATPase_family_AAA_domain-containing_protein_3B
ATAD3A  ATPase_family_AAA_domain-containing_protein_3A_isoform_3
C1orf70  transmembrane_protein_C1orf70
SSU72  RNA_polymerase_II_subunit_A_C-terminal_domain_phosphatase_SSU72
LOC643988  hypothetical_LOC643988
MIB2  E3_ubiquitin-protein_ligase_MIB2_isoform_5
MMP23B  matrix_metalloproteinase-23_precursor
CDK11B  cell_division_protein_kinase_11B_isoform_3
4   427989       chr1  NT_004350.19  1806494-2234483    RER1  protein_RER1
PEX10  peroxisome_biogenesis_factor_10_isoform_2
PLCH2  1-phosphatidylinositol-4,5-bisphosphate_phosphodiesterase_eta-2
PANK4  pantothenate_kinase_4
HES5  transcription_factor_HES-5
LOC115110  hypothetical_LOC115110
LOC100133445  hypothetical_LOC100133445
TNFRSF14  tumor_necrosis_factor_receptor_superfamily_member_14_precursor
LOC100506589  hypothetical_LOC100506589
C1orf93  hypothetical_protein_LOC127281_isoform_b
MMEL1  membrane_metallo-endopeptidase-like_1
TTC34  tetratricopeptide_repeat_protein_34
5   413058       chr5  NT_023133.13  22271415-22684473    FAM153C  hypothetical_protein_LOC653316
RPL19P9 
N4BP3  NEDD4-binding_protein_3
RMND5B  protein_RMD5_homolog_B
NHP2  H/ACA_ribonucleoprotein_complex_subunit_2_isoform_b
LOC645853 
GMCL1L  germ_cell-less_homolog_1_(Drosophila)-like
HNRNPAB  heterogeneous_nuclear_ribonucleoprotein_A/B_isoform_b
AGXT2L2  alanine--glyoxylate_aminotransferase_2-like_2
MRPL50P3  collagen_alpha-1(XXIII)_chain
7   393159       chr12  NT_024477.14  28635-421794    LOC100130238  hypothetical_LOC100130238
LOC100506978  hypothetical_LOC100506978
LOC100507023  hypothetical_protein_LOC100507023
LOC100507055  uncharacterized_protein_LOC645277-like_isoform_2
P2RX2  P2X_purinoceptor_2_isoform_I
POLE  DNA_polymerase_epsilon_catalytic_subunit_A
8   386286       chr9  NT_024000.16  169428-555714    NOTCH1  neurogenic_locus_notch_homolog_protein_1_preproprotein_preproprotein
LOC401561  FP7915_protein
LOC100505976  hypothetical_LOC100505976
MIR126  microRNA:hsa-mir-126
AGPAT2  1-acyl-sn-glycerol-3-phosphate_acyltransferase_beta_isoform_b
FAM69B  hypothetical_protein_LOC138311
SNORA17  small_nucleolar_RNA,_H/ACA_box_17
LCN10  epididymal-specific_lipocalin-10
LCN6  epididymal-specific_lipocalin-6_precursor
LOC100128593  hypothetical_LOC100128593
LCN8  epididymal-specific_lipocalin-8
LCN15  lipocalin-15_precursor
ATP6V1G1P3 
TMEM141  transmembrane_protein_141
KIAA1984  hypothetical_protein_LOC84960
LOC100131193  hypothetical_LOC100131193
MIR4292  microRNA_4292
C9orf172  chromosome_9_open_reading_frame_172
PHPT1  14_kDa_phosphohistidine_phosphatase_isoform_2
MAMDC4  apical_endosomal_glycoprotein_precursor
EDF1  endothelial_differentiation-related_factor_1_isoform_beta


Posfai@neb.com
May 11, 2011