Distribution of restriction sites in the human genome

Enzyme:  ClaI               Longest uncut segments
Specificity:  ATCGAT               Repeats in uncut segments
Number of sites:  85091               Genes in uncut segments
Mean distance between sites:  33626 base pairs
Standard deviation:  35270 base pairs
Site density 29.7 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   647243  chr15  NT_037852.6  1255774-1903017    13.86 % in   381 repeats    2.96 % in 3 genes
2   492771  chr6  NT_167244.1  1820515-2313286    14.91 % in   299 repeats    17.27 % in 11 genes
3   474874  chr6  NT_167244.1  2326429-2801303    7.85 % in   149 repeats    3.94 % in 2 genes
4   462928  chr17  NT_010783.15  5578220-6041148    46.91 % in   1050 repeats    78.40 % in 18 genes
5   412844  chr2  NT_005403.17  54359304-54772148    49.47 % in   915 repeats    55.29 % in 6 genes
6   412011  chr15  NT_010194.17  46235072-46647083    46.34 % in   931 repeats    61.66 % in 12 genes
7   399111  chr19  NT_011109.16  15465806-15864917    56.74 % in   616 repeats    52.26 % in 8 genes
8   391486  chr9  NT_008413.18  4701472-5092958    56.48 % in   763 repeats    56.02 % in 6 genes
9   381373  chr20  NT_011362.10  4899186-5280559    44.80 % in   867 repeats    0.00 % in 0 genes
10   356219  chr12  NT_009775.17  11259621-11615840    61.12 % in   1113 repeats    0.00 % in 0 genes
11   356063  chr12  NT_029419.12  33620090-33976153    58.55 % in   566 repeats    0.00 % in 0 genes
12   355768  chr1  NT_032977.9  22939245-23295013    67.01 % in   1116 repeats    0.00 % in 0 genes
13   354361  chr6  NT_167247.1  1401812-1756173    25.34 % in   345 repeats    0.00 % in 0 genes
14   348797  chrY  NT_011875.12  8381724-8730521    81.63 % in   106 repeats    0.00 % in 0 genes
15   346749  chr2  NT_005403.17  29851154-30197903    43.27 % in   464 repeats    0.00 % in 0 genes
16   341449  chr11  NT_167190.1  4739868-5081317    55.21 % in   672 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 
647243  chr15  NT_037852.6  1255774-1903017    381  118       AluSx (24)  MIRb (13)  AT_rich (13) 
492771  chr6  NT_167244.1  1820515-2313286    299  87       AluSx (41)  L2a (14)  AluSg (13) 
474874  chr6  NT_167244.1  2326429-2801303    149  69       AluSx (11)  AluY (10)  AluJo (8) 
462928  chr17  NT_010783.15  5578220-6041148    1050  149       AluSx (192)  AluJo (63)  AluY (57) 
412844  chr2  NT_005403.17  54359304-54772148    915  187       AluSx (125)  AluY (51)  AT_rich (50) 
412011  chr15  NT_010194.17  46235072-46647083    931  178       AluSx (111)  AluJo (62)  AluJb (62) 
399111  chr19  NT_011109.16  15465806-15864917    616  91       L1MB3 (32)  L1MB1 (30)  L1MCa (27) 
391486  chr9  NT_008413.18  4701472-5092958    763  192       AluSx (51)  AT_rich (46)  AluJo (39) 
381373  chr20  NT_011362.10  4899186-5280559    867  141       AluSx (83)  MIR (82)  MIRb (79) 
10  356219  chr12  NT_009775.17  11259621-11615840    1113  150       AluSx (160)  AluY (76)  AluJo (61) 
11  356063  chr12  NT_029419.12  33620090-33976153    566  176       AT_rich (33)  MIR (32)  L2a (29) 
12  355768  chr1  NT_032977.9  22939245-23295013    1116  174       AluSx (145)  AluJb (62)  AluJo (50) 
13  354361  chr6  NT_167247.1  1401812-1756173    345  128       L2a (18)  L2c (14)  MIRc (13) 
14  348797  chrY  NT_011875.12  8381724-8730521    106  48       LTR12B (17)  L1PA16 (7)  AT_rich (7) 
15  346749  chr2  NT_005403.17  29851154-30197903    464  141       AT_rich (46)  MIRb (21)  L2c (21) 
16  341449  chr11  NT_167190.1  4739868-5081317    672  185       AluSx (47)  AT_rich (32)  MIRb (31) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   647243       chr15  NT_037852.6  1255774-1903017    LOC283804 
LOC727914 
LOC100418897 
2   492771       chr6  NT_167244.1  1820515-2313286    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
3   474874       chr6  NT_167244.1  2326429-2801303    HCG22  HLA_complex_group_22
MICB  MHC_class_I_polypeptide-related_sequence_B_precursor
4   462928       chr17  NT_010783.15  5578220-6041148    RAB5C  ras-related_protein_Rab-5C_isoform_b
KCNH4  potassium_voltage-gated_channel_subfamily_H_member_4
HCRT  orexin_precursor
GHDC  GH3_domain-containing_protein_isoform_3
STAT5B  signal_transducer_and_activator_of_transcription_5B
STAT5A  signal_transducer_and_activator_of_transcription_5A
STAT3  signal_transducer_and_activator_of_transcription_3_isoform_3
PTRF  polymerase_I_and_transcript_release_factor
ATP6V0A1  V-type_proton_ATPase_116_kDa_subunit_a_isoform_1_isoform_c
PTP4A2P1 
NAGLU  alpha-N-acetylglucosaminidase_precursor
HSD17B1P1 
HSD17B1  estradiol_17-beta-dehydrogenase_1
COASY  bifunctional_coenzyme_A_synthase_isoform_b
MLX  max-like_protein_X_isoform_gamma
PSMC3IP  homologous-pairing_protein_2_homolog_isoform_2
FAM134C  hypothetical_protein_LOC162427
TUBG1  tubulin_gamma-1_chain
5   412844       chr2  NT_005403.17  54359304-54772148    CYP20A1  cytochrome_P450_20A1
MRPL50P2 
TRNAE40P  abl_interactor_2
RAPH1  ras-associated_and_pleckstrin_homology_domains-containing_protein_1_isoform_3
LOC729532 
LOC100287498 
6   412011       chr15  NT_010194.17  46235072-46647083    RPL36AP45 
C15orf39  hypothetical_protein_LOC56905
LOC100128707 
LOC100506519  putative_golgin_subfamily_A_member_6C
LOC100506552  golgin_A6_family,_member_D
DNM1P34 
ANP32BP1 
COMMD4  COMM_domain-containing_protein_4
MIR631  microRNA:hsa-mir-631
MAN2C1  alpha-mannosidase_2C1
RPL13P4  paired_amphipathic_helix_protein_Sin3a
LOC100506579  hypothetical_protein_LOC100506579
7   399111       chr19  NT_011109.16  15465806-15864917    PSG3  pregnancy-specific_beta-1-glycoprotein_3_precursor
LOC100505701  hypothetical_LOC100505701
CEACAMP6 
PSG10  pregnancy_specific_beta-1-glycoprotein_10
PSG1  pregnancy-specific_beta-1-glycoprotein_1_isoform_1
PSG11  pregnancy-specific_beta-1-glycoprotein_11_isoform_2
CEACAMP8 
PSG2  pregnancy-specific_beta-1-glycoprotein_2_precursor
8   391486       chr9  NT_008413.18  4701472-5092958    AK3  GTP:AMP_phosphotransferase,_mitochondrial
LOC100420354 
RPS5P6 
MIR101-2  microRNA:hsa-mir-101-2
LOC100128701 
IGHEP2  tyrosine-protein_kinase_JAK2



Posfai@neb.com
May 11, 2011