Distribution of restriction sites in the human genome

Enzyme:  Sbo13I               Longest uncut segments
Specificity:  TCGCGA               Repeats in uncut segments
Number of sites:  14417               Genes in uncut segments
Mean distance between sites:  198470 base pairs
Standard deviation:  255722 base pairs
Site density 5.0 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   2964298  chr5  NT_006576.16  10980963-13945261    47.33 % in   4549 repeats    47.18 % in 5 genes
2   2820313  chrY  NT_011875.12  3072843-5893156    59.86 % in   4674 repeats    4.27 % in 9 genes
3   2432625  chr4  NT_022778.16  5929802-8362427    49.79 % in   3654 repeats    19.23 % in 7 genes
4   2388355  chr2  NT_022184.15  1-2388356    46.44 % in   3739 repeats    2.18 % in 4 genes
5   2379534  chr4  NT_016354.19  59050621-61430155    52.70 % in   3518 repeats    2.41 % in 7 genes
6   2344814  chr18  NT_010966.14  20344513-22689327    44.47 % in   3726 repeats    23.47 % in 6 genes
7   2323802  chr3  NT_005612.16  1693438-4017240    51.88 % in   3389 repeats    42.16 % in 10 genes
8   2302326  chr4  NT_016354.19  103276745-105579071    52.11 % in   3750 repeats    7.97 % in 2 genes
9   2224614  chr4  NT_016354.19  16996845-19221459    49.98 % in   3443 repeats    0.00 % in 0 genes
10   2165509  chr3  NT_022517.18  651313-2816822    47.14 % in   3539 repeats    0.00 % in 0 genes
11   2145521  chr11  NT_009237.18  20569033-22714554    52.53 % in   3784 repeats    0.00 % in 0 genes
12   2089323  chr2  NT_005403.17  48014624-50103947    47.08 % in   3668 repeats    0.00 % in 0 genes
13   2080223  chr2  NT_022135.16  35934033-38014256    46.76 % in   3132 repeats    0.00 % in 0 genes
14   2015014  chr5  NT_034772.6  43857354-45872368    49.24 % in   3455 repeats    0.00 % in 0 genes
15   2010478  chr13  NT_024524.14  39939616-41950094    46.44 % in   3334 repeats    0.00 % in 0 genes
16   1999559  chr14  NT_026437.12  43116735-45116294    52.97 % in   3403 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  2964298  chr5  NT_006576.16  10980963-13945261    4549  536       AT_rich (419)  L2a (183)  AluSx (143) 
2  2820313  chrY  NT_011875.12  3072843-5893156    4674  528       AT_rich (358)  AluSx (218)  AluJo (190) 
3  2432625  chr4  NT_022778.16  5929802-8362427    3654  480       AT_rich (455)  MIR (139)  L2a (133) 
4  2388355  chr2  NT_022184.15  1-2388356    3739  465       AT_rich (210)  MIRb (175)  L2c (159) 
5  2379534  chr4  NT_016354.19  59050621-61430155    3518  484       AT_rich (525)  L2a (135)  MIR (94) 
6  2344814  chr18  NT_010966.14  20344513-22689327    3726  494       AT_rich (296)  MIRb (163)  MIR (157) 
7  2323802  chr3  NT_005612.16  1693438-4017240    3389  499       AT_rich (435)  L2a (108)  MIR (100) 
8  2302326  chr4  NT_016354.19  103276745-105579071    3750  491       AT_rich (456)  AluSx (126)  L2a (122) 
9  2224614  chr4  NT_016354.19  16996845-19221459    3443  454       AT_rich (414)  L2a (179)  MIR (137) 
10  2165509  chr3  NT_022517.18  651313-2816822    3539  478       AT_rich (257)  MIR (187)  MIRb (182) 
11  2145521  chr11  NT_009237.18  20569033-22714554    3784  435       MIRb (261)  MIR (225)  AT_rich (225) 
12  2089323  chr2  NT_005403.17  48014624-50103947    3668  442       AT_rich (266)  AluSx (211)  L2a (138) 
13  2080223  chr2  NT_022135.16  35934033-38014256    3132  457       AT_rich (296)  MIRb (126)  MIR (118) 
14  2015014  chr5  NT_034772.6  43857354-45872368    3455  409       MIRb (282)  AluSx (186)  MIR (184) 
15  2010478  chr13  NT_024524.14  39939616-41950094    3334  467       AT_rich (273)  L2a (155)  MIRb (126) 
16  1999559  chr14  NT_026437.12  43116735-45116294    3403  442       AluSx (194)  AT_rich (171)  MIRb (136) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   2964298       chr5  NT_006576.16  10980963-13945261    CTNND2  catenin_delta-2
LOC100420683  tumor_antigen_gene
RPS23P5 
RPL29P13 
DNAH5  dynein_heavy_chain_5,_axonemal
2   2820313       chrY  NT_011875.12  3072843-5893156    AGKP1  neuroligin-4,_Y-linked_isoform_2
MED13P1 
CYCSP46 
HDHD1P1 
STSP1 
SURF6P1 
FAM41AY1  family_with_sequence_similarity_41,_member_A,_Y-linked_1
TUBB1P2 
NCRNA00230B  non-protein_coding_RNA_230B
3   2432625       chr4  NT_022778.16  5929802-8362427    LOC401134  hypothetical_LOC401134
LOC100422019 
LOC100507063  hypothetical_LOC100507063
LOC100144602  hypothetical_LOC100144602
LOC728048 
MIR1269  microRNA:hsa-mir-1269
RPS23P3 
4   2388355       chr2  NT_022184.15  1-2388356    APOB  apolipoprotein_B-100_precursor
LOC100287183 
LOC100507562  hypothetical_LOC100507562
LOC100130841 
5   2379534       chr4  NT_016354.19  59050621-61430155    PABPC4L  polyadenylate-binding_protein_4-like
LOC345016 
LOC646272 
RPS2P27 
EEF1A1P35 
LOC100418792 
LOC100507528  hypothetical_LOC100507528
6   2344814       chr18  NT_010966.14  20344513-22689327    KC6  keratoconus_gene_6
NPM1P1 
LOC100301521 
PIK3C3  phosphatidylinositol_3-kinase_catalytic_subunit_type_3
RIT2  GTP-binding_protein_Rit2
SYT4  synaptotagmin-4
7   2323802       chr3  NT_005612.16  1693438-4017240    LOC100287639 
LOC644063 
LOC391556 
MTRNR2L12 
RPL18AP8 
LOC100131442 
LOC100129736 
EPHA6  ephrin_type-A_receptor_6_isoform_b
ARL6  ADP-ribosylation_factor-like_protein_6
LOC100506362  hypothetical_LOC100506362
8   2302326       chr4  NT_016354.19  103276745-105579071    LOC100506196  hypothetical_LOC100506196
RPL19P8 


Posfai@neb.com
May 11, 2011