Distribution of restriction sites in the human genome

Enzyme:  SenpCI               Longest uncut segments
Specificity:  CCGCGG               Repeats in uncut segments
Number of sites:  65238               Genes in uncut segments
Mean distance between sites:  43860 base pairs
Standard deviation:  107870 base pairs
Site density 22.8 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   2312892  chr2  NT_005403.17  61299302-63612194    41.67 % in   3443 repeats    62.08 % in 7 genes
2   2066442  chrX  NT_011669.17  3904892-5971334    72.93 % in   3320 repeats    28.97 % in 8 genes
3   1973303  chr14  NT_026437.12  65023241-66996544    45.18 % in   3215 repeats    0.35 % in 4 genes
4   1958699  chr12  NT_029419.12  45489151-47447850    53.67 % in   2993 repeats    12.03 % in 4 genes
5   1931649  chr10  NT_030059.13  57212777-59144426    47.16 % in   3267 repeats    32.46 % in 4 genes
6   1868985  chr5  NT_029289.11  3947948-5816933    53.42 % in   3268 repeats    20.07 % in 8 genes
7   1846168  chrX  NT_011786.16  10114037-11960205    71.63 % in   2626 repeats    0.71 % in 10 genes
8   1793317  chr12  NT_029419.12  34809682-36602999    55.79 % in   2723 repeats    22.81 % in 4 genes
9   1713761  chr2  NT_022171.15  8027226-9740987    48.91 % in   2558 repeats    0.00 % in 0 genes
10   1713351  chrX  NT_011651.17  16941077-18654428    73.53 % in   2564 repeats    0.00 % in 0 genes
11   1702946  chr14  NT_026437.12  29145534-30848480    55.92 % in   2520 repeats    0.00 % in 0 genes
12   1673158  chrX  NT_011651.17  4363678-6036836    80.64 % in   2443 repeats    0.00 % in 0 genes
13   1661572  chr10  NT_030059.13  34467488-36129060    48.88 % in   2694 repeats    0.00 % in 0 genes
14   1645002  chr18  NT_010966.14  22005031-23650033    53.00 % in   2636 repeats    0.00 % in 0 genes
15   1618142  chr1  NT_032977.9  49998211-51616353    50.39 % in   2535 repeats    0.00 % in 0 genes
16   1597962  chr4  NT_006238.11  4496889-6094851    56.93 % in   2549 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  2312892  chr2  NT_005403.17  61299302-63612194    3443  467       AT_rich (402)  MIR (149)  MIRb (146) 
2  2066442  chrX  NT_011669.17  3904892-5971334    3320  394       MIRb (187)  MIR (146)  AluSx (115) 
3  1973303  chr14  NT_026437.12  65023241-66996544    3215  464       AT_rich (307)  MIRb (132)  MIR (120) 
4  1958699  chr12  NT_029419.12  45489151-47447850    2993  452       AT_rich (307)  L2a (135)  MIRb (95) 
5  1931649  chr10  NT_030059.13  57212777-59144426    3267  435       MIRb (205)  MIR (183)  AT_rich (166) 
6  1868985  chr5  NT_029289.11  3947948-5816933    3268  423       MIRb (234)  L2a (207)  MIR (205) 
7  1846168  chrX  NT_011786.16  10114037-11960205    2626  411       AT_rich (178)  L2a (63)  MIRb (62) 
8  1793317  chr12  NT_029419.12  34809682-36602999    2723  458       AT_rich (283)  L2a (124)  MIRb (93) 
9  1713761  chr2  NT_022171.15  8027226-9740987    2558  380       AT_rich (225)  MIRb (85)  AluSx (82) 
10  1713351  chrX  NT_011651.17  16941077-18654428    2564  412       AT_rich (182)  (TA)n (64)  L1M1 (57) 
11  1702946  chr14  NT_026437.12  29145534-30848480    2520  425       AT_rich (247)  L2a (82)  AluSx (80) 
12  1673158  chrX  NT_011651.17  4363678-6036836    2443  381       AT_rich (124)  L1PA15 (56)  AluSx (56) 
13  1661572  chr10  NT_030059.13  34467488-36129060    2694  412       AT_rich (203)  MIRb (174)  AluSx (105) 
14  1645002  chr18  NT_010966.14  22005031-23650033    2636  425       AT_rich (220)  MIR (92)  MIRb (90) 
15  1618142  chr1  NT_032977.9  49998211-51616353    2535  435       AT_rich (270)  L2a (103)  MIR (93) 
16  1597962  chr4  NT_006238.11  4496889-6094851    2549  434       AT_rich (276)  MIR (105)  L2a (95) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   2312892       chr2  NT_005403.17  61299302-63612194    ACADL  long-chain_specific_acyl-CoA_dehydrogenase,_mitochondrial_precursor
MYL1  myosin_light_chain_1/3,_skeletal_muscle_isoform_isoform_3f
LANCL1  lanC-like_protein_1
CPS1IT  CPS1_intronic_transcript_(non-protein_coding)
LOC100420775 
RPS27P10 
MIR548F2  microRNA_548f-2
2   2066442       chrX  NT_011669.17  3904892-5971334    GPR165P 
LOC402408 
EDA2R  tumor_necrosis_factor_receptor_superfamily_member_27
LOC100129144  zinc_finger_protein_681
LOC100288853 
AR  androgen_receptor_isoform_2
LOC100127902 
LOC100288917  oligophrenin-1
3   1973303       chr14  NT_026437.12  65023241-66996544    LOC100421611 
RNU3P3 
LOC100506731  hypothetical_LOC100506731
FLRT2  leucine-rich_repeat_transmembrane_protein_FLRT2_precursor
4   1958699       chr12  NT_029419.12  45489151-47447850    TMTC2  transmembrane_and_TPR_repeat-containing_protein_2
RPL6P25 
LOC100128335 
SLC6A15  orphan_sodium-_and_chloride-dependent_neurotransmitter_transporter_NTT73_isoform_2
5   1931649       chr10  NT_030059.13  57212777-59144426    LOC100505890  hypothetical_LOC100505890
YWHAZP5 
RPL23AP59 
SORCS1  VPS10_domain-containing_receptor_SorCS1_isoform_a
6   1868985       chr5  NT_029289.11  3947948-5816933    RPL7P21  glucocorticoid_receptor_isoform_gamma
LOC100420513 
HMHB1  minor_histocompatibility_protein_HB-1
YIPF5  protein_YIPF5
KCTD16  BTB/POZ_domain-containing_protein_KCTD16
LOC100128121 
LOC100132712 
ASS1P10 
7   1846168       chrX  NT_011786.16  10114037-11960205    LOC100288421 
CXorf64  hypothetical_protein_LOC100130613
PNPLA10P 
LOC100420320 
ACTRT1  actin-related_protein_T1
LOC100129947 
LOC100419246 
LOC100128268 
RPL7AP72 
LOC392538 
8   1793317       chr12  NT_029419.12  34809682-36602999    LOC283392  hypothetical_LOC283392,_transcript_variant_2
LOC100422354  thyrotropin-releasing_hormone-degrading_ectoenzyme
LOC100507363  hypothetical_LOC100507363
RPL31P48 


Posfai@neb.com
May 11, 2011