Distribution of restriction sites in the human genome

Enzyme:  PliMI               Longest uncut segments
Specificity:  CGCCGAC               Repeats in uncut segments
Number of sites:  12022               Genes in uncut segments
Mean distance between sites:  238009 base pairs
Standard deviation:  432664 base pairs
Site density 4.2 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   7052207  chr12  NT_029419.12  47629881-54682088    50.15 % in   11819 repeats    24.13 % in 33 genes
2   6568573  chr5  NT_006576.16  21872645-28441218    52.08 % in   10744 repeats    21.36 % in 13 genes
3   6067031  chrX  NT_011651.17  16892928-22959959    62.09 % in   9315 repeats    25.22 % in 22 genes
4   5129370  chr8  NT_008046.16  25355029-30484399    49.16 % in   8141 repeats    28.77 % in 4 genes
5   4897598  chr2  NT_022135.16  12243098-17140696    54.80 % in   8283 repeats    18.56 % in 7 genes
6   4871759  chr4  NT_022778.16  3170669-8042428    53.66 % in   7431 repeats    12.51 % in 17 genes
7   4843631  chrX  NT_011651.17  2642081-7485712    75.51 % in   6798 repeats    17.35 % in 20 genes
8   4480536  chr11  NT_033899.8  5780444-10260980    49.67 % in   7534 repeats    36.74 % in 35 genes
9   4278343  chr18  NT_010966.14  16635262-20913605    42.02 % in   6515 repeats    0.00 % in 0 genes
10   4223086  chr10  NT_030059.13  16244764-20467850    53.57 % in   7129 repeats    0.00 % in 0 genes
11   4218876  chr3  NT_005612.16  70121479-74340355    53.62 % in   6633 repeats    0.00 % in 0 genes
12   4123865  chrX  NT_167197.1  23545816-27669681    52.73 % in   7147 repeats    0.00 % in 0 genes
13   3962158  chr1  NT_004487.19  43054366-47016524    51.90 % in   6515 repeats    0.00 % in 0 genes
14   3921243  chr3  NT_022459.15  11808913-15730156    44.42 % in   6103 repeats    0.00 % in 0 genes
15   3839664  chr13  NT_024524.14  48175675-52015339    46.56 % in   5980 repeats    0.00 % in 0 genes
16   3837201  chr7  NT_007933.15  20106222-23943423    44.47 % in   5769 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  7052207  chr12  NT_029419.12  47629881-54682088    11819  722       AT_rich (1092)  L2a (546)  MIRb (531) 
2  6568573  chr5  NT_006576.16  21872645-28441218    10744  728       AT_rich (1295)  AluSx (345)  AluY (307) 
3  6067031  chrX  NT_011651.17  16892928-22959959    9315  665       AT_rich (631)  L2c (312)  AluSx (306) 
4  5129370  chr8  NT_008046.16  25355029-30484399    8141  655       AT_rich (962)  L2a (323)  MIRb (273) 
5  4897598  chr2  NT_022135.16  12243098-17140696    8283  655       MIRb (510)  AT_rich (503)  MIR (324) 
6  4871759  chr4  NT_022778.16  3170669-8042428    7431  663       AT_rich (953)  L2a (243)  (TA)n (205) 
7  4843631  chrX  NT_011651.17  2642081-7485712    6798  580       AT_rich (416)  AluSx (177)  MIRb (153) 
8  4480536  chr11  NT_033899.8  5780444-10260980    7534  645       AT_rich (607)  MIRb (382)  L2a (328) 
9  4278343  chr18  NT_010966.14  16635262-20913605    6515  592       AT_rich (515)  MIRb (296)  MIR (253) 
10  4223086  chr10  NT_030059.13  16244764-20467850    7129  654       AT_rich (583)  AluSx (270)  MIRb (257) 
11  4218876  chr3  NT_005612.16  70121479-74340355    6633  604       AT_rich (771)  L2a (211)  MIRb (197) 
12  4123865  chrX  NT_167197.1  23545816-27669681    7147  608       AT_rich (603)  L2a (248)  AluSx (239) 
13  3962158  chr1  NT_004487.19  43054366-47016524    6515  591       AT_rich (727)  L2a (254)  AluSx (201) 
14  3921243  chr3  NT_022459.15  11808913-15730156    6103  591       AT_rich (685)  MIR (211)  L2a (207) 
15  3839664  chr13  NT_024524.14  48175675-52015339    5980  610       AT_rich (799)  L2a (183)  MIR (172) 
16  3837201  chr7  NT_007933.15  20106222-23943423    5769  585       AT_rich (738)  MIR (211)  L2a (209) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   7052207       chr12  NT_029419.12  47629881-54682088    LRRIQ1  leucine-rich_repeat_and_IQ_domain-containing_protein_1_isoform_2
ALX1  ALX_homeobox_protein_1
LOC441643 
LOC100129589 
RASSF9  ras_association_domain-containing_protein_9
NTS  neurotensin/neuromedin_N_preproprotein_preproprotein
MGAT4C  alpha-1,3-mannosyl-glycoprotein_4-beta-N-acetylglucosaminyltransferase_C
RPL23AP68 
LOC100507559  hypothetical_LOC100507559
CYCSP30 
LOC100420357  makorin_ring_finger_protein_9,_pseudogene
RPS4XP15 
C12orf50  hypothetical_protein_LOC160419
C12orf29  hypothetical_protein_LOC91298
LOC100420011  centrosomal_protein_of_290_kDa
TMTC3  transmembrane_and_TPR_repeat-containing_protein_3
KITLG  kit_ligand_isoform_b_precursor
LOC728084  hypothetical_LOC728084
LOC100287355 
MRPS6P4 
DUSP6  dual_specificity_protein_phosphatase_6_isoform_b
GALNT4  polypeptide_N-acetylgalactosaminyltransferase_4
ATP2B1  plasma_membrane_calcium-transporting_ATPase_1_isoform_1a
LOC338758  hypothetical_LOC338758
MRPL2P1 
LOC100287505 
LOC100507594  hypothetical_LOC100507594
C12orf12  hypothetical_protein_LOC196477
EPYC  epiphycan_precursor
KERA  keratocan_precursor
LUM  lumican_precursor
DCN  decorin_isoform_e_precursor
BTG1  protein_BTG1
2   6568573       chr5  NT_006576.16  21872645-28441218    GCNT1P2  pro-melanin-concentrating_hormone-like_1
LOC100420804 
LOC391771 
PRDM9  histone-lysine_N-methyltransferase_PRDM9
LOC100130746 
CDH10  cadherin-10_isoform_2
LOC100422502 
LOC340107  hypothetical_LOC340107
LOC100506287  hypothetical_protein_LOC100506287
MSNL1 
-  tRNA-Lys
LOC100131678 
CDH9  cadherin-9_preproprotein_preproprotein
3   6067031       chrX  NT_011651.17  16892928-22959959    PAICSP7 
CCNB1IP1P3 
MIR548M  microRNA_548m
CALM1P1 
LOC100129001 
LOC100128595 
RPS7P13 
LOC100420872 
LOC648927 
RPS29P28 
LOC643486  bromodomain,_testis-specific_pseudogene
LOC100130500 
LOC100422431  replication_protein_A_30_kDa_subunit
LOC100131072 
RPL6P29 
LOC100420955 
EEF1A1P15 
LOC100419995 
LOC100422469  X-ray_repair_complementing_defective_repair_pseudogene
LOC643605 
RPSAP8 
PCDH19  protocadherin-19_isoform_c_precursor
4   5129370       chr8  NT_008046.16  25355029-30484399    EEF1A1P37 
RPL18P7  microRNA:hsa-mir-2053
LOC100420746 
LOC100506910  hypothetical_LOC100506910
5   4897598       chr2  NT_022135.16  12243098-17140696    MKI67IP  MKI67_FHA_domain-interacting_nucleolar_phosphoprotein
TSN  translin
LOC100422580 
LOC100131284 
CNTNAP5  contactin-associated_protein-like_5_precursor
LOC100422417 
LOC150554 
6   4871759       chr4  NT_022778.16  3170669-8042428    RPS15AP17 
RPL21P47 
LOC100289193 
LOC100131441 
LOC644534 
LOC644548 
LOC644578  hypothetical_protein_LOC644578
TECRL  trans-2,3-enoyl-CoA_reductase-like
LOC391657 
RPS6P5 
LOC401134  hypothetical_LOC401134
LOC100422019 
LOC100507063  hypothetical_LOC100507063
LOC100144602  hypothetical_LOC100144602
LOC728048 
MIR1269  microRNA:hsa-mir-1269
RPS23P3 
7   4843631       chrX  NT_011651.17  2642081-7485712    FAM46D  hypothetical_protein_LOC169966
LOC727874 
HK2P1 
LOC100422286  bromodomain_and_WD_repeat-containing_protein_3
VDAC1P1 
LOC100421037 
HMGN5  high_mobility_group_nucleosome-binding_domain-containing_protein_5
SH3BGRL  SH3_domain-binding_glutamic_acid-rich-like_protein
LOC100422471 
LOC100129843 
RPL22P22 
LOC266683 
POU3F4  POU_domain,_class_3,_transcription_factor_4
TERF1P4 
CYLC1  cylicin-1
RPS6KA6  ribosomal_protein_S6_kinase_alpha-6
MIR548I4  microRNA:hsa-mir-548i-4
HDX  highly_divergent_homeobox_isoform_2
LOC642869 
UBE2DNL  ubiquitin-conjugating_enzyme_E2D_N-terminal_like_(pseudogene)
8   4480536       chr11  NT_033899.8  5780444-10260980    BIRC2  baculoviral_IAP_repeat-containing_protein_2
TMEM123  porimin_precursor
LOC727869  hypothetical_LOC727869
MMP7  matrilysin_preproprotein_preproprotein
MMP20  matrix_metalloproteinase-20_preproprotein_preproprotein
MMP27  matrix_metalloproteinase-27_precursor
MMP8  neutrophil_collagenase_preproprotein_preproprotein
LOC100421658 
MMP10  stromelysin-2_preproprotein_preproprotein
CSNK1A1P2  interstitial_collagenase_isoform_2
MMP3  stromelysin-1_preproprotein_preproprotein
MMP12  macrophage_metalloelastase_preproprotein_preproprotein
LOC100288111 
MMP13  collagenase_3_preproprotein_preproprotein
RPL21P96 
DCUN1D5  DCN1-like_protein_5
LOC100506721  cytoplasmic_dynein_2_heavy_chain_1_isoform_2
LOC100190922 
DDI1  protein_DDI1_homolog_1
LOC100506742  inactive_caspase-12-like_isoform_2
LOC643733  caspase_4,_apoptosis-related_cysteine_peptidase_pseudogene,_transcript_variant_2
CASP4  caspase-4_isoform_gamma_precursor
CASP5  caspase-5_isoform_f_precursor
CASP1  caspase-1_isoform_gamma_precursor
CARD16  caspase_recruitment_domain-containing_protein_16_isoform_2
LOC440067 
CARD17  caspase_recruitment_domain-containing_protein_17
CARD18  caspase_recruitment_domain-containing_protein_18
OR2AL1P 
HSPD1P13  glutamate_receptor_4_isoform_3_precursor
KIAA1826  hypothetical_protein_LOC84437
KBTBD3  kelch_repeat_and_BTB_domain-containing_protein_3
AASDHPPT  L-aminoadipate-semialdehyde_dehydrogenase-phosphopantetheinyl_transferase
LOC643855 
LOC100422300  guanylate_cyclase_soluble_subunit_alpha-2


Posfai@neb.com
May 11, 2011