Distribution of restriction sites in the human genome

Enzyme:  SgrAI               Longest uncut segments
Specificity:  CRCCGGYG               Repeats in uncut segments
Number of sites:  14831               Genes in uncut segments
Mean distance between sites:  192930 base pairs
Standard deviation:  297350 base pairs
Site density 5.2 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   4931754  chr2  NT_022184.15  57055887-61987641    49.58 % in   7762 repeats    23.68 % in 14 genes
2   4593141  chr2  NT_005403.17  42549734-47142875    49.81 % in   7306 repeats    19.74 % in 15 genes
3   3574100  chr12  NT_029419.12  20847492-24421592    54.13 % in   5583 repeats    16.49 % in 7 genes
4   3390597  chr6  NT_007592.15  47353249-50743846    49.61 % in   5276 repeats    24.63 % in 32 genes
5   3233709  chrX  NT_011651.17  5290145-8523854    72.47 % in   4417 repeats    22.85 % in 17 genes
6   2883399  chr5  NT_006713.15  34274796-37158195    52.93 % in   4567 repeats    1.43 % in 12 genes
7   2875767  chr7  NT_007914.15  5780946-8656713    46.77 % in   4681 repeats    0.13 % in 4 genes
8   2757258  chr9  NT_008413.18  24125256-26882514    51.65 % in   4271 repeats    3.86 % in 4 genes
9   2719436  chr14  NT_026437.12  21232343-23951779    55.47 % in   4146 repeats    0.00 % in 0 genes
10   2663257  chr6  NT_007592.15  21772047-24435304    47.09 % in   4301 repeats    0.00 % in 0 genes
11   2627340  chr8  NT_008046.16  22367577-24994917    50.35 % in   4449 repeats    0.00 % in 0 genes
12   2582129  chr15  NT_010274.17  1394288-3976417    47.44 % in   4251 repeats    0.00 % in 0 genes
13   2552176  chr3  NT_022517.18  1733017-4285193    47.37 % in   4369 repeats    0.00 % in 0 genes
14   2550285  chr5  NT_034772.6  16475019-19025304    52.76 % in   3881 repeats    0.00 % in 0 genes
15   2544398  chr3  NT_022517.18  60256143-62800541    42.90 % in   4506 repeats    0.00 % in 0 genes
16   2480909  chr4  NT_016354.19  36089928-38570837    46.79 % in   4116 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  4931754  chr2  NT_022184.15  57055887-61987641    7762  672       AT_rich (648)  MIRb (306)  MIR (291) 
2  4593141  chr2  NT_005403.17  42549734-47142875    7306  632       AT_rich (814)  AluSx (239)  L2a (211) 
3  3574100  chr12  NT_029419.12  20847492-24421592    5583  581       AT_rich (531)  MIRb (220)  MIR (203) 
4  3390597  chr6  NT_007592.15  47353249-50743846    5276  556       AT_rich (491)  MIRb (213)  L2a (191) 
5  3233709  chrX  NT_011651.17  5290145-8523854    4417  483       AT_rich (283)  MIRb (118)  L2c (104) 
6  2883399  chr5  NT_006713.15  34274796-37158195    4567  533       AT_rich (554)  AluSx (132)  MIR (125) 
7  2875767  chr7  NT_007914.15  5780946-8656713    4681  516       AT_rich (432)  AluSx (192)  L2a (172) 
8  2757258  chr9  NT_008413.18  24125256-26882514    4271  522       AT_rich (383)  MIRb (239)  MIR (165) 
9  2719436  chr14  NT_026437.12  21232343-23951779    4146  523       AT_rich (479)  L2a (113)  MIRb (103) 
10  2663257  chr6  NT_007592.15  21772047-24435304    4301  512       AT_rich (299)  AluSx (217)  MIRb (162) 
11  2627340  chr8  NT_008046.16  22367577-24994917    4449  523       AT_rich (378)  MIRb (201)  L2a (187) 
12  2582129  chr15  NT_010274.17  1394288-3976417    4251  461       MIRb (392)  MIR (236)  AT_rich (173) 
13  2552176  chr3  NT_022517.18  1733017-4285193    4369  486       MIRb (275)  MIR (244)  AT_rich (213) 
14  2550285  chr5  NT_034772.6  16475019-19025304    3881  484       AT_rich (300)  MIRb (151)  MIR (142) 
15  2544398  chr3  NT_022517.18  60256143-62800541    4506  460       MIRb (322)  MIR (280)  AluSx (240) 
16  2480909  chr4  NT_016354.19  36089928-38570837    4116  467       AT_rich (384)  AluSx (214)  MIRb (175) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   4931754       chr2  NT_022184.15  57055887-61987641    CYCSP6 
LOC100421651 
REG3G  regenerating_islet-derived_protein_3-gamma_precursor
REG1B  lithostathine-1-beta_precursor
REG1A  lithostathine-1-alpha_precursor
REG1P  regenerating_islet-derived_1_pseudogene
REG3A  regenerating_islet-derived_protein_3-alpha_precursor
LRRTM1  leucine-rich_repeat_transmembrane_neuronal_protein_1_precursor
LOC100287912 
LOC100130209 
LOC100507201  hypothetical_LOC100507201
LOC100420968 
LOC100286883 
LOC100419683  dihydrofolate_reductase_pseudogene
2   4593141       chr2  NT_005403.17  42549734-47142875    OBFC2A  SOSS_complex_subunit_B2
SDPR  serum_deprivation-response_protein
DNAJB1P1  hypothetical_LOC100506977
TMEFF2  tomoregulin-2_precursor
LOC100506993  hypothetical_LOC100506993
RPS17P8  prostate-specific_transcript_1_(non-protein_coding)
LOC100420669 
LOC645314 
GLULP6 
LOC100287191 
LOC100419812 
LOC100420970 
LOC391470 
SLC39A10  zinc_transporter_ZIP10_precursor
LOC100420572  dynein_heavy_chain_7,_axonemal
3   3574100       chr12  NT_029419.12  20847492-24421592    LOC100506869  hypothetical_LOC100506869,_transcript_variant_2
LRIG3  leucine-rich_repeats_and_immunoglobulin-like_domains_protein_3_isoform_1
RPS6P22 
LOC644915 
SLC16A7  monocarboxylate_transporter_2
PGBD3P1 
RPS3P6  family_with_sequence_similarity_19_(chemokine_(C-C_motif)-like),_member_A2_precursor
4   3390597       chr6  NT_007592.15  47353249-50743846    LOC100421517  CD2-associated_protein
GPR111  probable_G-protein_coupled_receptor_111
GPR115  probable_G-protein_coupled_receptor_115_precursor
RPL27AP7 
OPN5  opsin_5,_transcript_variant_2
LOC100505931  hypothetical_LOC100505931
LOC389395 
RBMXP1 
LOC100506698 
LOC100418956 
LOC100287991 
LOC100287991 
RNU7-65P 
LOC442215 
LOC100505950  hypothetical_LOC100505950
MUT  methylmalonyl-CoA_mutase,_mitochondrial_precursor
CENPQ  centromere_protein_Q
GLYATL3  glycine_N-acyltransferase-like_protein_3
C6orf141  hypothetical_protein_LOC135398
RHAG  ammonium_transporter_Rh_type_A
CRISP2  cysteine-rich_secretory_protein_2_precursor
CRISP3  cysteine-rich_secretory_protein_3_isoform_2_precursor
PGK2  phosphoglycerate_kinase_2
CRISP1  cysteine-rich_secretory_protein_1_isoform_2_precursor
DEFB133  beta-defensin_133
DEFB114  beta-defensin_114_precursor
DEFB113  beta-defensin_113_precursor
DEFB110  beta-defensin_110_isoform_a
DEFB112  beta-defensin_112_precursor
LOC100505985  hypothetical_LOC100505985
TFAP2D  transcription_factor_AP-2-delta
TFAP2B  transcription_factor_AP-2-beta
5   3233709       chrX  NT_011651.17  5290145-8523854    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)
APOOL  apolipoprotein_O-like_precursor
SATL1  spermidine/spermine_N(1)-acetyltransferase-like_protein_1
LOC100421745 
ZNF711  zinc_finger_protein_711
POF1B  protein_POF1B
MIR1321  microRNA_1321
LOC730792 
CHM  rab_proteins_geranylgeranyltransferase_component_A_1_isoform_b
6   2883399       chr5  NT_006713.15  34274796-37158195    EDIL3  EGF-like_repeat_and_discoidin_I-like_domain-containing_protein_3_precursor
LOC100289244 
RPL5P17 
LOC645181 
RPS2P25 
LOC100129564 
NBPF22P  neuroblastoma_breakpoint_family,_member_22_(pseudogene)
LOC100421863 
COX7C  cytochrome_c_oxidase_subunit_7C,_mitochondrial_precursor
LOC100505878  hypothetical_LOC100505878
RPL10AP9 
MIR4280  microRNA_4280
7   2875767       chr7  NT_007914.15  5780946-8656713    CNTNAP2  contactin-associated_protein-like_2_precursor
LOC100420074 
MIR548F4  microRNA_548f-4
LOC100507538  hypothetical_LOC100507538
8   2757258       chr9  NT_008413.18  24125256-26882514    TUSC1  tumor_suppressor_candidate_gene_1_protein
LOC100421478 
LOC100506422  putative_deoxyuridine_5'-triphosphate_nucleotidohydrolase-like_protein_FLJ16323-like
C9orf82  hypothetical_protein_LOC79886_isoform_2


Posfai@neb.com
May 11, 2011