Distribution of restriction sites in the human genome

Enzyme:  RsrII               Longest uncut segments
Specificity:  CGGWCCG               Repeats in uncut segments
Number of sites:  9384               Genes in uncut segments
Mean distance between sites:  304917 base pairs
Standard deviation:  506969 base pairs
Site density 3.3 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   9927468  chr13  NT_024524.14  41920357-51847825    49.29 % in   15548 repeats    16.17 % in 27 genes
2   5726025  chr4  NT_016354.19  18004637-23730662    48.97 % in   8915 repeats    51.90 % in 16 genes
3   5606393  chrY  NT_011875.12  1749807-7356200    59.85 % in   8836 repeats    14.71 % in 67 genes
4   5418629  chr4  NT_016354.19  83382556-88801185    51.53 % in   8740 repeats    27.57 % in 20 genes
5   5318921  chr3  NT_005612.16  66614017-71932938    55.10 % in   8687 repeats    14.75 % in 25 genes
6   5264160  chr14  NT_026437.12  5951016-11215176    48.90 % in   7963 repeats    19.22 % in 24 genes
7   4854041  chr21  NT_011512.11  7542208-12396249    49.05 % in   8210 repeats    12.69 % in 13 genes
8   4628134  chr3  NT_022459.15  15540539-20168673    48.18 % in   7073 repeats    29.22 % in 6 genes
9   4541037  chr4  NT_016354.19  59346802-63887839    50.34 % in   6780 repeats    0.00 % in 0 genes
10   4512033  chr8  NT_008046.16  22368049-26880082    50.95 % in   7458 repeats    0.00 % in 0 genes
11   4369756  chr3  NT_005612.16  7890906-12260662    51.48 % in   6981 repeats    0.00 % in 0 genes
12   4366502  chr12  NT_029419.12  34200872-38567374    52.40 % in   7077 repeats    0.00 % in 0 genes
13   4302945  chr4  NT_022778.16  3671874-7974819    53.40 % in   6489 repeats    0.00 % in 0 genes
14   4280263  chrX  NT_011669.17  85525-4365788    77.91 % in   5885 repeats    0.00 % in 0 genes
15   4234204  chr4  NT_016354.19  72761076-76995280    49.84 % in   7414 repeats    0.00 % in 0 genes
16   4222572  chr2  NT_022184.15  26834408-31056980    46.27 % in   6841 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  9927468  chr13  NT_024524.14  41920357-51847825    15548  814       AT_rich (2012)  L2a (517)  AluSx (431) 
2  5726025  chr4  NT_016354.19  18004637-23730662    8915  663       AT_rich (901)  L2a (397)  MIR (363) 
3  5606393  chrY  NT_011875.12  1749807-7356200    8836  652       AT_rich (622)  AluSx (451)  AluJo (312) 
4  5418629  chr4  NT_016354.19  83382556-88801185    8740  695       AT_rich (853)  AluSx (353)  L2a (280) 
5  5318921  chr3  NT_005612.16  66614017-71932938    8687  689       AT_rich (987)  L2a (279)  AluSx (256) 
6  5264160  chr14  NT_026437.12  5951016-11215176    7963  638       AT_rich (749)  L2a (289)  MIR (275) 
7  4854041  chr21  NT_011512.11  7542208-12396249    8210  637       AT_rich (962)  AluY (274)  AluSx (267) 
8  4628134  chr3  NT_022459.15  15540539-20168673    7073  617       AT_rich (914)  L2a (211)  AluSx (207) 
9  4541037  chr4  NT_016354.19  59346802-63887839    6780  631       AT_rich (911)  L2a (230)  AluSx (201) 
10  4512033  chr8  NT_008046.16  22368049-26880082    7458  653       AT_rich (767)  L2a (288)  MIRb (281) 
11  4369756  chr3  NT_005612.16  7890906-12260662    6981  632       AT_rich (721)  L2a (211)  MIR (210) 
12  4366502  chr12  NT_029419.12  34200872-38567374    7077  625       AT_rich (661)  L2a (319)  MIRb (269) 
13  4302945  chr4  NT_022778.16  3671874-7974819    6489  625       AT_rich (863)  L2a (207)  (TA)n (188) 
14  4280263  chrX  NT_011669.17  85525-4365788    5885  509       MIRb (220)  MIR (211)  AluSx (194) 
15  4234204  chr4  NT_016354.19  72761076-76995280    7414  593       AT_rich (519)  AluSx (447)  MIRb (282) 
16  4222572  chr2  NT_022184.15  26834408-31056980    6841  595       AT_rich (539)  AluSx (344)  MIRb (296) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   9927468       chr13  NT_024524.14  41920357-51847825    TDRD3  tudor_domain-containing_protein_3_isoform_2
EIF4A1P6 
MIR3169  microRNA_3169
PCDH20  protocadherin-20
RPL32P28 
OR7E156P  olfactory_receptor,_family_7,_subfamily_E,_member_156_pseudogene
LOC647264  hypothetical_LOC647264
LOC100128626 
LOC100507505  hypothetical_protein_LOC100507505
OR7E104P 
NFYAP1 
LGMN2P 
STARP1 
LOC387933 
PCDH9  protocadherin-9_isoform_2_precursor
LOC730236  hypothetical_protein_LOC730236
RPSAP53 
LOC390411 
OR7E111P 
OR7E33P 
RPL37P21 
RPL12P34 
LOC730239 
LOC100421079 
LOC100128625 
LOC100420198  kelch-like_protein_1
ATXN8OS  ATXN8_opposite_strand_(non-protein_coding)
2   5726025       chr4  NT_016354.19  18004637-23730662    LOC100422562  glutamate_receptor_delta-2_subunit_precursor
ATOH1  protein_atonal_homolog_1
LOC644429 
SMARCAD1  SWI/SNF-related_matrix-associated_actin-dependent_regulator_of_chromatin_subfamily_A_containing_DEAD/H_box_1_isoform_b
HPGDS  hematopoietic_prostaglandin_D_synthase
RPL35AP11 
PDLIM5  PDZ_and_LIM_domain_protein_5_isoform_e
LOC100507012  hypothetical_LOC100507012
BMPR1B  bone_morphogenetic_protein_receptor_type-1B_precursor
UNC5C  netrin_receptor_UNC5C_precursor
RPL30P6 
PDHA2  pyruvate_dehydrogenase_E1_component_subunit_alpha,_testis-specific_form,_mitochondrial_precursor
LOC100418701 
COX7A2P2 
RPL5P12  hypothetical_protein_LOC285555
RPL21P48  rap1_GTPase-GDP_dissociation_stimulator_1_isoform_6
3   5606393       chrY  NT_011875.12  1749807-7356200    UTY  histone_demethylase_UTY_isoform_1
TMSB4Y  thymosin_beta-4,_Y-chromosomal
PSIP1P2 
KALP 
VCY1B  testis-specific_basic_protein_Y_1
VCY  testis-specific_basic_protein_Y_1
LOC100462832 
PNPLA4P1 
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
KIAA0664P1 
TAF9P1 
TCEB1P14 
CDY5P 
PRYP1 
ACTG1P2 
XKRY  testis-specific_XK-related_protein,_Y-linked_2
TRAPPC2P3 
OFD1P1Y 
TCEB1P6 
CDY2B  testis-specific_chromodomain_protein_Y_2
CDY6P 
USP9YP7 
USP9YP6 
CDY7P 
LOC387361 
CDY8P 
CDY2A  testis-specific_chromodomain_protein_Y_2
TCEB1P12 
OFD1P2Y 
TRAPPC2P8 
XKRY2  testis-specific_XK-related_protein,_Y-linked_2
ACTG1P11 
PRYP2 
CDY9P 
TAF9P2 
KIAA0664P2 
NCRNA00230A  non-protein_coding_RNA_230A
TUBB1P1 
FAM41AY2  family_with_sequence_similarity_41,_member_A,_Y-linked_2
TCEB1P13 
OFD1P4Y 
USP9YP5 
XKRYP1 
TCEB1P7 
USP9YP1 
HSFY1  heat_shock_transcription_factor,_Y-linked_isoform_1
TTTY9B  testis-specific_transcript,_Y-linked_9B_(non-protein_coding)
OFD1P5Y 
TRAPPC2P7 
OFD1P6Y 
TTTY9A  testis-specific_transcript,_Y-linked_9A_(non-protein_coding)
HSFY2  heat_shock_transcription_factor,_Y-linked_isoform_1
USP9YP2 
XKRYP2 
USP9YP10 
OFD1P7Y 
NCRNA00185  non-protein_coding_RNA_185
ZNF839P1 
CD24  signal_transducer_CD24_precursor
4   5418629       chr4  NT_016354.19  83382556-88801185    RPL6P11 
FAM198B  protein_ENED_isoform_2
LOC100422445 
TMEM144  transmembrane_protein_144
LOC646890 
LOC100131038 
RXFP1  relaxin_receptor_1
C4orf46  hypothetical_protein_LOC201725
ETFDH  electron_transfer_flavoprotein-ubiquinone_oxidoreductase,_mitochondrial_precursor
PPID  peptidyl-prolyl_cis-trans_isomerase_D
FNIP2  folliculin-interacting_protein_2
FABP5P12  hypothetical_protein_LOC152940
LOC100505930  hypothetical_LOC100505930
RAPGEF2  rap_guanine_nucleotide_exchange_factor_2
RPS14P7 
FSTL5  follistatin-related_protein_5_isoform_c
LOC100131135 
NAF1  H/ACA_ribonucleoprotein_complex_non-core_subunit_NAF1_isoform_a
LOC133332 
NPY1R  neuropeptide_Y_receptor_type_1
5   5318921       chr3  NT_005612.16  66614017-71932938    MIR16-2  microRNA:hsa-mir-16-2
TRIM59  tripartite_motif-containing_protein_59
B3GAT3P1 
LOC100507647  hypothetical_LOC100507647
SCARNA7  small_Cajal_body-specific_RNA_7
KRT8P12 
RPL6P8 
ARL14  ADP-ribosylation_factor-like_protein_14
PPM1L  protein_phosphatase_1L
B3GALNT1  UDP-GalNAc:beta-1,_3-N-acetylgalactosaminyltransferase_1
NMD3  60S_ribosomal_export_protein_NMD3
LOC100129403 
LOC646085 
C3orf57  small_subunit_of_serine_palmitoyltransferase_B
RPL23AP42 
OTOL1  otolin-1_precursor
TOMM22P6 
RPS6P4 
LOC647107  hypothetical_LOC647107
RNU7-82P 
LOC730129 
MIR1263  microRNA:hsa-mir-1263
MIR720  microRNA:hsa-mir-720
SI  sucrase-isomaltase,_intestinal
SLITRK3  SLIT_and_NTRK-like_protein_3_precursor
6   5264160       chr14  NT_026437.12  5951016-11215176    CMA1  chymase_preproprotein_preproprotein
CTSG  cathepsin_G_preproprotein_preproprotein
GZMH  granzyme_H_precursor
GZMB  granzyme_B_precursor
STXBP6  syntaxin-binding_protein_6
HMGN2L6 
OR7K1P 
LOC401767 
LOC100289051 
NOVA1  RNA-binding_protein_Nova-1_isoform_3
MIR4307  microRNA_4307
UNGP2 
RPS27AP4 
LOC100505967  hypothetical_LOC100505967,_transcript_variant_3
BNIP3P 
RPL26P3 
EIF4A1P12 
BTF3P2 
FOXG1  forkhead_box_protein_G1
C14orf23  chromosome_14_open_reading_frame_23,_transcript_variant_2
LOC100420424 
LOC100506004  hypothetical_LOC100506004
LOC100506026  hypothetical_LOC100506026
PRKD1  serine/threonine-protein_kinase_D1
7   4854041       chr21  NT_011512.11  7542208-12396249    LOC100421083 
C21orf131  chromosome_21_open_reading_frame_131
LOC100288185 
NCAM2  neural_cell_adhesion_molecule_2_precursor
LOC100420035 
MAPK6PS2 
ZNF299P 
LOC100130310 
EEF1A1P1 
TUBAP 
VN2R20P 
LOC100419737 
RPL13AP7 
8   4628134       chr3  NT_022459.15  15540539-20168673    LOC100419178  1,4-alpha-glucan-branching_enzyme
RPL7AP23 
CYP51P1 
SRRM1P2 
LOC100130326  similar_to_MUF1_protein
LOC100422711  cell_adhesion_molecule_2_isoform_3


Posfai@neb.com
May 11, 2011