Distribution of restriction sites in the human genome

Enzyme:  FseI               Longest uncut segments
Specificity:  GGCCGGCC               Repeats in uncut segments
Number of sites:  13281               Genes in uncut segments
Mean distance between sites:  215446 base pairs
Standard deviation:  390072 base pairs
Site density 4.6 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   5060503  chr12  NT_029419.12  49883372-54943875    50.31 % in   8738 repeats    12.17 % in 25 genes
2   4943511  chr7  NT_007933.15  60314894-65258405    51.10 % in   7919 repeats    33.24 % in 28 genes
3   4887751  chr3  NT_005612.16  7399797-12287548    52.75 % in   7933 repeats    21.70 % in 22 genes
4   4858522  chr2  NT_005403.17  61041706-65900228    45.10 % in   7517 repeats    65.85 % in 16 genes
5   4810861  chr2  NT_022184.15  34700065-39510926    46.48 % in   7101 repeats    22.31 % in 16 genes
6   4276013  chr2  NT_005403.17  37228957-41504970    50.75 % in   7030 repeats    34.10 % in 32 genes
7   4256389  chr4  NT_016354.19  72081694-76338083    47.77 % in   6846 repeats    52.81 % in 15 genes
8   4115246  chr13  NT_024524.14  18105339-22220585    48.15 % in   6770 repeats    35.80 % in 29 genes
9   4103589  chr10  NT_030059.13  3638145-7741734    47.14 % in   6485 repeats    0.00 % in 0 genes
10   4003347  chr5  NT_034772.6  6398391-10401738    55.37 % in   6268 repeats    0.00 % in 0 genes
11   4002825  chr7  NT_007933.15  51266317-55269142    43.09 % in   6430 repeats    0.00 % in 0 genes
12   3845128  chr13  NT_009952.14  16432160-20277288    39.23 % in   5884 repeats    0.00 % in 0 genes
13   3779666  chr8  NT_008046.16  17149459-20929125    48.77 % in   6472 repeats    0.00 % in 0 genes
14   3756443  chr18  NT_010966.14  3445920-7202363    44.74 % in   6315 repeats    0.00 % in 0 genes
15   3691065  chr6  NT_007299.13  12490112-16181177    55.91 % in   5708 repeats    0.00 % in 0 genes
16   3633936  chr4  NT_016354.19  55507692-59141628    54.95 % in   5738 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  5060503  chr12  NT_029419.12  49883372-54943875    8738  643       AT_rich (666)  MIRb (439)  L2a (426) 
2  4943511  chr7  NT_007933.15  60314894-65258405    7919  631       AT_rich (662)  MIRb (267)  L2a (266) 
3  4887751  chr3  NT_005612.16  7399797-12287548    7933  662       AT_rich (768)  AluSx (269)  L2a (242) 
4  4858522  chr2  NT_005403.17  61041706-65900228    7517  648       AT_rich (807)  MIR (315)  L2a (303) 
5  4810861  chr2  NT_022184.15  34700065-39510926    7101  595       AT_rich (582)  MIRb (323)  MIR (288) 
6  4276013  chr2  NT_005403.17  37228957-41504970    7030  620       AT_rich (696)  AluSx (303)  MIRb (229) 
7  4256389  chr4  NT_016354.19  72081694-76338083    6846  591       AT_rich (534)  AluSx (306)  MIRb (280) 
8  4115246  chr13  NT_024524.14  18105339-22220585    6770  622       AT_rich (456)  AluSx (305)  MIRb (288) 
9  4103589  chr10  NT_030059.13  3638145-7741734    6485  603       AT_rich (664)  MIRb (317)  MIR (299) 
10  4003347  chr5  NT_034772.6  6398391-10401738    6268  604       AT_rich (657)  AluSx (216)  L2a (176) 
11  4002825  chr7  NT_007933.15  51266317-55269142    6430  553       AT_rich (641)  MIRb (259)  MIR (242) 
12  3845128  chr13  NT_009952.14  16432160-20277288    5884  555       AT_rich (616)  MIRb (234)  L2a (215) 
13  3779666  chr8  NT_008046.16  17149459-20929125    6472  595       AT_rich (456)  MIRb (343)  AluSx (297) 
14  3756443  chr18  NT_010966.14  3445920-7202363    6315  565       AT_rich (384)  AluSx (340)  MIRb (285) 
15  3691065  chr6  NT_007299.13  12490112-16181177    5708  547       AT_rich (509)  AluSx (256)  L2a (181) 
16  3633936  chr4  NT_016354.19  55507692-59141628    5738  626       AT_rich (774)  L2a (168)  AluSx (156) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   5060503       chr12  NT_029419.12  49883372-54943875    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
RPL21P106 
2   4943511       chr7  NT_007933.15  60314894-65258405    LOC100422456  RING_finger_protein_148_precursor
TAS2R16  taste_receptor_type_2_member_16
SLC13A1  solute_carrier_family_13_member_1
LOC100129401 
IQUB  IQ_and_ubiquitin-like_domain-containing_protein
NDUFA5  NADH_dehydrogenase_[ubiquinone]_1_alpha_subcomplex_subunit_5
ASB15  ankyrin_repeat_and_SOCS_box_protein_15
LMOD2  leiomodin-2
WASL  neural_Wiskott-Aldrich_syndrome_protein
HYALP1  hyaluronoglucosaminidase_pseudogene_1
HYAL4  hyaluronidase-4
SPAM1  hyaluronidase_PH-20_isoform_2
TMEM229A  transmembrane_protein_229A
LOC136157 
RPS2P31 
GPR37  probable_G-protein_coupled_receptor_37_precursor
LOC154872  hypothetical_protein_LOC154872
POT1  protection_of_telomeres_protein_1_isoform_4
LOC646837 
LOC100420864 
RPL31P39 
LOC100134507 
LOC100506664  hypothetical_LOC100506664
MIR592  microRNA:hsa-mir-592
LOC646873 
ZNF800  zinc_finger_protein_800
LOC100506682  hypothetical_LOC100506682
GCC1  GRIP_and_coiled-coil_domain-containing_protein_1
3   4887751       chr3  NT_005612.16  7399797-12287548    IMPG2  interphotoreceptor_matrix_proteoglycan_2_precursor
BTF3P16  protein_FAM136A-like
FAM172B  family_with_sequence_similarity_172,_member_B_pseudogene
RG9MTD1  mitochondrial_ribonuclease_P_protein_1
RPS18P5  PEST_proteolytic_signal-containing_nuclear_protein
RPL32P7 
ZBTB11  zinc_finger_and_BTB_domain-containing_protein_11
LOC100009676  hypothetical_LOC100009676
RPL24  60S_ribosomal_protein_L24
LOC285359  phosducin-like_3_pseudogene
CEP97  centrosomal_protein_of_97_kDa
FAM55C  hypothetical_protein_LOC91775_precursor
NFKBIZ  NF-kappa-B_inhibitor_zeta_isoform_b
LOC152225  hypothetical_LOC152225
ZPLD1  zona_pellucida-like_domain-containing_protein_1
LOC100287880 
LOC644681 
LOC100128179 
TRNAE27P 
LOC391562 
ALCAM  CD166_antigen_precursor
CBLB  E3_ubiquitin-protein_ligase_CBL-B
4   4858522       chr2  NT_005403.17  61041706-65900228    SNAI1P1  protein_unc-80_homolog_isoform_2
RPE  ribulose-phosphate_3-epimerase_isoform_2
RPL6P6  hypothetical_protein_LOC151050
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
LOC646249 
IKZF2  zinc_finger_protein_Helios_isoform_2
RPL5P8  sperm-associated_antigen_16_protein_isoform_2
VWC2L  von_Willebrand_factor_C_domain-containing_protein_2-like_precursor
ENSAP3 
BARD1  BRCA1-associated_RING_domain_protein_1
5   4810861       chr2  NT_022184.15  34700065-39510926    PNPT1  polyribonucleotide_nucleotidyltransferase_1,_mitochondrial_precursor
EFEMP1  EGF-containing_fibulin-like_extracellular_matrix_protein_1_precursor
MIR217  microRNA:hsa-mir-217
MIR216A  microRNA:hsa-mir-216a
MIR216B  microRNA:hsa-mir-216b
LOC100129434  hypothetical_LOC100129434
CCDC85A  coiled-coil_domain-containing_protein_85A
EIF2S2P7 
LOC100131953 
VRK2  serine/threonine-protein_kinase_VRK2_isoform_2
FANCL  E3_ubiquitin-protein_ligase_FANCL_isoform_2
EIF3FP3 
LOC644456 
FLJ30838  hypothetical_LOC400955
LOC100506891  hypothetical_LOC100506891
LOC100506934  hypothetical_LOC100506934
6   4276013       chr2  NT_005403.17  37228957-41504970    RPL23AP35 
LOC100131051 
DPRXP1  zinc_finger_CCCH_domain-containing_protein_15
ITGAV  integrin_alpha-V_isoform_2
FAM171B  KIAA1946
ZSWIM2  E3_ubiquitin-protein_ligase_ZSWIM2
IMPDH1P7 
GAPDHP59  calcitonin_gene-related_peptide_type_1_receptor_precursor
TFPI  tissue_factor_pathway_inhibitor_isoform_b_precursor
ST13P2 
LOC729141 
GULP1  PTB_domain-containing_engulfment_adapter_protein_1
DIRC1  disrupted_in_renal_carcinoma_protein_1
MIR1245  microRNA:hsa-mir-1245
MIR3129  microRNA_3129
KRT18P19 
WDR75  WD_repeat-containing_protein_75
LOC100420666 
SLC40A1  solute_carrier_family_40_member_1
ASNSD1  asparagine_synthetase_domain-containing_protein_1
ANKAR  ankyrin_and_armadillo_repeat-containing_protein
OSGEPL1  probable_O-sialoglycoprotein_endopeptidase_2
ORMDL1  ORM1-like_protein_1
LOC100421409  PMS1_protein_homolog_1_isoform_c
LOC100287965 
LOC653447 
RNF11P1 
MSTN  growth/differentiation_factor_8_precursor
C2orf88  hypothetical_protein_LOC84281
HIBCH  3-hydroxyisobutyryl-CoA_hydrolase,_mitochondrial_isoform_2_precursor
INPP1  inositol_polyphosphate_1-phosphatase
MFSD6  major_facilitator_superfamily_domain-containing_protein_6
7   4256389       chr4  NT_016354.19  72081694-76338083    POU4F2  POU_domain,_class_4,_transcription_factor_2
TTC29  tetratricopeptide_repeat_protein_29
LOC100505596  hypothetical_LOC100505596
RPL31P26 
LOC100420927 
GTF2F2P1  endothelin-1_receptor_isoform_b_precursor
TMEM184C  transmembrane_protein_184C
PRMT10  putative_protein_arginine_N-methyltransferase_10
LOC100420036  rho_GTPase-activating_protein_10
NR3C2  mineralocorticoid_receptor_isoform_2
ASS1P8 
ATP5LP4 
LOC100216487  hypothetical_LOC285423
DCLK2  serine/threonine-protein_kinase_DCLK2_isoform_b
LOC729566  protein_archease-like
8   4115246       chr13  NT_024524.14  18105339-22220585    C13orf36  hypothetical_protein_LOC400120
GAPDHP34 
LOC646879 
RFXAP  regulatory_factor_X-associated_protein
SMAD9  mothers_against_decapentaplegic_homolog_9_isoform_b
LOC100130119 
RPL29P28 
EIF4A1P5 
ALG5  dolichyl-phosphate_beta-glucosyltransferase_isoform_2
EXOSC8  exosome_complex_exonuclease_RRP43
FAM48A  family_with_sequence_similarity_48,_member_A_isoform_b
CSNK1A1L  casein_kinase_I_isoform_alpha-like
RPS12P24 
POSTN  periostin_isoform_4
TRPC4  short_transient_receptor_potential_channel_4_isoform_zeta
HSPD1P9 
UFM1  ubiquitin-fold_modifier_1_precursor
LOC100128902 
FREM2  FRAS1-related_extracellular_matrix_protein_2_precursor
LOC100420281 
LOC646929 
STOML3  stomatin-like_protein_3_isoform_2
C13orf23  hypothetical_protein_LOC80209_isoform_2
NHLRC3  NHL_repeat-containing_protein_3_isoform_b
LHFP  lipoma_HMGIC_fusion_partner_precursor
RNY4P14  microRNA_4305
FLJ42392  hypothetical_LOC400123
LOC646982  twelve-thirteen_translocation_leukemia_gene,_transcript_variant_TTL-T
LOC100507202  hypothetical_LOC100507202


Posfai@neb.com
May 11, 2011