Distribution of restriction sites in the human genome

Enzyme:  SwaI               Longest uncut segments
Specificity:  ATTTAAAT               Repeats in uncut segments
Number of sites:  225541               Genes in uncut segments
Mean distance between sites:  12686 base pairs
Standard deviation:  16793 base pairs
Site density 78.8 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   521001  chr6  NT_167244.1  2356293-2877294    7.22 % in   161 repeats    6.85 % in 9 genes
2   502104  chr15  NT_037852.6  1384128-1886232    2.32 % in   33 repeats    0.00 % in 0 genes
3   444815  chr19  NT_011255.14  4056673-4501488    54.64 % in   1215 repeats    78.73 % in 19 genes
4   413433  chr19  NT_011295.11  5271496-5684929    57.59 % in   1221 repeats    68.28 % in 16 genes
5   407492  chr16  NT_010393.16  999009-1406501    24.91 % in   528 repeats    56.32 % in 18 genes
6   396279  chr19  NT_011255.14  794691-1190970    34.46 % in   755 repeats    76.14 % in 20 genes
7   387418  chr22  NT_011520.12  17317742-17705160    52.53 % in   1060 repeats    61.48 % in 16 genes
8   383492  chr20  NT_011362.10  30970436-31353928    19.73 % in   416 repeats    52.77 % in 12 genes
9   376832  chr8  NT_037704.5  1760-378592    29.65 % in   519 repeats    0.00 % in 0 genes
10   357342  chr7  NT_007933.15  38734833-39092175    58.21 % in   957 repeats    0.00 % in 0 genes
11   353959  chr1  NT_004350.19  2681236-3035195    17.21 % in   320 repeats    0.00 % in 0 genes
12   346304  chr19  NT_011295.11  1269013-1615317    56.69 % in   993 repeats    0.00 % in 0 genes
13   344908  chr16  NT_010393.16  490382-835290    22.42 % in   404 repeats    0.00 % in 0 genes
14   339698  chr22  NT_011520.12  22799672-23139370    41.89 % in   745 repeats    0.00 % in 0 genes
15   339622  chr19  NT_011109.16  14631304-14970926    45.65 % in   794 repeats    0.00 % in 0 genes
16   327893  chr19  NT_011295.11  8581167-8909060    56.50 % in   956 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  521001  chr6  NT_167244.1  2356293-2877294    161  69       AluSx (19)  AluY (11)  AluJo (8) 
2  502104  chr15  NT_037852.6  1384128-1886232    33  19       L1MDa (6)  Tigger2 (5)  MER49 (2) 
3  444815  chr19  NT_011255.14  4056673-4501488    1215  145       AluSx (224)  AluY (93)  AluJo (89) 
4  413433  chr19  NT_011295.11  5271496-5684929    1221  161       AluSx (211)  AluJo (116)  AluSq (62) 
5  407492  chr16  NT_010393.16  999009-1406501    528  119       AluSx (54)  AluJo (31)  AluJb (25) 
6  396279  chr19  NT_011255.14  794691-1190970    755  110       AluSx (108)  AluJo (60)  AluY (59) 
7  387418  chr22  NT_011520.12  17317742-17705160    1060  135       AluSx (167)  MIRb (90)  AluY (64) 
8  383492  chr20  NT_011362.10  30970436-31353928    416  118       AluSx (28)  MIRb (24)  AluY (18) 
9  376832  chr8  NT_037704.5  1760-378592    519  104       AluSx (88)  GC_rich (37)  AluY (35) 
10  357342  chr7  NT_007933.15  38734833-39092175    957  149       AluSx (196)  AluJo (120)  AluSq (48) 
11  353959  chr1  NT_004350.19  2681236-3035195    320  97       (TG)n (20)  MIR3 (19)  MIR (19) 
12  346304  chr19  NT_011295.11  1269013-1615317    993  147       AluSx (158)  AluJo (113)  AluJb (59) 
13  344908  chr16  NT_010393.16  490382-835290    404  100       AluSx (50)  AluY (32)  GC_rich (28) 
14  339698  chr22  NT_011520.12  22799672-23139370    745  131       AluSx (106)  MIRb (81)  MIR (42) 
15  339622  chr19  NT_011109.16  14631304-14970926    794  130       AluSx (86)  MIRb (55)  AluJb (42) 
16  327893  chr19  NT_011295.11  8581167-8909060    956  135       AluSx (171)  AluJo (78)  AluY (56) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   521001       chr6  NT_167244.1  2356293-2877294    MICB  MHC_class_I_polypeptide-related_sequence_B_precursor
PPIAP9 
RPL15P4 
MCCD1  mitochondrial_coiled-coil_domain_protein_1_precursor
SNORD117  small_nucleolar_RNA,_C/D_box_117
TNF  tumor_necrosis_factor
LTB  lymphotoxin-beta_isoform_b
LST1  leukocyte-specific_transcript_1_protein_isoform_5
NCR3  natural_cytotoxicity_triggering_receptor_3_isoform_c
3   444815       chr19  NT_011255.14  4056673-4501488    MAP2K2  dual_specificity_mitogen-activated_protein_kinase_kinase_2
CREB3L3  cyclic_AMP-responsive_element-binding_protein_3-like_protein_3
SIRT6  NAD-dependent_deacetylase_sirtuin-6_isoform_2
ANKRD24  ankyrin_repeat_domain-containing_protein_24
EBI3  interleukin-27_subunit_beta_precursor
CCDC94  coiled-coil_domain-containing_protein_94
SHD  SH2_domain-containing_adapter_protein_D
TMIGD2  transmembrane_and_immunoglobulin_domain-containing_protein_2_isoform_2_precursor
FSD1  fibronectin_type_III_and_SPRY_domain-containing_protein_1
STAP2  signal-transducing_adaptor_protein_2_isoform_2
LOC100506931  eukaryotic_translation_initiation_factor_1-like
SH3GL1  endophilin-A2
CHAF1A  chromatin_assembly_factor_1_subunit_A
UBXN6  UBX_domain-containing_protein_6_isoform_2
HDGFRP2  hepatoma-derived_growth_factor-related_protein_2_isoform_2
PLIN4  perilipin-4
PLIN5  perilipin-5
LRG1  leucine-rich_alpha-2-glycoprotein_precursor
SEMA6B  semaphorin-6B_precursor
4   413433       chr19  NT_011295.11  5271496-5684929    C19orf57  hypothetical_protein_LOC79173
CC2D1A  coiled-coil_and_C2_domain-containing_protein_1A
PODNL1  podocan-like_protein_1_isoform_1
DCAF15  DDB1-_and_CUL4-associated_factor_15
RFX1  MHC_class_II_regulatory_factor_RFX1
RLN3  relaxin-3_preproprotein_preproprotein
IL27RA  interleukin-27_receptor_subunit_alpha_precursor
PALM3  paralemmin-3
EEF1DP1 
LOC113230  hypothetical_LOC113230
C19orf67  UPF0575_protein_C19orf67
SAMD1  atherin
PRKACA  cAMP-dependent_protein_kinase_catalytic_subunit_alpha_isoform_2
ASF1B  histone_chaperone_ASF1B
LOC100507373  hypothetical_LOC100507373,_transcript_variant_1
LPHN1  latrophilin-1_isoform_2_precursor
5   407492       chr16  NT_010393.16  999009-1406501    LOC146336  hypothetical_LOC146336
SSTR5  somatostatin_receptor_type_5
C1QTNF8  complement_C1q_tumor_necrosis_factor-related_protein_8
GS85  hypothetical_LOC100128785
CACNA1H  voltage-dependent_T-type_calcium_channel_subunit_alpha-1H_isoform_b
TPSG1  tryptase_gamma_preproprotein
TPSB2  tryptase_beta-2_precursor
TPSAB1  tryptase_beta-1_precursor
TPSD1  tryptase_delta_precursor
PRSS29P 
TPSP1 
LOC650474 
UBE2I  SUMO-conjugating_enzyme_UBC9
RPS20P2 
BAIAP3  BAI1-associated_protein_3
C16orf42  hypothetical_protein_LOC115939
GNPTG  N-acetylglucosamine-1-phosphotransferase_subunit_gamma_precursor
UNKL  RING_finger_protein_unkempt-like_isoform_2
6   396279       chr19  NT_011255.14  794691-1190970    ELANE  neutrophil_elastase_preproprotein_preproprotein
CFD  complement_factor_D_preproprotein_preproprotein
MED16  mediator_of_RNA_polymerase_II_transcription_subunit_16
C19orf22  R3H_domain-containing_protein_C19orf22
KISS1R  kiSS-1_receptor
ARID3A  AT-rich_interactive_domain-containing_protein_3A
WDR18  WD_repeat-containing_protein_18
GRIN3B  glutamate_[NMDA]_receptor_subunit_3B_precursor
C19orf6  membralin_isoform_2
CNN2  calponin-2_isoform_b
ABCA7  ATP-binding_cassette_sub-family_A_member_7
HMHA1  minor_histocompatibility_protein_HA-1
POLR2E  DNA-directed_RNA_polymerases_I,_II,_and_III_subunit_RPABC1
GPX4  phospholipid_hydroperoxide_glutathione_peroxidase,_mitochondrial_isoform_C_precursor
SBNO2  protein_strawberry_notch_homolog_2_isoform_2
LOC729119 
STK11  serine/threonine-protein_kinase_11
C19orf26  protein_Dos
ATP5D  ATP_synthase_subunit_delta,_mitochondrial_precursor
MIDN  midnolin
7   387418       chr22  NT_011520.12  17317742-17705160    CDC42EP1  cdc42_effector_protein_1
LGALS2  galectin-2
GGA1  ADP-ribosylation_factor-binding_protein_GGA1_isoform_5
SH3BP1  SH3_domain-binding_protein_1
PDXP  pyridoxal_phosphate_phosphatase
LGALS1  galectin-1
NOL12  nucleolar_protein_12
TRIOBP  TRIO_and_F-actin-binding_protein_isoform_2
H1F0  histone_H1.0
GCAT  2-amino-3-ketobutyrate_coenzyme_A_ligase,_mitochondrial_isoform_2_precursor
GALR3  galanin_receptor_type_3
ANKRD54  ankyrin_repeat_domain-containing_protein_54
MIR658  microRNA:hsa-mir-658
MIR659  microRNA:hsa-mir-659
EIF3L  eukaryotic_translation_initiation_factor_3_subunit_L
MICALL1  MICAL-like_protein_1
8   383492       chr20  NT_011362.10  30970436-31353928    GTPBP5  GTP-binding_protein_5
HRH3  histamine_H3_receptor
FLJ44790  hypothetical_FLJ44790
OSBPL2  oxysterol-binding_protein-related_protein_2_isoform_2
ADRM1  proteasomal_ubiquitin_receptor_ADRM1_precursor
LOC100506553  hypothetical_LOC100506553
RPS21  40S_ribosomal_protein_S21
CABLES2  CDK5_and_ABL1_enzyme_substrate_2
C20orf151  hypothetical_protein_LOC140893
GATA5  transcription_factor_GATA-5
C20orf200  chromosome_20_open_reading_frame_200
MIR133A2  microRNA:hsa-mir-133a-2


Posfai@neb.com
May 11, 2011