Distribution of restriction sites in the human genome

Enzyme:  XamI               Longest uncut segments
Specificity:  GTCGAC               Repeats in uncut segments
Number of sites:  30676               Genes in uncut segments
Mean distance between sites:  93276 base pairs
Standard deviation:  101295 base pairs
Site density 10.7 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   1343037  chr1  NT_032977.9  21443537-22786574    61.81 % in   3520 repeats    70.86 % in 13 genes
2   1095871  chrX  NT_167197.1  31284761-32380632    62.79 % in   1649 repeats    0.48 % in 4 genes
3   994289  chr3  NT_022517.18  5184741-6179030    54.28 % in   1736 repeats    1.71 % in 2 genes
4   953599  chr12  NT_009714.17  3484789-4438388    52.38 % in   1479 repeats    50.10 % in 20 genes
5   931374  chr11  NT_033899.8  25131799-26063173    49.98 % in   1594 repeats    39.00 % in 4 genes
6   913850  chr14  NT_026437.12  26921614-27835464    63.19 % in   1339 repeats    0.00 % in 0 genes
7   894612  chr5  NT_006713.15  1393635-2288247    48.12 % in   1334 repeats    0.18 % in 2 genes
8   885627  chr9  NT_008413.18  31502686-32388313    57.10 % in   1346 repeats    1.79 % in 3 genes
9   880188  chr3  NT_022459.15  19461230-20341418    44.56 % in   1291 repeats    0.00 % in 0 genes
10   870069  chr7  NT_007933.15  26466350-27336419    51.23 % in   1329 repeats    0.00 % in 0 genes
11   852834  chr8  NT_167187.1  17810991-18663825    54.03 % in   2008 repeats    0.00 % in 0 genes
12   841025  chr2  NT_022184.15  10053563-10894588    59.31 % in   1323 repeats    0.00 % in 0 genes
13   834719  chr6  NT_007592.15  44034782-44869501    46.65 % in   1506 repeats    0.00 % in 0 genes
14   823974  chr5  NT_034772.6  8196414-9020388    54.58 % in   1181 repeats    0.00 % in 0 genes
15   823485  chr9  NT_008470.19  34741462-35564947    58.87 % in   1320 repeats    0.00 % in 0 genes
16   821399  chr6  NT_025741.15  1-821400    51.54 % in   1288 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  1343037  chr1  NT_032977.9  21443537-22786574    3520  380       AluSx (398)  MIRb (193)  AluJb (153) 
2  1095871  chrX  NT_167197.1  31284761-32380632    1649  334       AT_rich (132)  (TA)n (38)  MIRb (36) 
3  994289  chr3  NT_022517.18  5184741-6179030    1736  352       MIRb (101)  MIR (78)  AT_rich (71) 
4  953599  chr12  NT_009714.17  3484789-4438388    1479  291       AT_rich (110)  L2 (53)  MIR (51) 
5  931374  chr11  NT_033899.8  25131799-26063173    1594  298       MIRb (109)  AluSx (88)  L2c (78) 
6  913850  chr14  NT_026437.12  26921614-27835464    1339  305       AT_rich (126)  L2a (48)  MIRb (39) 
7  894612  chr5  NT_006713.15  1393635-2288247    1334  290       AT_rich (162)  MIR (50)  L2a (49) 
8  885627  chr9  NT_008413.18  31502686-32388313    1346  323       AT_rich (94)  MIRb (50)  MIR (37) 
9  880188  chr3  NT_022459.15  19461230-20341418    1291  286       AT_rich (162)  L2a (47)  (TA)n (46) 
10  870069  chr7  NT_007933.15  26466350-27336419    1329  290       AT_rich (153)  MIR (52)  MIRb (42) 
11  852834  chr8  NT_167187.1  17810991-18663825    2008  284       AluSx (240)  AluJo (139)  AluJb (119) 
12  841025  chr2  NT_022184.15  10053563-10894588    1323  294       MIRb (89)  AluSx (53)  MIR (41) 
13  834719  chr6  NT_007592.15  44034782-44869501    1506  286       AluSx (103)  MIRb (89)  MIR (72) 
14  823974  chr5  NT_034772.6  8196414-9020388    1181  282       AT_rich (125)  (TA)n (36)  MIR (29) 
15  823485  chr9  NT_008470.19  34741462-35564947    1320  313       AT_rich (124)  AluSx (38)  (TA)n (37) 
16  821399  chr6  NT_025741.15  1-821400    1288  285       AT_rich (143)  MIR (53)  L2c (40) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   1343037       chr1  NT_032977.9  21443537-22786574    C1orf185  hypothetical_protein_LOC284546
CFLP2 
LOC100128235 
RPS2P8  RING_finger_protein_11
TTC39A  tetratricopeptide_repeat_protein_39A_isoform_2
LOC100422413  epidermal_growth_factor_receptor_substrate_15_isoform_B
CALR4P 
OSBPL9  oxysterol-binding_protein-related_protein_9_isoform_b
MIR761  microRNA_761
RPS26P14  ras-related_protein_Rab-3B
KTI12  protein_KTI12_homolog
BTF3L4  transcription_factor_BTF3_homolog_4_isoform_2
ANAPC10P1  zinc_finger_FYVE_domain-containing_protein_9_isoform_2
2   1095871       chrX  NT_167197.1  31284761-32380632    LOC646506 
FAM47A  hypothetical_protein_LOC158724
FTH1P14 
LOC392439 
3   994289       chr3  NT_022517.18  5184741-6179030    EDEM1  ER_degradation-enhancing_alpha-mannosidase-like_1
MRPS35P1 
4   953599       chr12  NT_009714.17  3484789-4438388    KLRA1  killer_cell_lectin-like_receptor_subfamily_A,_member_1,_pseudogene
MAGOHB  protein_mago_nashi_homolog_2
STYK1  tyrosine-protein_kinase_STYK1
CSDA  DNA-binding_protein_A_isoform_b
LOC100286954  hypothetical_LOC100506226,_transcript_variant_1
TAS2R7  taste_receptor_type_2_member_7
TAS2R8  taste_receptor_type_2_member_8
TAS2R9  taste_receptor_type_2_member_9
TAS2R10  taste_receptor_type_2_member_10
LOC100420580 
TAS2R18  taste_receptor_type_2_member_30
PS5 
TAS2R42  taste_receptor_type_2_member_42
LOC100420583 
PRB3  basic_salivary_proline-rich_protein_3_precursor
PRB4  basic_salivary_proline-rich_protein_4_precursor
PRB1  basic_salivary_proline-rich_protein_1_isoform_3_preproprotein
PRB2  basic_salivary_proline-rich_protein_2
LOC100130073 
LOC100129640 
5   931374       chr11  NT_033899.8  25131799-26063173    LOC100507165  hypothetical_LOC100507165
MIR100  microRNA:hsa-mir-100
-  tRNA-Lys
GLULP3 
7   894612       chr5  NT_006713.15  1393635-2288247    LOC100128982 
RPS17P11 
8   885627       chr9  NT_008413.18  31502686-32388313    LOC100288563 
SLC25A5P8 
ACO1  cytoplasmic_aconitate_hydratase


Posfai@neb.com
May 11, 2011