Insertion Sequence Annotation (ISA) System - Browser

Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.
Fengfeng Zhou, Victor Olman and Ying Xu.
BMC Genomics 2008, 9:36.


It is worth mentioning that a single-copy IS element might also be active in the host genome. For example, a recently invaded IS element in a genome might not have enough time to accumulate more than one copy. But it's difficult to identify the complete structures of these IS elements. This work defines a recently active IS element as those with two other highly conserved copies in the same genome, and identifies the complete structures of the IS elements with recent activities by comparing the multiple copies of the same element.

Cyano_genomes
Anabaena variabilis ATCC 29413 Gloeobacter violaceus PCC 7421 Nostoc sp. PCC 7120
Prochlorococcus marinus str. MIT 9312 Prochlorococcus marinus str. MIT 9313 Prochlorococcus marinus str. NATL2A
Prochlorococcus marinus subsp. marinus str. CCMP1375 Prochlorococcus marinus subsp. pastoris str. CCMP1986 Synechococcus elongatus PCC 6301
Synechococcus elongatus PCC 7942 Synechococcus sp. CC9311 Synechococcus sp. CC9605
Synechococcus sp. CC9902 Synechococcus sp. JA-2-3B'a(2-13) Synechococcus sp. JA-3-3Ab
Synechococcus sp. WH 8102 Synechocystis sp. PCC 6803 Thermosynechococcus elongatus BP-1
Trichodesmium erythraeum IMS101

Archaea_genomes
Aeropyrum pernix K1 Archaeoglobus fulgidus DSM 4304 Haloarcula marismortui ATCC 43049
Halobacterium sp. NRC-1 Haloquadratum walsbyi DSM 16790 Methanocaldococcus jannaschii DSM 2661
Methanococcoides burtonii DSM 6242 Methanococcus maripaludis S2 Methanopyrus kandleri AV19
Methanosaeta thermophila PT Methanosarcina acetivorans C2A Methanosarcina barkeri str. Fusaro
Methanosarcina mazei Go1 Methanosphaera stadtmanae DSM 3091 Methanospirillum hungatei JF-1
Methanothermobacter thermautotrophicus str. Delta H Nanoarchaeum equitans Kin4-M Natronomonas pharaonis DSM 2160
Picrophilus torridus DSM 9790 Pyrobaculum aerophilum str. IM2 Pyrobaculum islandicum DSM 4184
Pyrococcus abyssi GE5 Pyrococcus furiosus DSM 3638 Pyrococcus horikoshii OT3
Sulfolobus acidocaldarius DSM 639 Sulfolobus solfataricus P2 Sulfolobus tokodaii str. 7
Thermococcus kodakarensis KOD1 Thermofilum pendens Hrk 5 Thermoplasma acidophilum DSM 1728
Thermoplasma volcanium GSS1

 

Nostoc_sp
     
 

Distribution of recently active Insertion Sequence elements (raIS) and A+T contents (window size: 1,000 bp) of each chromosomes and plasmids:

raIS elements annotated with different colors based on the IS families and groups they belong to. The information could be found details .
1 A+T contents ranging in [0%, 100%]
2 Positions of annotated raIS
3 A+T content of the chromosome or plasmid
 


   NC_003272 Click to view the full size in a separate window.
   NC_003276 Click to view the full size in a separate window.
   NC_003240 Click to view the full size in a separate window.
   NC_003267 Click to view the full size in a separate window.
   NC_003273 Click to view the full size in a separate window.
   NC_003241 Click to view the full size in a separate window.
   NC_003270 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Nostoc_sp

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_003272 5531710-5532919 (+) IS14999 8 details 17232120, (all)
1 NC_003272 2356170-2357367 (-) IS14999 8 details 17229463, 17229464, (all)
2 NC_003272 2473736-2474933 (-) IS14999 8 details 17229558, 17229559, (all)
3 NC_003272 3370746-3371941 (+) IS14999 8 details 17230265, 17230266, (all)
4 NC_003272 2216711-2217910 (+) IS14999 8 details 17229345, 17229346, (all)
5 NC_003272 2075746-2076940 (+) IS14999 8 details 17229218, 17229219, (all)
6 NC_003272 644481-645676 (+) IS14999 8 details 17228048, 17228049, (all)
7 NC_003272 5798056-5799253 (-) IS14999 8 details 17232359, 17232360, (all)
8 NC_003273 6942-8619 (+) IS892 9 details 17232883, (all)
9 NC_003276 90930-92610 (-) IS892 9 details 17233121, 17233122, (all)
10 NC_003276 1715-3391 (-) IS892 9 details 17233020, 17233021, (all)
11 NC_003276 95843-97519 (-) IS892 9 details 17233127, 17233128, (all)
12 NC_003276 313183-314859 (-) IS892 9 details 17233318, 17233319, (all)
13 NC_003276 397063-398741 (-) IS892 9 details 62946472, 62946473, (all)
14 NC_003276 357658-359335 (+) IS892 9 details 62946420, (all)
15 NC_003276 282848-284524 (-) IS892 9 details 17233284, (all)
16 NC_003276 176941-178621 (-) IS892 9 details 17233193, 17233194, (all)
17 NC_003272 348482-349766 (-) IS492 12 No TIRs detected. 17227802, (all)
18 NC_003272 854123-855407 (-) IS492 12 No TIRs detected. 17228227, (all)
19 NC_003272 1286987-1288271 (-) IS492 12 No TIRs detected. 17228594, (all)
20 NC_003272 4388727-4390012 (+) IS492 12 No TIRs detected. 17231128, (all)
21 NC_003272 4313977-4315262 (+) IS492 12 No TIRs detected. 17231063, (all)
22 NC_003272 2379127-2380409 (-) IS492 12 No TIRs detected. 17229478, (all)
23 NC_003272 2472381-2473665 (-) IS492 12 No TIRs detected. 17229557, (all)
24 NC_003272 4441627-4442911 (-) IS492 12 No TIRs detected. 17231174, (all)
25 NC_003272 4509378-4510662 (-) IS492 12 No TIRs detected. 17231226, (all)
26 NC_003272 1429352-1430637 (+) IS492 12 No TIRs detected. 17228707, (all)
27 NC_003272 5668286-5669570 (-) IS492 12 No TIRs detected. 17232248, (all)
28 NC_003272 266703-267988 (+) IS492 12 No TIRs detected. 17227745, (all)
29 NC_003276 331904-333277 (+) ISAsp1 3 details 17233321, (all)
30 NC_003272 3288052-3289425 (+) ISAsp1 3 details 17230190, (all)
31 NC_003272 4094972-4096054 (+) ISNsp1 7 details 17230876, (all)
32 NC_003272 3275233-3276315 (+) ISNsp1 7 details 17230175, (all)
33 NC_003272 4374481-4375563 (-) ISNsp1 7 details 17231116, (all)
34 NC_003272 1835199-1836281 (+) ISNsp1 7 details 17229061, (all)
35 NC_003272 3285356-3286438 (+) ISNsp1 7 details 17230186, (all)
36 NC_003272 3231773-3232855 (-) ISNsp1 7 details 17230156, (all)
37 NC_003272 1170302-1171384 (+) ISNsp1 7 details 17228494, (all)
38 NC_003272 6156672-6157568 (+) ISMac15 7 details 17232649, 17232650, (all)
39 NC_003272 5322283-5323179 (+) ISMac15 7 details 17231930, 17231931, (all)
40 NC_003272 4361022-4361948 (+) ISMac15 7 details 17231102, 17231103, (all)
41 NC_003272 5275703-5276599 (-) ISMac15 7 details 17231891, 17231892, (all)
42 NC_003272 3284218-3285114 (-) ISMac15 7 details 17230184, 17230185, (all)
43 NC_003272 12710-13606 (-) ISMac15 7 details 17227511, 17227512, (all)
44 NC_003272 5735433-5736329 (-) ISMac15 7 details 17232308, 17232309, (all)
45 NC_003267 6554-7919 (-) IS891 5 No TIRs detected. 17227384, (all)
46 NC_003272 4944637-4946071 (+) IS891 5 No TIRs detected. 17231596, (all)
47 NC_003272 4801327-4802690 (-) IS891 5 No TIRs detected. 17231478, (all)
48 NC_003272 5350243-5351605 (-) IS891 3 No TIRs detected. 17231957, (all)
49 NC_003276 245632-247066 (+) IS891 5 No TIRs detected. 17233247, (all)
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Disclaimer:
The dataset and this website is freely available to academic users. Commercial users should contact the CSBL lab.

Website created by Fengfeng Zhou © 2007

Last updated: Oct-26-2007.