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

 

Methanosarcina_acetivorans
     
 

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_003552 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Methanosarcina_acetivorans

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_003552 3428785-3430387 (-) ISMac8 3 details 20091571, (all)
1 NC_003552 4365456-4367058 (+) ISMac8 3 details 20092337, (all)
2 NC_003552 4732969-4734575 (-) ISMac8 3 details 20092648, (all)
3 NC_003552 2407121-2408613 (-) ISPpu20 8 No TIRs detected.  
4 NC_003552 2457741-2459447 (-) ISMac20 6 details 20090834, (all)
5 NC_003552 552773-554438 (-) ISMac20 6 No TIRs detected. 20089361, (all)
6 NC_003552 1123096-1124761 (-) ISMac20 6 No TIRs detected. 20089822, (all)
7 NC_003552 5150054-5151722 (-) ISMac20 6 No TIRs detected. 20093017, (all)
8 NC_003552 1246815-1248480 (-) ISMac20 6 No TIRs detected. 20089917, (all)
9 NC_003552 3326161-3327825 (-) ISMac20 6 No TIRs detected. 20091501, (all)
10 NC_003552 1575771-1576320 (-) ISMac16 16 details 20090177, (all)
11 NC_003552 1977741-1978504 (-) ISMac16 16 details 20090502, 20090503, (all)
12 NC_003552 5030105-5030888 (-) ISMac16 16 details 20092900, 20092901, (all)
13 NC_003552 3473416-3473971 (+) ISMac16 16 details 20091608, (all)
14 NC_003552 3409927-3410482 (-) ISMac16 16 details 20091558, (all)
15 NC_003552 4171897-4172452 (-) ISMac16 16 details 20092189, (all)
16 NC_003552 4347062-4347818 (-) ISMac16 16 details 20092319, (all)
17 NC_003552 5148212-5149001 (-) ISMac16 16 details 20093014, 20093015, (all)
18 NC_003552 4085139-4085895 (+) ISMac16 16 details 20092126, 20092127, (all)
19 NC_003552 3738290-3738839 (-) ISMac16 16 details 20091823, (all)
20 NC_003552 3985379-3986174 (-) ISMac16 16 details 20092037, 20092038, (all)
21 NC_003552 3679781-3680563 (+) ISMac16 16 details 20091765, (all)
22 NC_003552 2669508-2670106 (-) ISMac16 16 details 20091004, (all)
23 NC_003552 2317005-2317560 (+) ISMac16 16 details 20090729, (all)
24 NC_003552 3064727-3065519 (+) ISMac16 16 details 20091301, 20091302, (all)
25 NC_003552 4728690-4729457 (-) ISMac16 16 details 20092643, 20092644, (all)
26 NC_003552 1250417-1251596 (-) ISMac17 3 details  
27 NC_003552 1236771-1237971 (+) ISMac17 3 No TIRs detected.  
28 NC_003552 1708156-1709335 (+) ISMac17 3 details  
29 NC_003552 2566675-2568350 (+) ISMac12 3 details 20090920, (all)
30 NC_003552 4338594-4340277 (-) ISMac12 3 details 20092312, (all)
31 NC_003552 3672422-3674099 (-) ISMac12 3 details 20091761, (all)
32 NC_003552 1258475-1260413 (+) ISMac19 7 No TIRs detected.  
33 NC_003552 2709076-2711334 (-) ISMac9 7 details 20091042, 20091043, (all)
34 NC_003552 2573934-2576192 (-) ISMac9 7 details 20090925, 20090926, (all)
35 NC_003552 3880191-3882449 (-) ISMac9 7 details 20091941, 20091942, (all)
36 NC_003552 4139947-4142205 (-) ISMac9 7 details 20092167, 20092168, (all)
37 NC_003552 4102863-4105120 (+) ISMac9 7 details 20092140, 20092141, (all)
38 NC_003552 3417707-3419964 (+) ISMac9 7 details 20091561, 20091562, (all)
39 NC_003552 1261581-1263836 (+) ISMac9 7 details 20089928, (all)
40 NC_003552 3630452-3631986 (-) ISMba20 4 No TIRs detected. 20091728, (all)
41 NC_003552 3444977-3446511 (+) ISMba20 4 No TIRs detected. 20091585, (all)
42 NC_003552 4495463-4496997 (-) ISMba20 4 No TIRs detected. 20092446, (all)
43 NC_003552 3403992-3405526 (-) ISMba20 4 No TIRs detected. 20091553, (all)
44 NC_003552 2585628-2587253 (-) ISMma11 8 No TIRs detected. 20090932, (all)
45 NC_003552 3396515-3398236 (-) ISMma11 8 details 20091549, (all)
46 NC_003552 176945-178569 (+) ISMma11 8 No TIRs detected. 20089047, (all)
47 NC_003552 3092230-3093856 (-) ISMma11 8 No TIRs detected. 20091325, (all)
48 NC_003552 3252236-3253860 (-) ISMma11 8 No TIRs detected. 20091449, (all)
49 NC_003552 470590-472214 (-) ISMma11 8 No TIRs detected. 20089285, (all)
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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.