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

 

Synechocystis_PCC6803
     
 

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_005229 Click to view the full size in a separate window.
   NC_000911 Click to view the full size in a separate window.
   NC_005230 Click to view the full size in a separate window.
   NC_005231 Click to view the full size in a separate window.
   NC_005232 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Synechocystis_PCC6803

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_000911 2443967-2444919 (+) ISTcSa 22 No TIRs detected. 16331366, (all)
1 NC_000911 52189-53142 (-) ISTcSa 22 No TIRs detected. 16329212, (all)
2 NC_000911 379032-379985 (+) ISTcSa 22 No TIRs detected. 16329519, (all)
3 NC_000911 3512244-3513200 (-) ISTcSa 22 No TIRs detected. 16332278, (all)
4 NC_000911 3097402-3098356 (+) ISTcSa 22 No TIRs detected. 16331943, (all)
5 NC_000911 2533994-2535137 (+) ISTcSa 22 details 16331436, (all)
6 NC_000911 1623652-1624605 (-) ISTcSa 22 No TIRs detected. 16330637, (all)
7 NC_000911 1098294-1099243 (+) ISTcSa 22 No TIRs detected. 16330163, (all)
8 NC_000911 123429-124380 (-) ISTcSa 22 No TIRs detected. 16329277, 16329278, (all)
9 NC_000911 421693-422648 (-) ISTcSa 22 No TIRs detected. 16329556, 16329557, (all)
10 NC_000911 1710738-1711445 (-) ISTcSa 3 details 16330726, 16330727, (all)
11 NC_000911 1877208-1878053 (+) ISTcSa 3 No TIRs detected. 16330878, 16330879, (all)
12 NC_000911 2235529-2236481 (+) ISTcSa 22 No TIRs detected. 16331192, 16331193, (all)
13 NC_000911 1725359-1726310 (-) ISTcSa 22 No TIRs detected. 16330742, 16330743, (all)
14 NC_000911 1901313-1902264 (-) ISTcSa 22 No TIRs detected. 16330899, 16330900, (all)
15 NC_000911 1463424-1464375 (+) ISTcSa 22 No TIRs detected. 16330493, 16330494, (all)
16 NC_000911 2524501-2525453 (-) ISTcSa 22 No TIRs detected. 16331427, 16331428, (all)
17 NC_000911 605469-606422 (-) ISTcSa 22 No TIRs detected. 16329717, (all)
18 NC_000911 1626006-1626885 (+) ISTcSa 22 details 16330641, 16330642, (all)
19 NC_000911 1346433-1347365 (+) ISTcSa 22 details 16330389, 16330390, (all)
20 NC_000911 3405462-3406338 (+) ISTcSa 3 No TIRs detected. 16332196, 16332197, (all)
21 NC_005230 100746-101701 (+) ISTcSa 22 No TIRs detected. 38505772, 38505773, (all)
22 NC_005231 41021-41976 (+) ISTcSa 22 No TIRs detected. 38505820, 38505821, (all)
23 NC_005231 38496-39448 (-) ISTcSa 22 No TIRs detected. 38505817, 38505818, (all)
24 NC_000911 1200292-1201467 (-) IS4Sa 10 No TIRs detected. 16330249, (all)
25 NC_000911 2326939-2328114 (+) IS4Sa 10 No TIRs detected. 16331269, (all)
26 NC_000911 2048398-2049594 (+) IS4Sa 10 details 16331039, (all)
27 NC_000911 3400583-3401526 (-) IS4Sa 10 details 16332191, (all)
28 NC_000911 1728928-1730103 (-) IS4Sa 10 No TIRs detected. 16330747, (all)
29 NC_000911 1970859-1971739 (-) IS4Sa 10 details 16330964, (all)
30 NC_000911 573419-574594 (+) IS4Sa 10 No TIRs detected. 16329690, (all)
31 NC_005229 117261-118437 (-) IS4Sa 10 No TIRs detected. 38505666, (all)
32 NC_005232 99571-100747 (+) IS4Sa 10 details 38505930, (all)
33 NC_005230 4167-5342 (+) IS4Sa 10 No TIRs detected. 38505676, (all)
34 NC_000911 3096324-3097186 (+) IS5Sb 13 details 16331941, (all)
35 NC_000911 2441034-2441896 (+) IS5Sb 13 details 16331363, (all)
36 NC_000911 2482728-2483590 (-) IS5Sb 13 details 16331397, (all)
37 NC_000911 3093893-3094755 (-) IS5Sb 13 details 16331937, (all)
38 NC_000911 3109765-3110622 (-) IS5Sb 11 details 16331953, 16331954, (all)
39 NC_000911 967542-968424 (-) IS5Sa 13 details 16330046, (all)
40 NC_000911 1275357-1276219 (-) IS5Sa 13 details 16330321, (all)
41 NC_000911 1513161-1514023 (+) IS5Sa 11 details 16330535, (all)
42 NC_000911 2921596-2922452 (+) IS5Sa 11 details 16331789, (all)
43 NC_000911 2328184-2329044 (-) IS5Sa 10 details 16331270, 16331271, (all)
44 NC_000911 2210275-2211136 (+) IS5Sa 10 details 16331166, 16331167, (all)
45 NC_000911 473029-473746 (+) IS5Sa 3 details 16329603, (all)
46 NC_005229 38792-39654 (+) IS5Sa 11 details 38505575, (all)
47 NC_000911 1614419-1615836 (+) IS4Sa2 3 details 16330626, (all)
48 NC_000911 1384731-1385603 (+) IS5Sa2 3 No TIRs detected. 16330423, (all)
49 NC_000911 1386016-1386475 (-) IS1Sa 3 details 16330426, (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.