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

 

Sulfolobus_tokodaii
     
 

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_003106 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Sulfolobus_tokodaii

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_003106 1157550-1159397 (+) ISSis2 3 No TIRs detected. 15921416, 15921417, 15921418, (all)
1 NC_003106 2562505-2564304 (-) ISSis2 4 No TIRs detected. 15922886, 15922887, (all)
2 NC_003106 660647-662441 (-) ISSis2 3 No TIRs detected. 15920900, 15920901, 15920902, (all)
3 NC_003106 1907713-1909559 (+) ISSis2 3 No TIRs detected. 15922219, 15922220, 15922221, (all)
4 NC_003106 1164029-1164879 (+) ISSto2 6 details 15921423, (all)
5 NC_003106 833259-834107 (+) ISSto2 6 details 15921092, (all)
6 NC_003106 2269440-2270274 (+) ISSto2 6 details 15922590, (all)
7 NC_003106 163506-164346 (+) ISSto2 6 details 15920321, (all)
8 NC_003106 1993428-1994266 (-) ISSto2 6 details 15922298, (all)
9 NC_003106 269896-270743 (+) ISSto2 6 details 15920440, (all)
10 NC_003106 1114411-1115612 (-) ISSto5 3 No TIRs detected. 15921377, (all)
11 NC_003106 1910490-1911775 (+) ISSto5 3 No TIRs detected. 15922223, (all)
12 NC_003106 1175090-1176367 (+) ISSto5 3 No TIRs detected. 15921433, 15921434, (all)
13 NC_003106 1957126-1958513 (-) ISC1205 3 details 15922266, 15922267, (all)
14 NC_003106 885024-886346 (-) ISC1234 6 details 15921143, (all)
15 NC_003106 1164949-1166265 (+) ISC1234 6 details 15921424, (all)
16 NC_003106 823496-824818 (+) ISC1234 6 details 15921082, (all)
17 NC_003106 2239404-2240719 (+) ISC1234 6 details 15922560, (all)
18 NC_003106 189310-190569 (-) ISC1234 3 No TIRs detected. 15920340, (all)
19 NC_003106 777594-778867 (-) ISC1234 3 details 15921032, (all)
20 NC_003106 1723807-1725070 (-) ISC1234 3 No TIRs detected. 15922028, (all)
21 NC_003106 2000023-2001329 (+) ISC1234 6 details 15922303, (all)
22 NC_003106 1961223-1962671 (+) ISSto10 3 details 15922269, (all)
23 NC_003106 2181214-2182424 (-) ISSto10 3 No TIRs detected. 15922509, (all)
24 NC_003106 1964768-1966130 (+) ISSto8 3 details 15922273, (all)
25 NC_003106 73052-74399 (+) ISSto8 3 details 15920233, (all)
26 NC_003106 1786137-1787492 (-) ISSto8 3 details 15922080, (all)
27 NC_003106 1134265-1135060 (-) ISSto9 7 details 15921396, (all)
28 NC_003106 1909714-1910511 (+) ISSto9 6 details 15922222, (all)
29 NC_003106 1066271-1067066 (-) ISSto9 6 details 15921335, (all)
30 NC_003106 654314-655109 (+) ISSto9 6 details 15920893, (all)
31 NC_003106 162716-163505 (+) ISSto9 6 details 15920320, (all)
32 NC_003106 1155998-1156791 (-) ISSto9 7 details 15921412, 15921413, 15921414, (all)
33 NC_003106 2031271-2032055 (+) ISSto9 3 details 15922334, 15922335, (all)
34 NC_003106 2563808-2564474 (-) ISSep3 7 No TIRs detected. 15922887, (all)
35 NC_003106 661946-662612 (-) ISSep3 7 No TIRs detected. 15920902, (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.