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

 

Halobacterium_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_002607 Click to view the full size in a separate window.
   NC_002608 Click to view the full size in a separate window.
   NC_001869 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Halobacterium_sp

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_002607 16129-17714 (+) ISH10B 5 details 15789357, (all)
1 NC_002608 63091-64674 (+) ISH10B 5 details 16120048, (all)
2 NC_002608 332792-334375 (-) ISH10B 5 details 16120314, (all)
3 NC_001869 63091-64674 (+) ISH10B 5 details 10803610, (all)
4 NC_001869 158713-160296 (-) ISH10B 5 details 10803693, (all)
5 NC_001869 34452-35395 (+) ISMbu10 4 details 10803581, (all)
6 NC_001869 187992-188935 (-) ISMbu10 4 details 10803722, (all)
7 NC_002608 34452-35395 (+) ISMbu10 4 details 16120013, (all)
8 NC_002608 362071-363014 (-) ISMbu10 4 details 16120349, (all)
9 NC_001869 1716-4029 (+) ISH7B 4 No TIRs detected. 10803551, 10803552, (all)
10 NC_002608 1716-4029 (+) ISH7B 4 No TIRs detected. 16119983, (all)
11 NC_001869 86693-89009 (+) ISH7B 4 No TIRs detected. 10803631, 10803632, (all)
12 NC_002608 86693-89009 (+) ISH7B 4 No TIRs detected. 16120073, (all)
13 NC_001869 79682-81104 (+) ISH8E 5 details  
14 NC_002608 276584-278035 (+) ISH8E 5 details 16120247, (all)
15 NC_002608 136940-138366 (+) ISH8E 5 details 16120109, (all)
16 NC_002608 79682-81104 (+) ISH8E 5 details 16120065, (all)
17 NC_002607 1231046-1232448 (+) ISH8E 7 details 15790603, (all)
18 NC_002608 35630-37510 (+) ISH5 4 details 16120014, (all)
19 NC_002608 359956-361836 (-) ISH5 4 details 16120348, (all)
20 NC_002608 36992-38309 (+) ISH5 4 No TIRs detected. 16120015, (all)
21 NC_002608 359159-360476 (-) ISH5 4 No TIRs detected. 16120347, (all)
22 NC_001869 35630-37510 (+) ISH5 4 details 10803582, (all)
23 NC_001869 185877-187757 (-) ISH5 4 details 10803721, (all)
24 NC_001869 36992-38309 (+) ISH5 4 No TIRs detected. 10803583, 10803584, (all)
25 NC_001869 185080-186397 (-) ISH5 4 No TIRs detected. 10803719, 10803720, (all)
26 NC_001869 34452-35395 (+) ISH9 4 details 10803581, (all)
27 NC_001869 187992-188935 (-) ISH9 4 details 10803722, (all)
28 NC_002608 34452-35395 (+) ISH9 4 details 16120013, (all)
29 NC_002608 362071-363014 (-) ISH9 4 details 16120349, (all)
30 NC_002607 1184712-1185779 (+) ISH11 7 details 15790556, (all)
31 NC_002607 178274-179341 (+) ISH11 7 details 15789516, (all)
32 NC_001869 36764-37831 (+) ISH11 7 details 10803583, (all)
33 NC_001869 185556-186623 (-) ISH11 7 details 10803720, (all)
34 NC_002608 323318-324387 (-) ISH11 7 details 16120302, (all)
35 NC_002608 36764-37831 (+) ISH11 7 details 16120015, (all)
36 NC_002608 359635-360702 (-) ISH11 7 details 16120347, (all)
37 NC_002608 124376-125185 (-) IS231H 6 No TIRs detected.  
38 NC_001869 14194-15595 (+) ISH8 16 details 10803559, (all)
39 NC_001869 30609-32009 (-) ISH8 16 details 10803579, (all)
40 NC_001869 58502-59904 (+) ISH8 16 details 10803606, (all)
41 NC_001869 163485-164886 (-) ISH8 16 details 10803697, (all)
42 NC_001869 132341-133742 (-) ISH8 21 details 10803666, (all)
43 NC_002608 309813-311213 (-) ISH8 16 details 16120283, (all)
44 NC_002608 14194-15595 (+) ISH8 16 details 16119991, (all)
45 NC_002608 30609-32009 (-) ISH8 16 details 16120011, (all)
46 NC_002608 122259-123661 (+) ISH8 16 details 16120097, (all)
47 NC_002608 58502-59904 (+) ISH8 16 details 16120043, (all)
48 NC_002608 337564-338965 (-) ISH8 16 details 16120319, (all)
49 NC_002608 265438-266839 (-) ISH8 21 details 16120237, 16120238, (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.